This application claims priority to Korean Patent Application No. 10-2022-0162494 filed on Nov. 29, 2022, and all the benefits accruing therefrom under 35 U.S.C. § 119, the contents of which in its entirety are herein incorporated by reference.
The instant application contains a Sequence Listing which has been submitted electronically in a computer readable Sequence Listing XML format and is hereby incorporated by reference in its entirety. Said computer readable Sequence Listing in XML format was created on Nov. 22, 2023, is named G1035-26201_SequenceListing.xml and is 472,398 bytes in size.
The present disclosure relates to a peptide having an independently stabilized hydrophobic α-helix structure without help from outside, a peptide complex including the same, and a use thereof.
Magnetically responsive materials are highly valuable for biological and medical uses because the magnetic field is radiation-free and safe for humans. A variety of stimuli-responsive self-assembled materials have been developed to date. Although magnetically responsive self-assembled materials based on ferromagnetic/paramagnetic inorganic materials or composites of inorganic and organic materials have been developed, magnetically responsive self-assembled materials based solely on organic materials have not been reported. DNAs and some proteins have been shown to be magnetically responsive. However, there is difficulty in actual commercialization since an extremely strong magnetic field is required.
Self-assembled peptide structures are receiving a lot of attentions due to their potential for various biological applications such as medical or nanotechnological fields. The self-assembled peptide structures have inherently high biological stability because they are made up of short units. These peptide monomers can form secondary structures such as α-helix or β-sheet and can form various structures such as micelles, vesicles, nanofibers, hydrogels, etc. through hydrophobic bonds, hydrogen bonds, electrostatic attractions, π-π bonds, etc.
As such, peptides have attracted much attention as they can realize more precise and stable functional structures by providing not only various structures but also various functions depending on their properties. However, as representative diamagnetic organic molecules, they have been regarded as non-magnetic materials since they are not sensitive to strong magnetic fields of several teslas or higher.
Recently, it was found out that the α-helix structure, which is the secondary structure of peptide monomers, has slight magnetic responsiveness. However, there is a problem that the peptides with an α-helix structure do not maintain the α-helix structure in the monomer state or have the α-helix structure only when they exist in a protein.
Regarding magnetically responsive peptides, a one-dimensional nanostructure formed through self-assembly of dipeptides whose arrangement can be controlled with a magnetic field or an electric field is disclosed in the patent document 1. However, since the structure is limited in organic solvents and the peptide sequence is limited to Phe-Phe, wide application is impossible and an additional modification process is necessary to provide chemical and biological functions.
That is to say, although it should be possible to align the magnetic responsiveness along the direction of the magnetic field while forming a rod-shaped self-assembled peptide structure in order to use diamagnetic organic materials such as peptides as magnetically responsive organic materials capable of controlling the mechanical movement using magnetic force as a noninvasive stimulation source, related researches are very insufficient until now. In addition, although it is very important to maintain the secondary structure of the peptide stably for wide application through interaction with genetic materials, there are few related researches and no research has been conducted on the control of the formation and disassembly of self-assembled peptides.
The present disclosure is directed to providing a new peptide having an independently stabilized hydrophobic α-helix structure without help from outside and capable of forming various self-assembled structures through binding to hydrophilic molecules.
The present disclosure is also directed to providing a peptide complex including the hydrophobic peptide.
The present disclosure is also directed to providing a new system capable of safely storing nucleic acid information.
The present disclosure provides a hydrophobic peptide represented by General Formula 1 or 2:
-{[Aib]-[Xaa1]}m- [General Formula 1]
Xaa1-{[Aib]-[Xaa1]}m- [General Formula 2]
In General Formula 1, Xaa1 may be any one selected from a group consisting of Ala (A), Ile (I), Leu (L) and Met (M).
In General Formula 1, Xaa1 may be Ala (A) or Leu (L).
In General Formula 1, m may be any integer selected from 6 to 13.
In General Formula 1, m may be any integer selected from 6 to 10.
The hydrophobic peptide may be a rod-shaped hydrophobic peptide having an α-helix structure.
The hydrophobic peptide may be controlled to be arranged and oriented in the direction of an external magnetic field.
The present disclosure also provides a peptide complex including: the hydrophobic peptide; and at least one hydrophilic polymer or hydrophilic peptide bound to one or both ends of the hydrophobic peptide.
The hydrophilic polymer may be any one selected from a group consisting of polyethylene glycol (PEG), poly(N-(2-hydroxypropyl)methacrylamide), poly(2-(methacryloyloxy)ethyl phosphorylcholine), poly(hydroxyalkyl L-asparagine) and poly(hydroxyalkyl L-glutamine).
The hydrophilic peptide may consist of 3-20 amino acid sequences, wherein 70-100% of the amino acid sequences are hydrophilic amino acids, and the hydrophilic amino acid may be one or more selected from a group consisting of H (histidine), N (asparagine), Q (glutamine), S (serine), T (threonine), C (cysteine), G (glycine), K (lysine), R (arginine), E (glutamic acid) and D (aspartic acid).
The hydrophilic peptide may be any one selected from a group consisting of SEQ ID NOS 98-105.
The peptide complex may be cyclic with both ends of the peptide complex linked.
The peptide complex may further include a positively charged peptide consisting of positively charged 1-4 amino acid residues at the N- or C-terminal.
The positively charged peptide may be any one selected from SEQ ID NOS 108-119.
The peptide complex may self-assemble into a spherical nanoparticle such as a micellar structure or a vesicular structure in solution.
The peptide complex may self-assemble into an anisotropic planar nanostructure or a cruciform anisotropic nanostructure under the condition where a magnetic field is applied.
The intensity of the magnetic field may be 0.1-2 T.
The present disclosure also provides a composition for safely storing nucleic acid information, which contains: the peptide complex; and a nucleic acid material.
The peptide complex and the nucleic acid material may self-assemble into a nanoribbon or a nanostructure having an artificial chromosome-like structure via noncovalent bonding.
A nanoribbon structure may be formed through self-assembly as the peptide complex binds to the nucleic acid material and a nanostructure with an artificial chromosome-like structure may be formed through self-assembly as the nanoribbon is folded and stacked.
The nucleic acid material may be one or more selected from a group consisting of an RNA, a DNA, an siRNA (short interfering RNA), an aptamer, an antisense ODN (oligodeoxynucleotide), an antisense RNA, a ribozyme and a DNAzyme.
The nanostructure may be degraded at a magnetic field intensity of 0.1-2 T and induce the release of the nucleic acid material.
The magnetic field intensity may be 0.1-0.5 T based on a rotating magnetic field.
The present disclosure relates to a novel hydrophobic peptide consisting of short amino acid sequences as repeat units, having a perfectly stabilized α-helix structure without help from outside. The peptide has no cytotoxicity and has magnetic responsiveness, i.e., its arrangement and orientation are controlled by a magnetic field. In addition, the hydrophobic peptide according to the present disclosure can not only form complexes of various structures with hydrophilic molecules but also provide suitable nanostructures such as nanoribbons and artificial chromosome-like structures through stepwise association with nucleic acid materials.
A peptide complex including the hydrophobic peptide according to the present disclosure can provide a magnetically responsive material with a new structure that can completely protect nucleic acid materials from external environment and the assembly and degradation of which can be controlled with a magnetic field.
Since the peptide complex according to the present disclosure forms a nanostructure by associating with a nucleic acid material and can be applied directly to analysis methods such as PCR for identifying the genetic information of the nucleic acid material, it can be usefully used in various drug delivery systems, drug therapy technologies, cosmetic compositions, molecular machines, etc.
Hereinafter, the present disclosure is described in detail.
The present disclosure is directed to providing a magnetically responsive peptide that can be applied to magnetic applications and a peptide nanostructure including the same. For this, the inventors of the present disclosure have developed a monomeric, nonpolar and perfect α-helix (MNP-helix) that has the propensity to self-assemble and align parallel to the applied magnetic field.
The hydrophobic peptide according to the present disclosure has an α-helix structure from among common secondary structures. Similarly to aromatic rings, the resonance-stabilized peptide bond has a meaningful value of the diamagnetic anisotropy due to it partial double bond character (
The hydrophobic peptide according to the present disclosure can form a peptide complex with a rod-coil structure by binding to a hydrophilic molecule since it acts as a supramolecular building block.
The hydrophobic peptide according to the present disclosure acts as a hydrophobic block with a rigid rod structure and forms an amphiphilic peptide complex with a rod-coil structure by binding to a hydrophilic block with a flexible coil structure.
The peptide complex having a rod-coil structure has more advantages over the existing molecules with a coil-coil structure in terms of well-defined, dynamic and responsive assembly because the hydrophobic block consisting of hydrophobic peptides imparts orientational organization and the entropic penalty associated with chain stretching in coil-coils can be reduced.
The existing peptides having an α-helix rod structure cannot maintain the α-helix structure in the monomeric state. Also, in proteins, most α-helix peptide sequences can be stabilized only when they make noncovalent interactions with other residues of the proteins. Single α-helix structures found in proteins and some of designed peptides are highly helical in the monomeric state. These helix structures cannot be used as supramolecular building blocks because all of them are highly charged and hydrophilic.
In order to solve the problems described above, the inventors of the present disclosure have explored the synergistic effect of the α-helix and rod-coil structures to develop organic molecules responsive to the magnetic field produced by permanent magnets. To this end, they have designed a new hydrophobic peptide having an MNP α-helix structure as a first step.
By using the hydrophobic peptide according to the present disclosure as a rod block of a rod-coil peptide complex having amphiphilicity, they have confirmed that the self-assembly and disassembly processes can be controlled under a relatively weak magnetic field (0.07-0.25 T).
In addition, since the peptide complex including the hydrophobic peptide of the present disclosure is positively charged, it interacts with negatively charged materials. Especially, it self-assembles with genetic materials (nucleic acid, etc.) to form a nanostructure with an artificial chromosome-like structure. The nanostructure is a new-concept magnetically responsive organic molecule that can safely store and deliver a genetic material by packaging tightly and the release of the genetic material can be controlled with a magnetic field. It was found out that the nanostructure can be usefully used in various fields of applied researches such as medicine, cosmetics, stimuli-responsive molecular machines, motion control of organic materials, etc. because its magnetic responsiveness can be controlled variously.
In an aspect, the present disclosure relates to a hydrophobic peptide represented by General Formula 1 or 2.
-{[Aib]-[Xaa1]}m- [General Formula 1]
-[Xaa2]n-{[Aib]-[Xaa1]}m- [General Formula 2]
In the present specification, the term “peptide” or “polypeptide” refers to a linear molecule formed as 4-100, specifically 4-80, more specifically 10-80, more specifically 20-80, most specifically 20-40, amino acid residues are linked by peptide bonds.
The hydrophobic peptide represented by General Formula 1 or 2 may be represented by SEQ ID NO 121 or 122. It is not derived from existing proteins but was designed to include [Aib]-[Xaa1] or [Xaa1]-[Aib] as a repeat unit (hereinafter, also referred to as ‘a’) through numerous combinations of existing amino acid residues so as to stably maintain the α-helix structure and impart hydrophobicity and a rod structure.
Through experiments, the inventors of the present disclosure have identified that the hydrophobic peptide has a stable α-helix structure and rod structure despite the short sequence length. In addition, they have identified that it can be aligned in real time in response to a weak magnetic field and forms an artificial chromosome-like structure by interacting with a genetic material.
In the present disclosure, the hydrophobic peptide of General Formula 1 or 2 is a newly designed sequence derived from nowhere. Among the existing peptide secondary structures, the α-helix structure is known to have increased stability as the length of the peptide chain increases. However, as the peptide length increases, it is difficult to synthesize the peptide and to prepare a supramolecular building block having a specific structure. As a result of actually preparing peptides consisting of short repeat units through various combinations of amino acid residues, it was confirmed that most of them failed to form α-helix structures or, even if they did, the structures existed in unfolded states.
Through the experiments described above, the inventors of the present disclosure have identified that a peptide having a repeat unit prepared from a hydrophobic amino acid residue such as alanine (Ala or A) and Aib (2-aminoisobutyric acid, U) has a stable α-helix structure while having appropriate hydrophobicity for self-assembly and can be aligned highly by a magnetic field.
In a specific exemplary embodiment of the present disclosure, the hydrophobic peptide of the present disclosure is advantageous in that it has a perfectly stabilized α-helix structure while existing as monomeric state in solution without aggregation.
In a specific exemplary embodiment of the present disclosure, m may be any integer selected from 4 to 50, more specifically any integer selected from 6 to 13, further more specifically any integer selected from 6 to 10, most specifically 10.
In a specific exemplary embodiment of the present disclosure, Xaa1 may be any one selected from a group consisting of Ala (A), Ile (I), Leu (L) and Met (M), specifically Ala (A) or Leu (L).
In the formulas, Xaa1 may be most specifically alanine (Ala or A) so that the peptide has a stable α-helix structure while having appropriate hydrophobicity for self-assembly and can be aligned highly by a magnetic field.
In addition, in a specific exemplary embodiment of the present disclosure, Xaa1 may be an L-amino acid residue or a D-amino acid residue, although not being specially limited thereto.
In a specific exemplary embodiment of the present disclosure, the hydrophobic peptide represented by General Formula 1 or General Formula 2 is a polypeptide consisting of a repeat unit with the shortest sequence having a newly designed α-helix structure. The hydrophobic peptide may be any one selected from SEQ ID NOS 1-36, specifically any one selected from SEQ ID NOS 5-19 and 24-36, more specifically any one selected from SEQ ID NOS 13-14 and 32-33.
The hydrophobic peptide has a stable α-helix secondary structure while exhibiting hydrophobicity, is aligned along the direction of an external magnetic field and has superior responsiveness to a weak magnetic field of 1 T or lower.
Due to the characteristics described above, the hydrophobic peptide according to the present disclosure has a rigid rod structure capable of stably maintaining a plurality of α-helix structures.
The arrangement and orientation of the hydrophobic peptide according to the present disclosure are controlled under a magnetic field. As described above, the peptide is aligned and oriented parallel to the direction of an external magnetic field.
The existing peptide cannot maintain its α-helix structure unless it exists within a specific structure and cannot respond to a magnetic field because it is a very weak diamagnetic material. In contrast, the peptide of the present disclosure, which consists of a repeat unit with the shortest sequence, [Aib]-[Xaa1] or [Xaa1]-[Aib] (hereinafter, also referred to as ‘a’), maintains a stable α-helix structure in monomeric state even when it is not constrained in a ring or a large protein. In addition, it is a new magnetically responsive peptide that is aligned and oriented parallel to the direction of an external magnetic field.
Furthermore, since the hydrophobic peptide according to the present disclosure is easy to impart new functions through binding with a hydrophilic polymer or a hydrophilic peptide without losing the above-described characteristics and can be stored and delivered in the form of micelle particles through self-assembly, it can be usefully used in various fields such as medicine, stimuli-responsive molecular machines, cosmetics, etc.
In addition, since the hydrophobic peptide according to the present disclosure does not affect the genetic information analysis method such as PCR, even when mixed with a nucleic acid material, without generating noises, it can be advantageously used for analysis of a nucleic acid material without an additional purification process.
In another aspect, the present disclosure provides a peptide complex: including the hydrophobic peptide; and at least one hydrophilic polymer or hydrophilic peptide bound to one or both ends of the hydrophobic peptide.
As described above, in the peptide complex according to the present disclosure, one or more hydrophilic polymer or hydrophilic peptide may be bound to one or both ends of the hydrophobic peptide.
The description of the hydrophobic peptide will be omitted to avoid redundancy.
The one end of the hydrophobic peptide refers to any of the N-terminal or C-terminal of the hydrophobic peptide, and the both ends refers to both the N-terminal and C-terminal of the hydrophobic peptide.
The ‘N-terminal’ refers to the first amino acid residue in the hydrophobic peptide sequence. The N-terminal residue contains a free α-amino group. The ‘C-terminal’ refers to the last amino acid residue in the hydrophobic peptide sequence. The C-terminal residue contains a free carboxylate group.
In the present disclosure, the ‘polymer’ refers to a macromolecule having repeat units linked by covalent bonds. The polymer may be hydrophilic, hydrophobic or amphiphilic. Specifically, it may be a hydrophilic polymer exhibiting hydrophilicity. The polymer may include a homopolymer, a random copolymer and a block copolymer.
The ‘hydrophilic polymer’ is not specially limited as long as it substantially miscible with water. It may be specifically polyethylene glycol (PEG), poly(N-(2-hydroxypropyl)methacrylamide), poly(2-(methacryloyloxy)ethyl phosphorylcholine), poly(hydroxyalkyl L-asparagine) or poly(hydroxyalkyl L-glutamine), more specifically polyethylene glycol (PEG).
Specifically, the hydrophilic polymer may be an unbranched, non-crosslinked linear polymer and may have a molecular weight of about 1-100 kDa, specifically about 1-75 kDa, more specifically about 5-50 kDa, further more specifically about 5-25 kDa.
The polyethylene glycol (PEG) contains PEG monomers and may be represented by the chemical formula CH3—O(CH2CH2O)n— or —O(CH2CH2O)n—, wherein n is a positive integer from about 10 to about 2,300.
The ‘hydrophilic peptide’ is not specially limited as long as it is a peptide exhibiting hydrophilicity. As known to those skilled in the art, it refers to a peptide exhibiting hydrophilicity as a whole with a high proportion of polar amino acid or hydrophilic amino acid residues. The hydrophilic amino acids may include H (histidine), N (asparagine), Q (glutamine), S (serine), T (threonine), C (cysteine), G (glycine), K (lysine), R (arginine), E (glutamic acid) and D (aspartic acid).
The hydrophilic peptide may consist of 3-100, specifically 3-60, more specifically 3-20, amino acid sequences and the content of the hydrophilic amino acids may be 70-100%.
The hydrophilic peptide is not specially limited as long as the above-described conditions are satisfied. Specifically, it may be an optional ligand that may or may not be present, selected from RGD, transferrin, folate, a signal peptide or signal sequence, a localization signal or sequence, a nuclear localization signal or sequence (NLS), an antibody, a cell-penetrating peptide (e.g., TAT or KALA), a ligand of a receptor, a cytokine, a hormone, a growth factor, a small molecule, a carbohydrate such as mannose and galactose, a synthetic ligand, a small-molecule agonist and an inhibitor or antagonist of a receptor (e.g., an RGD peptidomimetic analogue).
Specifically, the hydrophilic peptide may include or consist of the following amino acid sequences.
The hydrophobic peptide and the hydrophilic polymer or hydrophilic peptide are linked by a chemical bond. They may be linked either directly or indirectly via a linker.
The linkage via a chemical bond or a linker may vary depending on the terminal sequence of the peptide and the terminal group of the polymer. It may be for example, an amide bond, an ether bond, a thioether bond, an ester bond, a thioester bond, a carbonate bond, a carbamate bond, a phosphate bond or an oxime bond. Specifically, it may be an amide bond.
The linker may be any one that can be linked to the terminal of the hydrophobic peptide, the terminal of the hydrophilic peptide or the terminal of the hydrophilic polymer and can form the chemical bonds described above.
For example, dicyclohexylcarbodimide (DCC), 1,4-bis-maleimidobutane (BMB), 1,11-bismaleimidotetraethylene glycol (BM(PEG)4), 11-ethyl-3-[3-dimethylaminopropyl]carbodiimide hydrochloride (EDC), succinimidyl-4-[N-maleimidomethylcyclohexane-1-carboxy-[6-amidocaproate] (SMCC) and a sulfonate thereof (sulfo-SMCC), succinimidyl 6-[3-(2-pyridyldithio)-ropionamido]hexanoate (SPDP) and a sulfonate thereof (sulfo-SPDP), m-maleimidobenzoyl-N-hydroxysuccinimide ester (MBS) and a sulfonate thereof (sulfo-MBS), succinimidyl[4-(p-maleimidophenyl) butyrate (SMPB) and a sulfonate thereof (sulfo-SMPB), etc., specifically dicyclohexylcarbodimide (DCC), may be used. A linker peptide consisting of 1-10 amino acids may also be used.
The linker peptide may consist of 1-10 amino acids selected from H (histidine), G (glycine) and R (arginine).
The peptide sequence may include silent mutations that may occur during an encoding process. The silent mutations may be intended implicitly. The peptide sequence of the present disclosure may include sequence variations for conservative substitutions that provide functionally similar amino acids widely known in the art.
The peptide complex of the present disclosure may further contain a positively charged peptide consisting of positively charged 1-4 amino acid residues at the N- or C-terminal.
The positively charged peptide may be linked to the hydrophobic peptide of the peptide complex of the present disclosure. Specifically, the positively charged peptide is linked via a linker or a direct bond. The design is intended to provide a new approach to easily form a bond with a negatively charged molecule such as an oligonucleotide for better efficiency such as delivery of a nucleic acid material, treatment, storage, etc.
The peptide complex of the present disclosure may form a nanostructure by binding easily to a nucleic acid material even without a positively charged peptide bound thereto. However, when it contains a positively charged peptide, a nanostructure with a highly functional structure in artificial chromosome form may be prepared more effectively.
The positively charged peptide may be any one selected from SEQ ID NOS 108-119.
The peptide complex of the present disclosure may be an amphiphilic molecule having a rod-coil structure. Since the peptide complex of the present disclosure has amphiphilic characteristics, it can form a self-assembled structure in an aqueous solvent through self-assembly.
The peptide complex of the present disclosure may self-assemble into a micelle structure in an aqueous solvent through self-assembly. The micelle structure refers to an aggregated nanostructure of amphiphilic molecules with regular size and shape. The micelle has various shapes including spherical, ellipsoid, cylindrical, ring and lamellar shapes. The peptide complex of the present disclosure may self-assemble to one or more shapes selected from spherical, ellipsoid, cylindrical, ring and lamellar shapes.
The self-assembled structure of the peptide complex of the present disclosure may have an average diameter of usually 10-400 nm.
The form of the self-assembled structure may be controlled by controlling the orientation of the peptide complex according to the present disclosure with a magnetic field. When an electric field is not applied, the peptide complex of the present disclosure is prepared into a spherical nanoparticle as the orientation of the α-helix structure disappears. When an electric field is applied, a self-assembled structure having an anisotropic planar nanostructure or cruciform anisotropic nanostructure may be prepared as the α-helix structure is oriented along the direction of the electric field.
The peptide complex according to the present disclosure responds sensitively to a very low magnetic field intensity of 0.1-2 T.
In another aspect, the present disclosure relates to a composition for storing nucleic acid information safely, which contains the peptide complex and a nucleic acid material.
The peptide complex and the nucleic acid material may self-assemble into a nanoribbon or a nanostructure having an artificial chromosome-like structure via noncovalent bonding.
The composition of the present disclosure can store and deliver the genetic material very stably since the nucleic acid material is surrounded and coated by the peptide complex through interaction between the peptide complex and the nucleic acid material. The above-described process is advantageous in that it proceeds easily and quickly because the self-assembly occurs automatically in the aqueous solvent. In addition, the composition of the present disclosure is advantageous in that the information of the genetic material can be confirmed by usefully used DNA analysis without an additional separation process because the peptide complex does not affect the analysis process such as PCR, etc.
A nanoribbon structure may be formed through self-assembly as the peptide complex binds to the nucleic acid material and a nanostructure with an artificial chromosome-like structure may be formed through self-assembly as the nanoribbon is folded and stacked.
In the present disclosure, the artificial chromosome-like structure refers to a structure formed by condensation of chromatin, a thread-like structure made of nucleic acids and proteins that carries the genetic information of living organisms such as human chromosomes. In the present disclosure, the nanoribbon is formed as the peptide binds to the nucleic acid material and the nanoribbon is condensed to form a chromosome-like system that stores a large amount of genetic information in the minimal space.
The nucleic acid material may be one or more selected from a group consisting of an RNA, a DNA, an siRNA (short interfering RNA), an aptamer, an antisense ODN (oligodeoxynucleotide), an antisense RNA, a ribozyme and a DNAzyme. For example, it may be an RNA, a DNA or a cDNA, and the sequence of the nucleic acid may be a coding region sequence or a non-coding region sequence (e.g., an antisense oligonucleotide or siRNA). As the nucleic acid cargo, a nucleotide may be a standard nucleotide (e.g., adenosine, cytosine, guanine, thymine, inosine or uracil) or an analog thereof (e.g., a phosphorothioate nucleotide). For example, the nucleic acid cargo may be an antisense sequence consisting of phosphorothioate nucleotides or RNAi.
Since the structural degradation of the nanostructure can be induced under a magnetic field intensity of 0.1-2 T, the material release of the nucleic acid can be induced at desired time depending on purposes. Using these properties, it is possible to implement a delivery system which allows the control of long-term storage and release of the nucleic acid material.
Since the composition according to the present disclosure requires 10 days or longer for complete degradation under static magnetic field intensity, the rotating magnetic field condition is preferred for degradation within 1 day. The intensity of the rotating magnetic field may be specifically 0.1-0.5 T, although it can be adjusted adequately depending on the time required for the degradation and purpose.
In a specific exemplary embodiment of the present disclosure, the composition according to the present disclosure is very useful as a system for storing and protecting the information of a nucleic acid material for a long time since it perfectly protects the nucleic acid material from external environment and can restore the genetic information at any time through analysis methods such as PCR.
The composition according to the present disclosure is advantageous in that the genetic information of the nucleic acid material can be confirmed directly through analysis methods such as PCR without an additional purification process.
Hereinafter, the present disclosure will be described in more detail through specific examples. However, these examples are only for describing the present disclosure more specifically and it will be obvious to those having ordinary knowledge in the art that the scope of the present disclosure is not limited by them.
To evaluate the structures of a linear plasmid DNA and peptides, CD spectra were analyzed using a Chirascan CD spectrometer (Applied Photophysics, UK). The concentration of the peptides typically ranged from 0.156 to 160 μM. The final concentration of the linear plasmid DNA was 30 ng/μL. All the samples were dissolved in H2O. For the formation of the artificial chromosome, a mixture of the peptide and the DNA was incubated for 12 days or longer. Scanning was performed using a 2-mm path-length cuvette. Each scan was repeated three times and averaged. MRE (mean residue ellipticity) was calculated based on the number of amino acid residues.
MCD (magnetic circular dichroism) spectra were obtained using a Jasco-815 159-L spectrophotometer (Jasco, Japan). The concentration of the peptides was 20 μM in distilled water. Measurements were performed using a 2-mm path-length cuvette. The magnetic field of the permanent magnet in the MCD accessory (PM-491) was 1.6 T. Each scan was repeated three times and averaged.
1H NMR and 2D 1H-15N IPAP-HSQC (in-phase/anti-phase heteronuclear single quantum coherence) NMR spectra were acquired at 298 K using a Bruker AVANCE IV 900 MHz spectrometer and a BrukerAVANCE Ill HD 700 MHz spectrometer, both equipped with cryogenic probes. The NMR sample of PEG30-α10-PEG30 was dissolved in methanol-d3/chloroform-d (1:1) containing 0.05% TFA at a concentration of 4.26 mM. The acquisition parameters of IPAP were 2048 t2×1024 t1 points, 8 scans, 0.2 second recycle delay, 14 ppm spectral width for 1H and 26 ppm spectral width for 15N. The acquired data were split into two data sets, IP and AP, using a TopSpin software (Bruker, Germany). Each spectrum was processed by zero-filling up to 8192×8192 points. Peak positions were assigned using an NMRFAM-SPARKY software.
AFM was performed using an NX10 system (Park Systems, Korea) in a non-contact mode with PPP-NCHR AFM probes (Nanosensors, Switzerland). The DNA concentration ranged from 1 to 30 ng/μL and the peptide concentration ranged from 1 to 32 μM (in H2O). 2 μL of the sample solution was cast onto a freshly cleaved mica surface and dried. The data obtained by the SmartScan program (Park Systems, Korea) was analyzed using the XEI program (Park Systems, Korea).
TEM was performed using a JEM-F200 multi-purpose electron microscope (JEOL, Japan) at 200 kV. 2 μL of the sample solution was loaded on a copper grid (carbon type-B grid or Formvar/silicon monoxide grid, 200 mesh copper grids with a 97 μm hole; Ted Pella, USA). 1 hour later, 2 μL of 1-2% uranyl acetate was added to the dried sample for less than 1 minute and the negative stain solution was wicked off with filter paper. To analyze the internal packing structure of the artificial chromosome, the electron diffraction (ED) pattern was observed in selected areas.
EMSA was performed to investigate the mode of interaction between the peptide complex and the linear plasmid DNA and their binding ratio. The concentration of the peptide complex was increased from 1.5 μM to 6214 μM, while the concentration of the linear plasmid DNA was fixed to 30 ng/μL. The same mixing protocol was used as in the artificial chromosome formation. After incubation at room temperature, 10% glycerol was added to the sample for gel loading. Electrophoresis was performed for 100 minutes at 90 V on 1% agarose gel. The bands were visualized by staining with an SYBR Safe DNA gel stain (Invitrogen, USA).
A sample (the linear plasmid DNA or the artificial chromosome) containing 60 ng (2 μL; 30 ng/μL) of DNA was mixed with 0.1 μL (0.2 unit) of DNase I and 1 μL of a 10× DNase I reaction buffer. The volume of the mixture was 10 μL. After 20 minutes of incubation at 37° C., 0.3 μL of 0.05 M EDTA was added to inactivate the enzyme. Then, the sample was mixed with 1.7 μL of 60% glycerol and electrophoresed on 1.1% agarose gel (120 minutes, 100 V). For visualization, the DNA was stained with an SYBR Safe DNA gel stain (Invitrogen, USA). To evaluate the time-dependent kinetics of DNA degradation, UV absorbance at 260 nm was recorded over time after the addition of DNase I. Each sample (71.2 μL) containing DNA (30 ng/μL) and a 10× DNase I reaction buffer (8 μL) was mixed in a cuvette. Then, DNase I (0.8 μL) was added to the cuvette and the sample was mixed by pipetting for about 90-105 seconds. UV absorbance at 260 nm (A260) was measured using a V-650 UV-vis spectrophotometer (JASCO, Japan). A quartz cuvette with a path length of 10 mm was used. The absorbance was recorded at intervals of 10 seconds.
To assess the capability of recovering DNA information stored in the artificial chromosome, PCR (polymerase chain reaction) was conducted to amplify a specific DNA fragment of the sample DNA. The specific 310-bp fragment was amplified using the sense primer 5′-ACG GAG ACT GGA GTC GAA GAG G-3′ (SEQ ID NO 106) and the antisense primer 5′-GTA GGG CAA CTA GTG CAT CTC CC-3′ (SEQ ID NO 107). Each reaction mixture (50 μL) contained 50 ng of DNA, 10 pmol of each primer and 25 μL of 2× Quick Taq HS DyeMix (Toyobo, Japan). PCR amplification (30 cycle) was performed using a T100 thermal cycler (Bio-Rad, USA). After the amplification, the product was electrophoresed for 120 minutes at 80 V on 2% agarose gel (TBE system). A SYBR Safe DNA gel stain (Invitrogen, USA) was used for DNA staining.
Hydrophobic α-helix peptides (α4-13) represented by SEQ ID NOS 1-36 were synthesized as follows. The peptides were synthesized by standard Fmoc solid-phase peptide synthesis (SPPS) on Rink Amide MBHA resin LL (100-200 mesh, 0.30-0.40 mmol g−1, Novabiochem, Germany). All Fmoc-amino acids, Fmoc-NH-PEG8-propionic acids and Fmoc-NH-PEG10-propionic acids were purchased from AAPPTec (USA).
Coupling reagent such as HCTU (2-(6-chloro-1H-benzotriazole-1-yl)-1,1,3,3-tetramethylaminium hexafluorophosphate), HOBt (1-hydroxybenzotriazole) and Fmoc-PEG2-Suc-OH (Fmoc-ebes-OH) were purchased from AnaSpec (USA). The synthesis scale was typically 0.1 mmol and the synthesis was conducted mostly in a 6-mL Resprep SPE (solid-phase extraction) tube (Restek, USA). The synthesized peptides were purified by HPLC (high-performance liquid chromatography) using a C4 reversed-phase column (Waters, USA) at room temperature. The eluents were distilled water (0.1% TFA) and acetonitrile (0.1% TFA). The molecular weight of the peptides was measured using a MALDI-TOF (matrix-assisted laser desorption/ionization time-of-flight) mass spectrometer (
Peptide complexes represented by SEQ ID NOS 37-45 were prepared. Their structures are shown in
The molecular weight of the peptide complexes was measured using a MALDI-TOF (matrix-assisted laser desorption/ionization time-of-flight) mass spectrometer. The purity of the peptide complexes was >95%, as determined by analytical HPLC.
Peptide complexes of Example 46-57 wherein (PEG2)5 or (PEG8)2 is bound to peptides represented by SEQ ID NOS 2, 8, 14 and 46-51 were prepared by solid-phase peptide synthesis (Table 2). The structures of some of the peptide complexes are shown in
Peptide complexes of Examples 58-97 wherein (PEG8)2, (PEG8)3, (PEG8)4, (PEG8)5 or glucose is bound to peptides represented by SEQ ID NOS 52-84 were prepared by solid-phase peptide synthesis (Table 3). The solid-phase peptide synthesis was performed by standard Fmoc solid-phase peptide synthesis (SPPS) on Rink Amide MBHA resin LL (100-200 mesh, 0.30-0.40 mmol g−1, Novabiochem, Germany) in the same manner as in Example 1.
Peptide complexes of Examples 98-111, which have the same sequences as the peptide complexes of Examples 46-51 but are cyclic, were prepared by solid-phase peptide synthesis (Table 4). The structures of some of the cyclic peptide complexes are shown in
Peptide complexes of Examples 112-128 wherein (PEG8)2, (PEG8)3, (PEG10)2 or (PEG10)3 is bound to peptides represented by SEQ ID NOS 2, 8, 14 and 91-97 were prepared by solid-phase peptide synthesis (Table 5). The solid-phase peptide synthesis was performed by standard Fmoc solid-phase peptide synthesis (SPPS) on Rink Amide MBHA resin LL (100-200 mesh, 0.30-0.40 mmol g−1, Novabiochem, Germany) in the same manner as in Example 1.
As shown in
Because the hydrophobic peptides of SEQ ID NOS 1-36 have high hydrophobicity, it is difficult to investigate their behaviors in an aqueous solvent. Therefore, peptide complexes with a hydrophilic material bound to one end of the hydrophobic peptides were used for analysis. That is to say, the peptide complexes prepared in Examples 37-40 (αm-(RGD)2) were analyzed by CD spectroscopy.
CD (circular dichroism) spectroscopy was performed as follows. The peptide complexes prepared in Examples 37-40 (αm-(RGD)2) were prepared at various concentrations (0.156-160 μM in H2O) and analyzed using a Chirascan CD spectrometer (Applied Photophysics, UK. A cuvette with a path length of 2 mm was used. Each scan was repeated three times and averaged. MRE (mean residue ellipticity) was calculated based on the number of amino acid residues.
As shown in
An amphiphilic molecule is a molecule consisting of a hydrophilic moiety and a hydrophobic moiety. The amphiphilic molecules can associate in solution due to hydrophobic effect to form self-assembled structures. The peptide complexes prepared in Examples 37, 39 and 40 (α4-RGD2, α7-RGD2, α10-RGD2) of the present disclosure are amphiphilic molecules. Although it was confirmed in Test Example 2 that the peptide complexes prepared in Examples 37, 39 and 40 have the α-helix structure, this result only means that the α-helix structure is stabilized in the peptide complexes and it could not be confirmed whether this was due to the stabilized α-helix structure in the hydrophobic peptide or due to the stabilization of the helix structure through binding to the hydrophilic moiety (RGD2).
Therefore, the structure of the peptide complex prepared in Example 125 was analyzed (CD spectroscopy and AFM measurement). Since the peptide complex prepared in Example 125 has hydrophilic moieties bound to both ends of the hydrophobic peptide, the possibility of the stabilization of the α-helix structure through structural restraint via self-assembly is excluded. The peptide complex prepared in Example 125 had a coil-rod-coil structure.
The CD spectroscopy was performed in the same manner as in Test Example 2 and the AFM was performed using the NX10 system (Park Systems, Korea) in a non-contact mode with PPP-NCHR AFM probes (Nanosensors, Switzerland). The peptide complex concentration ranged from 1 to 32 μM (in H2O). 2 μL of the sample solution was cast onto a freshly cleaved mica surface and dried. The data obtained by the SmartScan program (Park Systems, Korea) were analyzed using the XEI program (Park Systems, Korea).
As shown in
As shown in
The [θ]222/[θ]203 ratio of the peptide complex of Example 125 (PEG16-α10-PEG16) was maintained at 1.1-1.2, indicating that the peptide complex of Example 125 (PEG16-α10-PEG16) has a perfect α-helix structure and exists in monomeric state without self-assembly.
Typically, a [θ]222/[θ]203 ratio higher than 1.0 is regarded as a coiled coil structure in which the α-helix structure is stabilized. However, because the peptide complex of the present disclosure has a ratio of 1.0 or lower, it can be seen that the α-helix structure exists independently.
The peptide complexes of Examples 37, 39 and 40 are peptide complexes having the rod-coil structure. They self-assembled into spherical particles such as micelles in an aqueous solvent. In contrast, the peptide complex of Example 125 has a coil-rod-coil structure and did not self-assemble in an aqueous solvent. That is to say, it can be seen that the α-helices of the peptide complex of Example 125 do not interact with each other.
From these results, it was confirmed that α10 (Example 14; SEQ ID NO 14) consisting of the shortest repeat unit has a monomeric, nonpolar and perfect α-helix (MNP-helix) structure.
Anisotropic diamagnetic molecules placed in an isotropic solution are aligned when a magnetic field is applied. The behavior of the peptide according to the present disclosure under a magnetic field was analyzed. For this, RDCs (residual dipolar couplings) between 1H-15N amide pairs (1DNH) were measured by NMR (nuclear magnetic resonance) at 16.45 T (700.400 MHz) and 21.14 T (900.230 MHz).
The peptide complex of Example 128 (PEG30-α10-PEG30) was used as a sample. The NMR sample was prepared by dissolving in a methanol-d3/chloroform-d (1:1) mixture containing 0.05% TFA to a concentration of 4.26 mM.
Specifically, 1H NMR and 2D 1H-15N IPAP-HSQC (in-phase/anti-phase heteronuclear single quantum coherence) NMR spectra were analyzed at 298 K using a BrukerAVANCE IV 900 MHz spectrometer and a BrukerAVANCE Ill HD 700 MHz spectrometer equipped with cryogenic probes. The NMR sample was prepared by dissolving in a methanol-d3/chloroform-d (1:1) mixture containing 0.05% TFA to a concentration of 4.26 mM. The acquisition parameters of IPAP were 2048 t2×1024 t1 points, 8 scans, 0.2 second recycle delay, 14 ppm spectral width for 1H and 26 ppm spectral width for 15N. The acquired data were split into two data sets, IP and AP, using the TopSpin software (Bruker, Germany). Each spectrum was processed by zero-filling up to 8192×8192 points. Peak positions were analyzed using the NMRFAM-SPARKY software.
Magnetic isotropy can be defined by Equation 1.
If Δχ is positive, the molecule will align with the direction of the magnetic field and vice versa. It is known that α-helices are aligned parallel to the external magnetic field because Δχ is positive.
N-H couplings (1JNH+1DNH) for 21 amino acid residues of the peptide of SEQ ID NO 10 (α10) in the peptide complex of Example 128 (PEG30-α10-PEG30) according to the present disclosure were measured. The result is shown in
1H
15N
1JNH + 1DNH
1H
15N
1JNH + 1DNH
Table 8 shows the experimental RDCs (1DNH, exp) of the peptide complex of Example 128 (PEG30-α10-PEG30). The experimental RDCs are calculated from Equation 2.
1DNH, exp
As shown in
The magnitude of the average RDC value (2.007 Hz) of the α10 peptide in the peptide complex of Example 128 is fairly high for an organic molecule. These results reveal that the peptide bonds in all 21 residues of the α10 peptide (SEQ ID NO 14) are involved in the formation of the α-helix structure.
Taken together, it can be seen that the hydrophobic peptides of the present disclosure (SEQ ID NOS 1-36) have superior magnetic responsiveness and the superior responsiveness to a magnetic field can be maintained even when the hydrophobic peptides are prepared into amphiphilic or hydrophilic molecules through binding with a polymer exhibiting hydrophilicity or a peptide exhibiting hydrophilicity.
In order to investigate whether the self-assembly process of the peptide complexes according to the present disclosure can be controlled with a magnetic field, the peptide complexes of Examples 46-50 having a linear rod-coil structure and the peptide complexes of Examples 98-102 having a cyclic rod-coil structure were prepared. The chemical structures of the peptide complexes of Examples 46-50 and the peptide complexes of Examples 98-102 are compared in
The CD spectra were analyzed using a Chirascan CD spectrometer (Applied Photophysics, UK). The peptide complex concentration ranged from 0.156 to 160 μM. All the samples were dissolved in H2O. Each scan was repeated three times using a 2-mm path-length cuvette and averaged. MRE (mean residue ellipticity) was calculated based on the number of amino acid residues.
MCD (magnetic circular dichroism) spectra were obtained using a Jasco-815 159-L spectrophotometer (Jasco, Japan). The concentration of the peptide complex was 20 μM in distilled water. Measurements were performed using a 2-mm path-length cuvette. The magnetic field of the permanent magnet in the MCD accessory (PM-491) was 1.6 T. Each scan was repeated three times and averaged.
AFM was performed using the NX10 system (Park Systems, Korea) in a non-contact mode with PPP-NCHR AFM probes (Nanosensors, Switzerland). The peptide complex (specimen) dispersed in an aqueous solvent was placed between neodymium magnets and measurements were compared before and after the application of a magnetic field. The magnetic field intensity was measured using a Model 450 gaussmeter (Lake Shore Cryotronics, USA).
an.d. = not determined
As shown in
MCD (magnetic circular dichroism) analysis was performed to investigate whether the helical stability of the αm peptide in the peptide complex according to the present disclosure is affected by the magnetic field. The peptide complexes of Examples 47 and 99 have partially stable α-helices. When a magnetic field of 1.6 T was applied to the peptide complexes of Examples 47 and 99 (
The extent of the increase in the [6]222/[θ]208 ratio was higher for the peptide complex of Example 99 (C-α5-PEG10) (from 0.89 to 1.01) than for the peptide complex of Example 47 (L-α5-PEG10) (from 0.86 to 0.91). This result suggests that the cyclic peptide complex responds more sensitively to a magnetic field than the linear peptide complex. That is to say, it was confirmed that the sensitivity to a magnetic field can be increased by structural difference even for the same sequence.
It was confirmed that the peptide complex according to the present disclosure is highly sensitive to a magnetic field and the α-helix structure can be controlled with a magnetic field. It was also investigated whether the self-assembly process of the peptide complex is affected by a magnetic field. The peptide complexes of Examples 51 and 99 were dissolved in aqueous solvents to induce self-assembly. The aqueous solvents were sonicated to prevent aggregation for clear observation. The aqueous solvent was placed in the equipment shown in
As shown in
Referring to
It was confirmed that the self-assembly behavior of the peptide complexes according to the present disclosure is changed by a very weak magnetic field of 0.07-0.25 T. It is because of the restriction in the motional degree of freedom of the peptide complex with the rod-coil during the self-assembly process due to the sensitivity of the MNP helix structure in the peptide complex to the magnetic field. Considering that molecules with the 1H-15N RDC values of about 20 kHz are considered to be fully oriented under a magnetic field, only a small fraction of the peptide complex of the present disclosure should be aligned in solution considering the experimental RDC value of α10 (see Table 3). However, the entropic penalty associated with self-assembly should be smaller for the aligned rod-coils than for the rod-coils randomly tumbling in solution (
It was investigated whether a complex can be formed through the interaction of the peptide complex according to the present disclosure and a negatively charged genetic material by applying a magnetic field. For this, the peptide complex of Example 60 (R-α10-PEG16) wherein a positively charged arginine (Arg or R) residue is added to the hydrophobic peptide and a linear plasmid DNA were prepared (
A linearized plasmid DNA with a sufficient length (estimated length: approximately 2.6 mm) was used for facile structural analysis by AFM and TEM. The cleavage map is shown in
The peptide complex of Example 60 (R-α10-PEG16) (34 μM in H2O) was slowly injected into a linear plasmid DNA of equal volume (30 ng/μL in H2O). Before the mixing, the peptide complex solution was sonicated to prevent nonspecific aggregation of the peptide complex. The peptide-DNA mixture solution was mixed further by gentle pipetting for 1 hour and incubated at room temperature for a prolonged period. Occasionally, 2 μL of the mixture was sampled and the morphological state was characterized by AFM and TEM.
EMSA was performed to investigate the mode of interaction between the peptide complex of Example 60 (R-α10-PEG16) and the linear plasmid DNA and their binding ratio. The concentration of the peptide complex was increased from 0 μM to 6214 μM, while the concentration of the linear plasmid DNA was fixed to 30 ng/μL (charge ratios (+/−): 0, 0.03, 0.06, 0.13, 0.25, 0.5, 1, 2, 4, 8, 16, 32, 64 and 128). After incubation at room temperature, 10% glycerol was added to the sample for gel loading. Electrophoresis was performed for 100 minutes at 90 V on 1% agarose gel. The bands were visualized by staining with the SYBR Safe DNA gel stain (Invitrogen, USA).
AFM was performed using the NX10 system (Park Systems, Korea) in a non-contact mode with PPP-NCHR AFM probes (Nanosensors, Switzerland). 2 μL of the sample solution was cast onto a freshly cleaved mica surface and dried. The data obtained with the SmartScan program (Park Systems, Korea) was analyzed using the XEI program (Park Systems, Korea).
TEM was performed using a JEM-F200 multi-purpose electron microscope (JEOL, Japan) at 200 kV. 2 μL of the sample solution was loaded on a copper grid (carbon type-B grid or Formvar/silicon monoxide grid, 200 mesh copper grids with a 97 μm hole; Ted Pella, USA). 1 hour later, 2 μL of 1-2% uranyl acetate was added to the dried sample for less than 1 minute and the negative stain solution was wicked off with filter paper. To analyze the internal packing structure of the artificial chromosome, the electron diffraction (ED) pattern was observed in selected areas.
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Through the EMSA, it was confirmed that the peptide-DNA nanostructure is formed when the charge ratio (+:−) of the peptide complex of Example 60 (R-α10-PEG16) and the linear plasmid DNA is between 0.5:1 and 1:1. A peptide-DNA nanostructure was prepared by mixing the peptide complex of Example 60 (R-α10-PEG16) and the linear plasmid DNA to have a charge ratio (+/− ratio) of 0.7, i.e., by mixing them at a charge ratio (+:−) of 0.5:1. The mixture was sampled 1 hour, 24 hours and 14 days later and then imaged by AFM and TEM.
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First, it was confirmed that the PD complex of the peptide complex of Example 60 (R-α10-PEG16) and the linear plasmid DNA successfully forms a nanostructure even at a charge ratio as low as 0.7.
From
As described above, the peptide complex according to the present disclosure self-assembles cooperatively with the genetic material, during which sequential assembly allows the formation of ordered nanostructures. Flat layers (terraces) and kinks were observed in the nanoribbons, indicating that they are formed by the epitaxial growth mechanism of crystal growth. The presence of steps and kinks between the flat layers (terraces) suggests that the nanoribbon growth can be described by the TSK (terrace-step-kink) model of crystal surface formation. The heights of the steps coincided with the diameter of DNA (2 nm) and its multiples. Thus, it was confirmed that the peptide-DNA nanostructure consists of multiple layers.
The peptide-DNA nanostructure in nanoribbon form according to the present disclosure has a living character. In polymer chemistry, the term “living” refers to the ability of an already formed polymer chain to further react with a freshly supplied monomer. Living behavior has been widely reported during the polymer synthesis such as living polymerization and living supramolecular polymerization. Recently, living behavior has also been found to occur in CDSA (living crystallization-driven self-assembly) or fibrilization of amyloid-β peptides. The discovery in the present disclosure is remarkable in that it presents a new structure.
The peptide-DNA nanostructure formed by mixing of the peptide complex of Example 60 (R-α10-PEG16) and the linear plasmid DNA has a living nanoribbon structure.
The peptide-DNA nanostructure having a living nanoribbon structure has been finally (2 weeks after incubation) confirmed as a nanostructure self-assembled into micrometer-scale objects, similar to human chromosomes in structure. The structure was termed ‘artificial chromosome’ structure. The ‘artificial chromosome’ structure of the peptide-DNA nanostructure was final and maintained for a long time.
As shown in
Through these results, it was confirmed that a nanostructure with an artificial chromosome-like structure is prepared through the following steps when the peptide complex of Example 60 (R-α10-PEG16) is mixed with the linear plasmid DNA: when the peptide complex of Example 60 (R-α10-PEG16) is mixed with the linear plasmid DNA, a nanostructure with a living nanoribbon structure is formed as the peptide complex surrounds the linear plasmid DNA and a nanostructure with an artificial chromosome structure is formed finally as the structure is stabilized gradually.
It is formed through charge interaction between the arginine residue (positively charged amino acid) in the peptide complex of Example 60 (R-α10-PEG16) and DNA and cooperative hydrophobic interaction between MNP-helices. The finally formed nanostructure in artificial chromosome form consists of a crystalline core and a solvated corona with a width of 200-500 nm and a length of 1-3 μm.
A linearized plasmid DNA with a sufficient length (estimated length: approximately 2.6 mm) was used for facile structural analysis by AFM and TEM. The cleavage map is shown in
The peptide complex of Example 60 (R-α10-PEG16) (34 μM in H2O) was slowly injected into a linear plasmid DNA of equal volume (30 ng/μL in H2O). Before the mixing, the peptide complex solution was sonicated to prevent nonspecific aggregation of the peptide complex. The peptide-DNA mixture solution was mixed further by gentle pipetting for 1 hour and incubated at room temperature for 14 days to prepare a peptide-DNA nanostructure (artificial chromosome form).
A sample (the linear plasmid DNA or the artificial chromosome) containing 60 ng (2 μL; 30 ng/μL) of DNA was mixed with 0.1 μL (0.2 unit) of DNase I and 1 μL of a 10× DNase I reaction buffer. The volume of the mixture was 10 μL. After 20 minutes of incubation at 37° C., 0.3 μL of 0.05 M EDTA was added to inactivate the enzyme. Then, the sample was mixed with 1.7 μL of 60% glycerol and electrophoresed on 1.1% agarose gel (120 minutes, 100 V). For visualization, the DNA was stained with an SYBR Safe DNA gel stain (Invitrogen, USA). To evaluate the time-dependent kinetics of DNA degradation, UV absorbance at 260 nm was recorded over time after the addition of DNase I. Each sample (71.2 μL) containing DNA (30 ng/μL) and a 10× DNase I reaction buffer (8 μL) was mixed in a cuvette. Then, DNase I (0.8 μL) was added to the cuvette and the sample was mixed by pipetting for about 90-105 seconds. UV absorbance at 260 nm (A260) was measured using a V-650 UV-vis spectrophotometer (JASCO, Japan). A quartz cuvette with a path length of 10 mm was used. The absorbance was recorded at intervals of 10 seconds.
4) Information Recovery from Artificial Chromosome
To assess the capability of recovering DNA information stored in the artificial chromosome, PCR (polymerase chain reaction) was conducted to amplify a specific DNA fragment of the sample DNA. The specific 310-bp fragment was amplified using the sense primer 5′-ACG GAG ACT GGA GTC GAA GAG G-3′ (SEQ ID NO 106) and the antisense primer 5′-GTA GGG CAA CTA GTG CAT CTC CC-3′ (SEQ ID NO 107). Each reaction mixture (50 μL) contained 50 ng of DNA, 10 pmol of each primer and 25 μL of 2× Quick Taq HS DyeMix (Toyobo, Japan). PCR amplification (30 cycle) was performed using a T100 thermal cycler (Bio-Rad, USA). After the amplification, the product was electrophoresed for 120 minutes at 80 V on 2% agarose gel (TBE system). A SYBR Safe DNA gel stain (Invitrogen, USA) was used for DNA staining.
As shown in
The peptide-DNA nanostructure (artificial chromosome form) according to the present disclosure is also very similar to human chromosomes (length: about 2-13 μm) in dimension and shape. Due to this structure, the peptide-DNA nanostructure (artificial chromosome form) according to the present disclosure can store a large quantity of biological data of genetic materials in minimal space. It can stably store the biological data without loss and the information of the genetic material can be retrieved through general analysis methods such as PCR, etc. Since the peptide-DNA nanostructure (artificial chromosome form) according to the present disclosure can store DNA information at high density, it can be utilized as a new DNA data storage medium.
To use the peptide-DNA nanostructure (artificial chromosome form) for the storage of genetic information and biological data, it should be able to protect DNA from enzymatic, chemical and physical damage. Therefore, the peptide-DNA nanostructure (artificial chromosome form) was exposed to DNase I for a long time and it was investigated whether the DNA is maintained without degradation.
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The peptide-DNA nanostructure prepared in Test Example 7 (nanoribbon form) was prepared. The peptide-DNA nanostructure (artificial chromosome form) was placed in the equipment shown in
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That is to say, it can be seen that the assembly or disassembly of the peptide-DNA nanostructure according to the present disclosure can be controlled effectively with a magnetic field.
The CD spectra of the hydrophobic peptides of Examples 1-36 were measured and the θ222 nm/θ208nm ratio was analyzed therefrom. The result is shown in Table 10. It can be seen that the helix structure is stabilized when the θ222nm/θ208nm ratio is 1.0-1.2.
As shown in Table 10, it was confirmed that the hydrophobic peptides of Examples 6-19 and 25-36 have a perfect α-helix structure. It can be seen that it is preferred that the repeat unit a constituting the hydrophobic peptide is repeated 6-13 times, most specifically 6-10 times, to achieve the most stable α-helix structure.
The peptide complexes of Examples 37-40, 46-53, 60-63, 66-67, 71-72 and 90-91 were purified by HPLC and analyzed by MALDI-TOF spectroscopy. The HPLC condition was as follows: C4 semiprep TFA ACN 15-35% 10-60 min, mobile phase: ACN (TFA 0.1%), gradient: 15-35%/10-60 min (+0.4%/min), flow rate: 2.000 mL/min, injection volume: 4.5 mL, injection solvent: ACN 5%, temperature: 25° C., UV detection: 230 nm.
As seen from
The CD spectra of the hydrophobic peptides of Examples 37-97 were measured and the θ222nm/θ208nm ratio was analyzed therefrom. The result is shown in Table 11. It can be seen that the helix structure is stabilized when the θ222nm/θ208nm ratio is 1.0-1.2.
As shown in Table 11, no minimum was observed at 222 and 208 nm in the RGD spectra of the peptide complexes of Example 67, 72 and 75. From the above results, it was confirmed that most of the peptide complexes according to the present disclosure have a stable α-helix structure. The peptide complexes of Example 37, 47, 52, 55 and 58, wherein the number of the repeat unit a constituting the hydrophobic peptide is 4, had the θ222nm/θ208nm ratio lower than 0.5. Accordingly, it is preferred to use the peptide complexes of Examples 39-45, 48-51, 53-55, 56-57 and 59-97, wherein the number of the repeat unit a constituting the hydrophobic peptide is 6-13.
The peptide complexes of Examples 37-40 were imaged by AFM. 25 μM of the peptide complex was dissolved in distilled water, sonicated for 5 minutes, incubated overnight and dropped on mica for measurement.
The peptide complexes other than the peptide complexes of Examples 37-40 were also imaged by AFM and their average diameters and the morphologies of self-assembled structures were observed.
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As shown in Table 12, it can be seen that the hydrophobic peptide having an α-helix structure according to the present disclosure successfully self-assembles into spherical particles in liquid not only with the RGD hydrophilic peptide but also with the hydrophilic polymer such as PEG, etc.
In addition, it can be seen that the peptide complex according to the present disclosure self-assembles into spherical nanoparticles with an average diameter of 20-400 nm in an aqueous solvent.
However, because irregular aggregation occurs when the number of the repeat unit of the hydrophobic peptide having α-helices is 6 or smaller, it is preferred to use the hydrophobic peptide having α-helices wherein the number of the repeat unit is 6 or larger.
1) Linear dsDNA
A large-scale plasmid DNA (pTWIN-Rev; 7,528 bp) was prepared using the NucleoBond Xtra Maxi Plus kit (Macherey-Nagel, Germany). The plasmid DNA was digested into linear double-stranded DNA with the BamH1 restriction enzyme (New England Biolabs, USA). The linear plasmid DNA was purified from the restriction digest using 1.1% agarose gel. Electrophoresis was conducted at 120 V for 180 minutes in a 1× TBE buffer. After the electrophoresis, the DNA was stained with the SYBR Safe DNA gel stain (Invitrogen, USA). A slice of the DNA band that corresponds to 7.5-kb linear dsDNA was cut out and the linear plasmid DNA was extracted using the MEGA Quick-Spin™ Plus kit (iNtRON, Korea). The purity of the DNA was found to be high (A260/A280 ratio was 1.8 and A260/A230 ratio was 2.0-2.2) as measured with a Nanodrop 1000 spectrophotometer (Thermo Scientific, USA).
The peptide complex of Example 60 was dissolved in distilled water and then sonicated. An R-α10-PEG16/dsDNA nanostructure was prepared by slowly adding dsDNA (1.8 ng/μL) of the same volume to the peptide complex. After reaction at room temperature for 2-3 minutes, the nanostructure was analyzed first by AFM and TEM. The second AFM and TEM analyses were performed after 12 days of reaction. The third AFM and TEM analyses were performed after 22 days of reaction.
60 ng of dsDNA (2 μL; 30 ng/μL) or R-α10-PEG16/dsDNA nanostructure (artificial chromosome form) was mixed with 0.1 μL (0.2 unit) of DNase I and 1 μL of a 10× DNase I reaction buffer. The volume of the mixture was 10 μL. After 20 minutes of incubation at 37° C., 0.3 μL of 0.05 M EDTA was added to inactivate the enzyme. Then, the sample was mixed with 1.7 μL of 60% glycerol and electrophoresed on 1.1% agarose gel (120 minutes, 100 V). For visualization, the DNA was stained with an SYBR Safe DNA gel stain (Invitrogen, USA). To evaluate the time-dependent kinetics of DNA degradation, UV absorbance at 260 nm was recorded over time after the addition of DNase I. Each sample (71.2 μL) containing DNA (30 ng/μL) and a 10× DNase I reaction buffer (8 μL) was mixed in a cuvette. Then, DNase I (0.8 μL) was added to the cuvette and the sample was mixed by pipetting for about 90-105 seconds. UV absorbance at 260 nm (A260) was measured using a V-650 UV-vis spectrophotometer (JASCO, Japan). A quartz cuvette with a path length of 10 mm was used. The absorbance was recorded at intervals of 10 seconds.
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Based on these results, the α-helix structure of the peptide complex of Example 60 (R-α10-PEG16), the dsDNA and the R-α10-PEG16/dsDNA nanostructure was compared.
It was investigated whether the R-α10-PEG16/dsDNA nanostructure also protects DNA stably from enzymatic degradation through the DNase I protection assay described above.
1) Linear dsDNA
First, a large-scale plasmid DNA (pTWIN-Rev; 7,528 bp) was prepared using the NucleoBond Xtra Maxi Plus kit (Macherey-Nagel, Germany). The plasmid DNA was digested into linear double-stranded DNA with the BamH1 restriction enzyme (New England Biolabs, USA). The linear plasmid DNA was purified from the restriction digest using 1.1% agarose gel. Electrophoresis was conducted at 120 V for 180 minutes in a 1× TBE buffer. After the electrophoresis, the DNA was stained with the SYBR Safe DNA gel stain (Invitrogen, USA). A slice of the DNA band that corresponds to 7.5-kb linear dsDNA was cut out and the linear plasmid DNA was extracted using the MEGA Quick-Spin™ Plus kit (iNtRON, Korea). The purity of the DNA was found to be high (A260/A280 ratio was 1.8 and A260/A230 ratio was 2.0-2.2) as measured with a Nanodrop 1000 spectrophotometer (Thermo Scientific, USA).
The peptide complex of Example 63 was dissolved in distilled water and then sonicated. An R4-α10-PEG16/dsDNA nanostructure was prepared by slowly adding dsDNA (145.2 ng/μL in H2O) of the same volume to the peptide complex at a concentration of 22.6 μM. After reaction at room temperature for 40 minutes, the nanostructure was analyzed first by AFM and TEM. The second AFM and TEM analyses were performed after 111 days of reaction.
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1) Preparation of Plasmid DNA, Linear dsDNA and ssDNA
First, a large-scale plasmid DNA (pTWIN-Rev; 7,528 bp) was prepared using the NucleoBond Xtra Maxi Plus kit (Macherey-Nagel, Germany). The plasmid DNA was digested into linear double-stranded DNA with the BamH1 restriction enzyme (New England Biolabs, USA) and purified using 1.1% agarose gel. Electrophoresis was conducted at 120 V for 180 minutes in a 1× TBE buffer. After the electrophoresis, the DNA was stained with the SYBR Safe DNA gel stain (Invitrogen, USA). A slice of the DNA band that corresponds to 7.5-kb linear dsDNA was cut out and the linear plasmid DNA was extracted using the MEGA Quick-Spin™ Plus kit (iNtRON, Korea). The purity of the DNA was found to be high (A260/A230 ratio was 1.8 and A260/A230 ratio was 2.0-2.2) as measured with a Nanodrop 1000 spectrophotometer (Thermo Scientific, USA).
As ssDNA, a short oligomer with a length of 20 nt prepared by Bioneer was used (SEQ ID NO 120).
The peptide complex of Example 63 was dissolved in distilled water and then sonicated. R-α10-PEG16/dsDNA and R-α10-PEG16/ssDNA nanostructures with the charge ratio (+/−) of the nucleic acid material and the peptide being 0, 0.03, 0.06, 0.12, 0.25, 0.5, 1, 2, 4, 8, 16, 32, 64 and 128 were prepared by slowly injecting dsDNA (30 ng/μL in H2O) or ssDNA (30 ng/μL in H2O) at various concentrations to the peptide complex of Example 60. EMSA was performed after 1 hour of incubation.
For EMSA (electrophoretic mobility shift assay), 10% glycerol was added to the sample. Electrophoresis was conducted at 100 V for 120 minutes on 1% agarose gel. The band was stained with the SYBR Safe DNA gel stain (Invitrogen, USA) for visualization.
From
Peptide-DNA nanostructures were prepared by mixing the peptide complexes of Examples 61-63 with dsDNA. A peptide-DNA nanostructure was prepared by mixing the peptide complex of Example 61 with a plasmid DNA (circular dsDNA, pTWIN-rev=7.5 kbp). The preparation process was the same as in Test Example 15. The R-α10-PEG16/pDNA, R-α10-PEG16/dsDNA nanostructures were prepared by mixing the nucleic acid material and the peptide at a charge ratio (+/−) of 0, 0.03, 0.06, 0.12, 0.25, 0.5, 1, 2, 4, 8, 16, 32, 64, 128 and 256. EMSA was performed after incubation for 1.5 hours.
For EMSA (electrophoretic mobility shift assay), 10% glycerol was added to the sample. The electrophoresis was performed for 120 minutes at 100 Von 1% agarose gel. The band was visualized by staining with the SYBR Safe DNA gel stain (Invitrogen, USA).
As shown in
The cyclic peptide complexes of Examples 98-111 were purified by HPLC and analyzed by MALDI-TOF and CD spectroscopy. The HPLC condition was as follows: C4 semiprep TFA ACN 15-35% 10-60 min, mobile phase: ACN (TFA 0.1%), gradient: 15-35%/10-60 min (+0.4%/min), flow rate: 2.000 mL/min, injection volume: 4.5 mL, injection solvent: ACN 5%, temperature: 25° C. UV detection: 230 nm.
Table 13 shows the result of analyzing the morphological characteristics of the cyclic peptide complexes of Examples 98-111 by CD spectroscopy.
an.d. = not determined
As shown in
Through the experiments described above, the self-assembly behaviors of the peptide complex according to the present disclosure and the nanostructure with an artificial chromosome-like structure prepared therefrom were elucidated and their interactions with genetic materials were investigated to confirm their potential as genetic material storage media and systems. For stable storage of genetic materials and use in the fields of cells, medicine and foods, cytotoxicity is also of great importance. Accordingly, the cytotoxicity of the peptide complex according to the present disclosure and the nanostructure with an artificial chromosome-like structure prepared therefrom were analyzed.
For investigation of cytotoxicity, WST-1 assay was performed using Hela cells. First, Hela cells were subcultured in DMEM supplemented with 10% FBS (fetal bovine serum). After dispensing the cells in each well at 5×04 Hela cells/well and culturing for 16 hours, they were treated with samples of various concentrations (5, 10 and 20 μM) and cultured at 37° C. for 24 hours. After adding WST-1 solution to the cultured cells, absorbance was measured at 450 nm 4 hours later using a microplate reader (Bio-Tek instrument Co., WA, USA).
The peptide complexes of Examples 40, 60 and 102 were prepared as the samples. In addition, as in Test Example 13 and Test Example 14, peptide-DNA nanostructures were prepared by mixing the peptide complexes of Examples 60 and 63 with linear plasmid DNA (artificial chromosome form, incubation for 12 days). Untreated normal cells were used as a control group.
The peptide complexes of Examples 112-128 have a coil-rod-coil structure. The peptide complexes were purified by HPLC and analyzed by MALDI-TOF and CD spectroscopy. The HPLC condition was as follows: C4 semiprep TFA ACN 15-35% 10-60 min, mobile phase: ACN (TFA 0.1%), gradient: 15-35%/10-60 min (+0.4%/min), flow rate: 2.000 mL/min, injection volume: 4.5 mL, injection solvent: ACN 5%, temperature: 25° C., UV detection: 230 nm.
As shown in
Number | Date | Country | Kind |
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10-2022-0162494 | Nov 2022 | KR | national |