Patent Application
20230332209
The present invention relates to a quencher having a quenching effect on a fluorescent material exhibiting a luminescent property at an excited energy level, and various uses thereof.
A quencher means a molecule capable of quenching the fluorescence of a fluorescent molecule, and a dye having a property of absorbing light is generally used.
A quenching phenomenon is known to occur through a mechanism including fluorescence resonance energy transfer (FRET), photo-induced electron transfer and dye coagulation such as H-dimer formation.
When a quencher is used to control or quench the fluorescence of a fluorescent dye, it is most important whether the absorption wavelength range of a quenching dye covers (overlaps) a considerable part or the entire region of the wavelength region of fluorescence exhibited by the fluorescent dye.
In order to obtain a quenching effect, the length between the fluorescence dye and the quencher is also important, and for example, the number of bases in the case of DNA or the number of amino acids in the case of a peptide/protein is considered. To obtain a higher quenching effect, the length of a linker labeled with a fluorescence dye and a quencher may be adjusted.
In the case of a quencher generally used commercially in the field of biology, although a fluorescence-fluorescent dye combination, which uses a FRET phenomenon, has been widely used, a dye structure does not emit light but only absorbs light is generally selected. The combined fluorescent-quenching, and fluorescent-fluorescent dyes may impart a kind of on/off function of fluorescence because the original fluorescence is restored or intensified when the distance between the two dyes increases or the two dyes are separated from a biomolecule, and in consideration of such a characteristic, may be widely used in designing biosensors or activation probes that can respond to biomarkers for specific proteins/enzymes.
When fluorescent or quenching dyes used in the field of biology are used alone, they are only limited to FDA-approved dyes such as indocyanine green or methylene blue, and a reactive group capable of binding to a substituent of a biomolecule is introduced. While various types of reactive groups described above are known, substituent selectivity, reaction rate, yield, reproducibility and stability have been verified by researchers for a long time. In recent years, reactive groups introduced to a dye for practical research or commercial purposes are limited to several.
For example, the most frequently used reactive groups for binding with an amine group of a protein molecule are succinimidyl ester and isothiocyanate, the most frequently used reactive group for binding with a thiol group of a protein molecule is maleimide, and as a reactive group for binding with a hydroxyl group of a protein molecule, dichlorotriazine is mainly used.
However, in most cases, the reactive groups are bound by substitution or it is difficult to maintain a long-term reaction and storage stability under a water-soluble condition.
The present invention is directed to providing a novel quencher as a compound that can be widely used to observe the identification of a biomolecule in the optical imaging field.
The present invention is also directed to providing an oligonucleotide, a composition and a support for detecting a nucleic acid, and a method of detecting a nucleic acid, including the novel quencher.
To solve the above-described technical problems, according to one aspect of the present invention, a quencher represented by Formula 1 or 2 below is provided.
Here,
In addition, according to another aspect of the present invention, a quencher represented by Formula 4 or 5 below is provided.
Here,
In addition, according to still aspect of the present invention, an oligonucleotide that includes the above-described quencher, a minor groove binder (MGB), and a fluorophore is provided.
In addition, according to yet another aspect of the present invention, a composition for detecting a nucleic acid, including the above-described oligonucleotide, is provided.
In addition, according to yet another aspect of the present invention, a support for detecting a nucleic acid, including the above-described quencher, a support, and a linker connecting the quencher and the support, is provided.
In addition, according to yet another aspect of the present invention, a method of detecting a nucleic acid, which includes (a) preparing a reaction mixture including a target nucleic acid, a reagent necessary for amplifying the target nucleic acid, and an oligonucleotide, (b) amplifying the target nucleic acid in the reaction mixture by a chain polymerase reaction, and (c) measuring the fluorescence intensity of the reaction mixture, is provided.
The present invention relates to a quencher exhibiting a quenching effect on a fluorescent material exhibiting a luminescent property at an excited energy level, and various uses thereof, and the quencher according to the present invention can exhibit an excellent quenching property due to high quenching efficiency compared to a conventional quencher.
In order to better understand the present invention, certain terms are defined herein for convenience. Unless defined otherwise herein, scientific and technical terms used herein will have meanings commonly understood by those of ordinary skill in the art.
In addition, unless specifically indicated otherwise, terms in a singular form also include plural forms, and terms in a plural form should be understood to include singular forms as well.
Novel Quencher
According to one aspect of the present invention, a quencher represented by Formula 1 or 2 below is provided.
In addition, according to another aspect of the present invention, a quencher represented by Formula 4 or 5 below is provided. Formula 4 represents the resonance structure of Formula 1, and Formula 5 represents the resonance structure of Formula 2. That is, the quencher exists as at least one structure selected from Formula 1 and Formula 4, or exists as at least one structure selected from Formula 2 and Formula 5.
In the quencher represented by Formula 1, 2, 4 or 5, Q is represented by Formula 3 below.
In the quencher represented by Formula 1, 2, 4 or 5, R1 to R6 and R9 to R14 are each independently (1) a moiety selected from hydrogen, deuterium, substituted or unsubstituted C1-C40 alkyl, substituted or unsubstituted C1-C40 heteroalkyl having at least one hetero atom, substituted or unsubstituted C2-C40 alkenyl, substituted or unsubstituted C2-C40 alkynyl, substituted or unsubstituted C3-C20 cycloalkyl, substituted or unsubstituted C3-C20 cycloalkenyl, substituted or unsubstituted C2-C20 heterocycloalkyl, hydroxy, oxido (—O−), substituted or unsubstituted C1-C40 alkoxy, substituted or unsubstituted C3-C40 cycloalkyloxy, substituted or unsubstituted C5-C40 aryloxy, substituted or unsubstituted C2-C40 heteroaryloxy, substituted or unsubstituted C5-C50 aryl, substituted or unsubstituted C2-C50 heteroaryl, substituted or unsubstituted C5-C50 aralkyl, substituted or unsubstituted C1-C40 alkylthio, substituted or unsubstituted C5-C40 arylthio, substituted or unsubstituted C3-C40 cycloalkylthio, substituted or unsubstituted C2-C40 heteroarylthio, substituted or unsubstituted acylamino, acyloxy, substituted or unsubstituted phosphino, carboxylate (—CO2−), trifluoromethylsulfonyl (—SO2CF3), substituted or unsubstituted ammonium, nitro, sulfonic acid (—SO3H), sulfonate, substituted sulfonyl, substituted sulfonic ester, substituted or unsubstituted sulfonamide, substituted thioketone, trihalomethyl (—CF3, —CCl3, —CBr3, —CI3), haloformyl (—COCl, —COBr, —COI), formyl (—CHO), acyl, carboxyl, substituted ester, substituted or unsubstituted aminocarbonyl, nitro, nitroso (—N═O), fluoro (—F), chloro (—Cl), bromo (—Br), iodo (—I), substituted or unsubstituted germanium, substituted or unsubstituted boron, substituted or unsubstituted aluminum, substituted or unsubstituted silyl, substituted or unsubstituted amide, carbamate, carboxylate, substituted or unsubstituted phosphine, substituted or unsubstituted phosphoric acid, phosphate, phosphonic acid, phosphonate, nitrile, hydrazine, acetal, ketal, and polyalkylene oxide,
Here, R9 and R10 are not electron-withdrawing groups.
Here, the electron-withdrawing group refers to a moiety having a tendency of withdrawing electrons due to an inductive effect or resonance effect, and may also be referred to as a deactivating group. Examples of the electron-withdrawing groups of the above-described moieties include trifluoromethylsulfonyl (—SO2CF3), substituted or unsubstituted ammonium (—NR3+), nitro, sulfonic acid (—SO3H), sulfonyl (—SO2R), nitrile, trihalomethyl (—CF3, —CCl3, —CBr3, —CI3), haloformyl (—COCl, —COBr, —COI), formyl (—CHO), acyl (—COR), carboxyl (—CO2H), substituted carbonyl (—CO2R), substituted or unsubstituted aminocarbonyl (—CONR2), and nitroso (—N═O). In addition, unless defined otherwise, the electron-withdrawing group may further include a moiety having a tendency of withdrawing electrons, other than the moieties exemplified above.
Accordingly, at R9 and R10, a moiety having a tendency of withdrawing electrons among the moieties exemplified above and a moiety having a tendency of withdrawing electrons, other than the moieties exemplified above, are not preferably located.
In addition, at least one of R1 to R14 is preferably (1) a moiety selected from carboxyl, carboxyl derivative, hydroxyl, haloalkyl, dienophile, aldehyde, substituted ketone, sulfonyl halide, thiol, substituted or unsubstituted amino, sulfhydryl, alkene, alkyne, halogen, hydrazine, azido, imido, ketene, isocyanate, epoxide, and phosphoramidite, or any moiety substituted with the moiety, (2) a reactive group enabling a covalent bond with a moiety selected from carboxyl, carboxyl derivative, hydroxyl, haloalkyl, dienophile, aldehyde, substituted ketone, sulfonyl halide, thiol, substituted or unsubstituted amino, sulfhydryl, alkene, alkyne, halogen, hydrazine, azido, imido, ketene, isocyanate, epoxide, and phosphoramidite, or any moiety substituted with the reactive group, or (3) a protecting group selected from an alcohol-derived protecting group, an amine-derived protecting group, a carbonyl-derived protecting group, a carboxylic acid-derived protecting group, a phosphate-derived protecting group, and an alkyne-derived protecting group. In addition, unless defined otherwise, the protecting group may be a moiety enabling introduction into a specific reactive group and removal thereof, other than the protecting group exemplified above.
Here, as a reactive group, (a) a carboxyl group and a derivative thereof: N-hydroxysuccinimide ester, N-hydroxy benztriazole ester, acyl halide, acyl imidazole, thioester, p-nitrophenyl ester, alkyl ester, alkenyl ester, alkynyl ester and aromatic ester; (b) hydroxyl that can be converted into ester, ether, or aldehyde; (c) haloalkyl that can be covalently attached to a different moiety by substituting a halogen, for example, with a nucleophilic moiety such as amine, a carboxylate anion, a thiol anion, a carboanion or an alkoxide ion; (d) a dienophile that can have a Diels-Elder reaction with, for example, a maleimido group; (e) aldehyde or ketone that can form a carbonyl derivative such as an imine, a hydrazone, a semi-carbazone, or an oxime; (f) sulfonyl halide that forms a sulfoamide by having a reaction with an amine; (g) thiol that can be converted into a disulfide or have a reaction with an acyl halide; (h) amine or sulfhydryl that can be acylated, alkylated or oxidized; (i) alkene which is involved in cycloaddition, acylation, or Michael reaction; (j) epoxide which is able to react with an amine or hydroxyl compound; (k) phosphoramidite, and other standard functional groups useful for a nucleic acid reaction may be used. Such a reactive group may be suitably selected so as to participate in or not to interfere with a reaction necessary for synthesizing a reactive quencher.
In another embodiment, these reactive groups may be protected with a protective group so as not to participate in a random reaction in the presence of the protective group.
The protecting group may be introduced by chemically converting a reactive group to impart reaction selectivity of at least some reactive groups during a continuous chemical or biological reaction process.
As the protecting group, an alcohol-derived protecting group, an amine-derived protecting group, a carbonyl-derived protecting group, a carboxylic acid-derived protecting group, a phosphate-derived protecting group, or an alkyne-derived protecting group is used. In addition, unless defined otherwise, the protecting group may be a group enabling introduction into a specific reactive group and removal thereof, other than the protecting group exemplified above.
For example, when a reactive group is hydroxyl, as a protecting group, acetyl, benzoyl, benzyl, β-methoxyethoxymethyl ether, dimethoxytrityl, methoxymethyl ether, methoxytrityl, p-methoxybenzyl ether, p-methoxyphenyl ether, methylthiomethyl ether, silyl ether, trityl or a derivative thereof may be used.
In addition, when a reactive group is amino, as a protecting group, tert-butyl carbamate, benzyl carbamate, acetamide, phthalimide, p-toluene sulfonamide or a derivative thereof may be used. For preferable examples of protective groups, reference may be made to contents of the following reference (Greene et al., PROTECTIVE GROUPS IN ORGANIC SYNTHESIS, John Wiley & Sons, New York, 1999; https://en.wikipedia.org/wiki/Protecting group).
Quenchers according to various embodiments of the present invention are capable of binding to and labeling a target biomolecule (e.g., nucleic acid) through the above-described reactive group.
The above-described reactive groups are functional groups that are able to react with a moiety such as an amino group, an imino group, a thiol group or a hydroxyl group of a target biomolecule, and may form a covalent bond, such as an amide bond, an imide bond, a urethane bond, an ester bond, a phosphite bond, a phosphate bond, or a guanine bond, between a quencher and a target biomolecule.
Meanwhile, in the quencher represented by Formula 1, 2, 4 or 5, the case in which all of R9 to R14 are hydrogen is excluded.
While R9 to R14 may each be independently present as the moieties defined above, in some embodiments, at least one of R9 to R14 may be bound with an adjacent substituent, thereby forming a substituted or unsubstituted ring (e.g., a 4-element ring, a 5-element ring, a 6-element ring, a ring consisting of more than 6 atoms, or a fused ring in which multiple rings are joined). In addition, the ring may be an aliphatic or aromatic ring. In addition, the ring may be a ring substituted with any moiety listed in (1) to (4) described above.
Specifically, when R13 of R9 to R14 is bound with an adjacent substituent to form a substituted or unsubstituted ring, R13 may be bound with R11 via C, N, Se or Si to form a substituted or unsubstituted ring, or may be bound with R11 by a single bond to form a substituted or unsubstituted ring.
In addition, when R14 of R9 to R14 is bound with an adjacent substituent to form a substituted or unsubstituted ring, R14 may be bound with R12 via C, N, Se or Si to form a substituted or unsubstituted ring, or may be bound with R12 by a single bond to form a substituted or unsubstituted ring.
The formation of substituted or unsubstituted rings by the above-described R13 and R14 is independent from each other, and thus the ring formed by bonding R11 and R13 in one compound together and the ring formed by bonding R12 and R14 in one compound together may be present simultaneously.
In addition, R1 and R2 may be bound with each other to form a substituted or unsubstituted ring, or R1 and/or R2 may be bound with adjacent R5 to form a substituted or unsubstituted ring.
In addition, R3 and R4 may be bound with each other to form a substituted or unsubstituted ring, or R3 and/or R4 may be bound with adjacent R6 to form a substituted or unsubstituted ring.
When adjacent moieties are bound with each other to form a substituted ring, any carbon in the ring may be substituted with any moiety listed in (1) to (4) described above.
In addition, when any one group of R1 to R14 is substituted, any carbon in the group may be substituted with any group listed in (1) to (4) described above.
In the present invention, when Ra (a is a natural number between 1 to 14) is alkenyl or alkynyl, sp2-hybrid carbon of alkenyl or sp-hybrid carbon of alkenyl may be directly bound, or indirectly bound by sp3-hybrid carbon of alkyl binding to sp2-hybrid carbon of alkenyl or sp-hybrid carbon of alkynyl.
In the present invention, a Ca-Cb moiety means a moiety that has a to b carbon atoms. For example, Ca-Cb alkyl means a saturated aliphatic group, including linear and branched alkyls having a to b carbon atoms. The linear or branched alkyls may have 40 or less Ca-Cb functional groups (e.g., C1-C10 linear or C3-C10 branched) in the main chain thereof.
Specifically, the alkyl may be methyl, ethyl, n-propyl, i-propyl, n-butyl, s-butyl, i-butyl, t-butyl, pent-1-yl, pent-2-yl, pent-3-yl, 3-methylbut-1-yl, 3-methylbut-2-yl, 2-methylbut-2-yl, 2,2,2-trimethyleth-1-yl, n-hexyl, n-heptyl, or n-octyl.
In addition, in the present invention, alkoxy means both of a —O-(alkyl) group and a —O-(unsubstituted cycloalkyl) group, and is linear or branched hydrocarbon having one or more ether groups and 1 to 10 carbon atoms.
Specifically, the alkoxy includes methoxy, ethoxy, propoxy, isopropoxy, n-butoxy, tert-butoxy, sec-butoxy, n-pentoxy, n-hexoxy, 1,2-dimethylbutoxy, cyclopropyloxy, cyclobutyloxy, cyclopentyloxy, and cyclohexyloxy, but the present invention is not limited thereto.
In addition, in the present invention, halogen means fluoro (—F), chloro (—Cl), bromo (—Br), or iodo (—I), and haloalkyl means alkyl substituted with the above-described halogen. For example, halomethyl means methyl in which at least one of the hydrogens is replaced with halogen (—CH2X, —CHX2 or —CX3).
In the present invention, aralkyl is the generic term for —(CH2)nAr, which is a moiety in which aryl substituted for a carbon of alkyl. As an example of the aralkyl includes benzyl (—CH2C6H5) or phenethyl (—CH2CH2C6H5).
In the present invention, aryl means, unless defined otherwise, an unsaturated aromatic ring including a single ring, or multiple rings (preferably, 1 to 4 rings) conjugated or connected by a covalent bond. Non-limiting examples of the aryl include phenyl, biphenyl, o-terphenyl, m-terphenyl, p-terphenyl, 1-naphthyl, 2-naphthyl, 1-anthryl, 2-anthryl, 9-anthryl, 1-phenanthrenyl, 2-phenanthrenyl, 3-phenanthrenyl, 4-phenanthrenyl, 9-phenanthrenyl, 1-phyrenyl, 2-phyrenyl, and 4-phyrenyl.
In the present invention, heteroaryl means a moiety in which one or more carbon atoms in the aryl defined above are substituted with a non-carbon atom such as nitrogen, oxygen or sulfur. Non-limiting examples of the hetero aryl include furyl, tetrahydrofuryl, pyrrolyl, pyrrolidinyl, thienyl, tetrahydrothienyl, oxazolyl, isoxazolyl, triazolyl, thiazolyl, isothiazolyl, pyrazolyl, pyrazolidinyl, oxadiazolyl, thiadiazolyl, imidazolyl, imidazolinyl, pyridyl, pyridaziyl, triazinyl, piperidinyl, morpholinyl, thiomorpholinyl, pyrazinyl, piperainyl, pyrimidinyl, naphthyridinyl, benzofuranyl, benzothienyl, indolyl, indolinyl, indolizinyl, indazolyl, quinolizinyl, quinolinyl, isoquinolinyl, cinnolinyl, phthalazinyl, quinazolinyl, quinoxalinyl, pteridinyl, quinuclidinyl, carbazoyl, acridinyl, phenazinyl, phenothizinyl, phenoxazinyl, purinyl, benzimidazolyl, benzothiazolyl, and analogs conjugated therewith.
In the present invention, unless defined otherwise, a hydrocarbon ring (cycloalkyl) or a hydrocarbon ring having a hetero atom (heterocycloalkyl) may be understood as a cyclic structure of an alkyl or heteroalkyl, respectively.
Non-limiting examples of the cycloalkyls include cyclopentyl, cyclohexyl, 1-cyclohexenyl, 3-cyclohexenyl, and cycloheptyl. Non-limiting examples of the heterocycloalkyls include 1-(1,2,5,6-tetrahyropyrinyl), 1-piperidinyl, 2-piperidinyl, 3-piperidinyl, 4-morpholinyl, 3-morpholinyl, tetrahydrofuran-2-yl, tetrahyrofuran-3-yl, tetrahydrothiene-2-yl, tetrahydrothiene-3-yl, 1-piperazinyl, and 2-piperazinyl.
In addition, the cycloalkyl or heterocycloalkyl may have a form with which cycloalkyl, heterocycloalkyl, aryl or hetero aryl is conjugated or connected by a covalent bond.
Here, the polyalkyleneoxide is a water-soluble polymer moiety, and includes polyethylene glycol (PEG), polypropylene glycol (PPG), a polyethylene glycol-polypropylene glycol (PEG-PPG) copolymer, and an N-substituted methacrylamide-containing polymer and copolymer.
The polyalkyleneoxide may be additionally substituted, as needed, as long as the characteristics of a polymer are maintained. For example, the substitution may be a chemical bond for increasing or decreasing the chemical or biological stability of a polymer. As a specific example, any carbon or terminal carbon in the polyalkyleneoxide may be substituted with hydroxy, alkyl ether (methyl ether, ethyl ether, propyl ether or the like), carboxylemethyl ether, carboxyethyl ether, benzyl ether, dibenzylmethyl ether, or dimethylamine. In one embodiment, the polyalkyleneoxide may be polyethyleneoxide terminated with methyl ether (mPEG), wherein mPEG is represented by the Formula —(CH2CH2O)nCH3, whose size may change depending on the size of n corresponding to the number of ethylene glycol repeat units.
In addition, the quenchers represented by Formulas 1, 2, 4 and 5 may have a structure further including a counter ion. The counter ion, which is an organic or inorganic anion, may be suitably selected in consideration of the solubility and stability of the quenchers.
Examples of the counter ions of the quencher according to one embodiment of the present invention include inorganic anions such as a phosphoric acid hexafluoride ion, a halogen ion, a phosphoric acid ion, a perchloric acid ion, a periodic acid ion, an antimony hexafluoride ion, a tartaric acid hexafluoride ion, a fluoroboric acid ion, and a tetrafluoride ion; and organic anions such as a thiocyanate ion, a benzenesulfonic acid ion, a naphthalenesulfonic acid ion, a p-toluenesulfonic acid ion, an alkysulfonic acid ion, a benzenecarboxylic acid ion, an alkylcarboxylic acid ion, a trihaloalkylcarboxylic acid ion, an alkyl sulfonic acid ion, a trihaloalkylsulfonic acid ion, and a nicotinic acid ion. In addition, metal compound ions such as bisphenylditol, thiobisphenol chelate, and bisdiol-α-diketone, metal ions such as sodium and potassium, and quaternary ammonium salts may also be selected as the counter ions.
Examples of the quenchers represented by Formulas 1, 2, 4 and 5 are as follows. Compounds 1 to 22 exemplified below may be synthesized by a known synthesis method with reference to preparation examples disclosed herein or the contents defined herein relating to the quenchers represented by Formulas 1, 2, 4 and 5.
A biomolecule targeting the quenchers represented by Formulas 1, 2, 4 and 5 disclosed herein may be at least one selected from an antibody, a lipid, a protein, a peptide, a carbohydrate, and a nucleic acid (including a nucleotide).
Specific examples of the lipids include fatty acids, phospholipids, and lipopolysaccharides, and specific examples of the carbohydrates include monosaccharides, disaccharides, and polysaccharides (e.g., dextran).
Here, as any moiety of the quenchers represented by Formulas 1, 2, 4 and 5, or a moiety for reacting with a reactive group binding to the quenchers represented by Formulas 1, 2, 4 and 5, the biomolecule may include at least one selected from amino, sulfhydryl(sulphydryl), carbonyl, hydroxyl, carboxyl, phosphate and thiophosphate, or have a derivative thereof.
In addition, the biomolecule may be an oxy- or deoxy-polynucleic acid which includes at least one selected from amino, sulfhydryl(sulphydryl), carbonyl, hydroxyl, carboxyl, phosphate and thiophosphate, or a derivative thereof.
Moreover, the quencher represented by Formula 1, 2, 4 or 5 may be used to label a drug including at least one selected from amino, sulfhydryl, carbonyl, hydroxyl, carboxyl, phosphate and thiophosphate, a hormone (including a receptor ligand), a receptor, an enzyme or enzyme substrate, a cell, a cell membrane, a toxin, a microorganism, or a nano biomaterial (polystyrene microsphere or the like), in addition to the biomolecule.
Oligonucleotide, Composition for Detecting Nucleic Acid and Support for Detecting Nucleic Acid, Including Novel Quencher
According to another aspect of the present invention, an oligonucleotide including at least one selected from the quenchers represented by Formulas 1, 2, 4 and 5 is provided.
The oligonucleotide refers to a polymer of one to hundreds of nucleotides, and includes DNA, RNA, or PNA. In addition, such oligonucleotides include analogs thereof, for example, those with chemically modified nucleotides or those that are easily modified by those of ordinary skill in the art, such as those to which a sugar binds, and are single-stranded or double-stranded.
The oligonucleotide preferably includes a probe. Such a probe is more preferably a probe capable of complementarily binding to a targeted nucleic acid, but the present invention is not limited thereto. Here, the probe may be selected from a nucleic acid, a peptide, a saccharide, an oligonucleotide, a protein, an antibody, or a combination thereof, but the present invention is not limited thereto.
In one embodiment, the oligonucleotide may include a fluorophore. For example, the 5′ end of the oligonucleotide may be labeled with a fluorophore, and the 3′ end thereof may be labeled with at least one selected from the quenchers represented by Formulas 1, 2, 4 and 5. Between the 5′ end and the 3′ end, a probe that is able to complimentarily bind to the targeted nucleic acid may be located.
The fluorophore may refer to the types of the fluorophores disclosed in the following references (Cardullo et al., Proc. Natl. Acad. Sci. USA 85: 8790-8794 (1988); Dexter, D. L., J. of Chemical Physics 21: 836-850 (1953); Hochstrasser et al., Biophysical Chemistry 45: 133-141 (1992); Selvin, P., Methods in Enzymology 246: 300-334 (1995); Steinberg, I. Ann. Rev. Biochem., 40: 83-114 (1971); Stryer, L. Ann. Rev. Biochem., 47: 819-846 (1978); Wang et al., Tetrahedron Letters 31: 6493-6496 (1990); Wang et al., Anal. Chem. 67: 1197-1203 (1995)).
In addition, non-limiting examples of the fluorophores that can be used herein include 4-acetamido-4′-isothiocyanatostilbene-2,2′disulfonic acid, acridine and derivatives thereof, 5-(2′-aminoethyl)aminonaphthalene-1-sulfonic acid (EDANS), 4-amino-N-[3-vinylsulfonyl)phenyl]naphthalimide-3,5 disulfonate, N-(4-anilino-1-naphthyl)maleimide, anthranilamide, BODIPY, Brilliant Yellow, coumarins (7-amino-4-methylcoumarin (AMC, Coumarin 120), and 7-amino-4-trifluoromethylcouluarin (Coumaran 151)) and derivatives thereof, cyanine dyes, cyanosine, 4′,6-diaminidino-2-phenylindole (DAPI), 5′,5″-dibromopyrogallol-sulfonaphthalein (Bromopyrogallol Red), 7-diethylamino-3-(4′-isothiocyanatophenyl)-4-methylcoumarin, diethylenetriamine pentaacetate, 4,4′-diisothiocyanatodihydro-stilbene-2,2′-disulfonic acid, 4,4′-diisothiocyanatostilbene-2,2′-disulfonic acid, 5-[dimethylamino]naphthalene-1-sulfonyl chloride (DNS, dansylchloride), 4-(4′-dimethylaminophenylazo)benzoic acid (DABCYL), 4-dimethylaminophenylazophenyl-4′-isothiocyanate (DABITC), eosin and a derivative thereof (eosin isocyanate), erythrosine and derivatives thereof (erythrosine B, erythrosine isocyanate), ethidium, fluorescein and derivatives thereof (5-carboxyfluorescein (FAM)), 5-(4,6-dichlorotriazin-2-yl)aminofluorescein (DTAF), 2′,7′-dimethoxy-4′5′-dichloro-6-carboxyfluorescein (JOE), QFITC (XRITC), fluorescamine, IR144, IR1446, Malachite Green isothiocyanate, 4-methylumbelliferone, ortho cresolphthalein, nitrotyrosine, pararosaniline, Phenol Red, B-phycoerythrin, o-phthaldialdehyde, pyrene and derivatives thereof (pyrene butyrate, succinimidyl 1-yprene butyrate), quantum dots, Reactive Red 4 (Cibacron Brilliant Red 3B-A), rhodamine and derivatives thereof (6-carboxy-X-rhodamine, 6-carboxyrhodamine, rhodamine B, rhodamine 123, rhodamine X isocyanate, sulforhodamine B, sulforhodamine 101, tetramethyl rhodamine, and tetramethyl rhodamine isocyanate), riboflavin, rosolic acid, pyrene, carbopyronin, oxazine, xanthene, thioxanthene, and terbium chelate derivatives.
In addition, the oligonucleotide according to the present invention may further include a minor groove binder (MGB) to improve the binding strength with a nucleic acid.
Such an oligonucleotide may be used in various ways in chemical and biological fields. Particularly, it may be useful for real time PCR or microassay, but the present invention is not limited thereto.
In addition, according to another aspect of the present invention, a composition for detecting a nucleic acid, including the oligonucleotide, is provided.
The composition for detecting a nucleic acid according to one embodiment of the present invention may further include an enzyme, a solvent (a buffer or the like) and other reagents for a reaction with a target biomolecule, in addition to an oligonucleotide including all of the quencher represented by Formula 1, 2, 4 or 5, MGB, and the fluorophore.
Here, as the solvent, a buffer selected from the group consisting of a phosphate buffer, a carbonate buffer and a Tris buffer, an organic solvent selected from dimethyl sulfoxide, dimethylformamide, dichloromethane, methanol, ethanol and acetonitrile, or water may be used, and it is possible to adjust solubility by introducing various functional groups to the quencher according to the type of solvent.
In addition, according to still another aspect of the present invention, a support for detecting a nucleic acid, which includes the quencher represented by Formula 1, 2, 4 or 5, a support, and a linker connecting the quencher and the support, is provided.
Accordingly, a biomolecule in a sample may be fixed on a supporting matrix through interaction with the quencher adhered onto the support.
The support may be manufactured with at least one selected from glass (e.g., CPG), cellulose, nylon, acrylamide gel, dextran, polystyrene, alginate, collagen, peptides, fibrin, hyaluronic acid, agarose, polyhydroxyethylmethacrylate, polyvinyl alcohol, polyethylene glycol, polyethyleneoxide, polyethylene glycol diacrylate, gelatin, Matrigel, polylactic acid, carboxymethylcellulose, chitosan, latex, and sepharose, and may be formed as a bead or a membrane.
Here, the linker, as a part connecting the quencher and the support, and any material capable of connecting the quencher and the support may be used as a linker intended by the present invention.
For example, the linker may be selected from substituted or unsubstituted C1-C30 alkyl, substituted or unsubstituted C3-C30 cycloalkyl, substituted or unsubstituted C2-C30 heteroalkyl having at least one hetero atom, substituted or unsubstituted C2-C30 heterocycloalkyl having at least one hetero atom, substituted or unsubstituted C2-C30 alkenyl, substituted or unsubstituted C6-C30 aryl, substituted or unsubstituted C3-C30 heteroaryl, amide (—CONH—), ester (—COO—), ketone (—CO—), nucleoside, and any combination thereof.
Examples of the connecting structures between the supports and the quenchers mediated by the linkers are as follows.
The linker merely connects a quencher and a support, but does not affect another reaction of a quencher or fluorophore, or fluorescence and quenching actions.
Method of Detecting Nucleic Acid
According to one embodiment of the present invention, a method of labeling a target nucleic acid through reaction with a quencher-labeled probe may be implemented. In addition, a biomolecule labeling method using a target-specific interaction may be implemented by introducing an appropriate reactive group to a quencher according to the type of target biomolecule. Moreover, a method of identifying the quencher-labeled biomolecule through electrophoresis may be implemented.
DNA Microarray
A DNA microarray is for measuring the fluorescence of a target nucleic acid by preparing a single-stranded probe nucleic acid which labels a target nucleic acid through reaction with a dye and has a complementary base sequence to the target nucleic acid, and hybridizing the probe nucleic acid with the target nucleic acid denatured into a single strand on a substrate.
In the labeling method, when gene expression is investigated, as the probe nucleic acid immobilized to the substrate, cDNA, which is prepared by amplifying a cDNA library, genome library, or any of all genomes as a template through PCR, may be used.
In addition, for investigation of a gene mutation, various oligonucleotides corresponding to mutations may be synthesized based on a known sequence serving as a reference and used.
A proper method for immobilizing the probe nucleic acid on the substrate may be selected according to the type of nucleic acid or substrate. For example, a method for electrostatic bonding to a substrate surface-treated with a cation such as polylysine using the charge of DNA may also be used.
The target nucleic acid denatured into a single strand is immobilized on the substrate, and hybridized with the oligonucleotide. Here, the 5′end of the oligonucleotide is labeled with a fluorophore, and the 3′end thereof is labeled with at least one selected from the quenchers represented by Formulas 1, 2, 4 and 5. Between the 5′ end and the 3′ end, a probe that is able to complimentarily bind to the targeted nucleic acid may be located.
Hybridization is preferably performed at room temperature to 70° C. for approximately 2 to 48 hours. Through hybridization, the target nucleic acid having a complementary base sequence with the probe nucleic acid is selectively bound with the probe nucleic acid. Afterward, the substrate is washed and dried at room temperature.
Here, the oligonucleotide is hybridized to the target nucleic acid by the probe, but the fluorophore at the 5′ end is present in a quenched state by the quencher at the 3′ end.
Subsequently, the oligonucleotide hybridized to the target nucleic acid is elongated by a polymerase and separated from the target nucleic acid by the exonuclease activity of the polymerase and degraded. The fluorophore at the 5′ end and the quencher at the 3′ end of the oligonucleotide are separated from each other, and thus the fluorophore may exhibit fluorescence.
Here, the intensity of the generated fluorescence is measured to measure the amplification amount of the target nucleic acid.
Hereinafter, specific examples of the present invention are suggested. However, the following examples are only for exemplifying or explaining the present invention in detail, and the present invention should not be limited thereto.
Synthesis of Intermediate 2
4-bromo-N,N-dimethylaniline (6.47 g, 32.34 mmol) and tetrahydrofuran (65 mL) were put into a 250 mL 3-neck reactor, and stirred under nitrogen atmosphere at −78° C. for 5 minutes. 1.6M n-butyl lithium (20.2 mL, 32.34 mmol) was slowly added dropwise to the reactor, and then stirred at −78° C. for 1 hour. Intermediate 1 (5.0 g, 10.78 mmol; synthesized with reference to Korean Unexamined Patent Application Publication No. 10-2019-0062162) was dissolved in tetrahydrofuran (50 mL) and added dropwise to the reactor, followed by stirring at room temperature for 12 hours. Hydrochloric acid (20 mL) was added to the reactor, and the resulting product was vigorously stirred for 30 minutes and concentrated, followed by performing column purification.
Synthesis of Intermediate 3
Intermediate 2 (4 g, 7.41 mmol), succinic anhydride (2.22 g, 22.2 mmol), triethylamine (3.37 g, 33.3 mmol), and dichloromethane (40 mL) were added to a 100 mL one-neck reactor and stirred at room temperature for 1 hour, and concentrated, followed by performing column purification.
Synthesis of Compound 1
Intermediate 3 (2 g, 3.31 mmol), dicyclohexylcarboimide (0.88 g, 4.31 mmol), N-hydroxysuccinimide (0.49 g, 4.31 mmol), and dichloromethane (40 mL) were added to a 100 mL one-neck reactor and stirred at room temperature for 1 hour. Subsequently, the obtained reaction solution was concentrated by filtration and then purified through a column.
1H-NMR of the obtained Compound 1 is as follows.
1H-NMR (400 MHz, CDCl3) d 7.66-7.64 (m, 2H), 7.34 (d, 2H, J=8.8 Hz), 7.22-7.11 (m, 2H), 7.05 (s, 1H), 6.98 (s, 1H), 6.89 (d, 2H, J=8.4 Hz), 3.75-3.69 (m, 12H), 3.14 (s, 6H), 1.79 (s, 6H), 1.49 (s, 9H)
Synthesis of Compound 2
Intermediate 4 was prepared using 4-bromo-N-methyl-N-phenylbenzeneamine instead of 4-bromo-N,N-dimethylaniline in the synthesis of Intermediate 2 of Preparation Example 1, and Compound 2 was prepared in the same manner as in the synthesis of Compound 1 using Intermediate 4.
1H-NMR of the obtained Intermediate 4 is as follows.
1H-NMR (400 MHz, CDCl3) d 7.68-7.62 (m, 2H), 7.46 (t, J=6.4 Hz, 2H), 7.31 (d, J=8.4 Hz, 2H), 7.27-7.14 (m, 5H), 7.03-6.97 (m, 4H), 3.76-3.45 (m, 12H), 3.45 (s, 3H), 1.79 (bs, 6H), 1.48 (s, 9H)
3-bromo-9-methylcarbazole (5.6 g, 22 mmol) and tetrahydrofuran (50 mL) were put into a 250 mL 3-neck reactor, and stirred under nitrogen atmosphere at −78° C. for 5 minutes. 1.6M n-butyl lithium (14 mL, 22 mmol) was slowly added dropwise to the reactor, and then stirred at −78° C. for 1 hour. Intermediate 1 (5.0 g, 11 mmol) was dissolved in tetrahydrofuran (50 mL) and added dropwise to the reactor, followed by stirring at room temperature for 12 hours. Hydrochloric acid (20 mL) was added to the reactor, vigorously stirred for 30 minutes, concentrated, and then purified using a column, thereby synthesizing 7.5 g (yield: 92%).
1H-NMR of the obtained Compound 12 is as follows.
1H-NMR (400 MHz, CDCl3) d 8.12-8.09 (m, 2H), 7.68 (d, J=8.4 Hz, 1H), 7.58-7.51 (m, 5H), 7.33 (t, J=6.8 Hz, 1H), 7.18-7.08 (m, 4H), 4.00 (s, 3H), 3.77-3.69 (m, 12H), 1.8 (bs, 6H), 1.49 (s, 9H)
To evaluate the extinction property of Compounds 1, 2 and 12 synthesized according to Preparation Examples 1 to 3 as quenchers, the absorption spectrum (PBS solvent), molar extinction coefficient (ε, Lmol−1 cm−1) and quantum efficiency (φ) of Compounds 1, 2 and 12 were measured by known methods.
The measurement results are shown in
As shown in
5′-GCGGGAGATGATATGGACTT-3′ as a forward primer for black queen cell virus (BQCV) and 5′-CCGTCTGAGATGCATGAATAC-3′ as a reverse primer were synthesized at 1 μmol scale each using a Universal UnyLinker Support (Chemgene, 500 Å), and the primers were then separated from the Support, followed by purification by RP-HPLC.
First, 5′-CCATCTTTATCGGTACGCCGCCC-Compound 1-3′ and 5′-CCATCTTTATCGGTACGCCGCCC-MGB-Compound 1-3′ were synthesized as single labeled probes using Compound 1-CPG (synthesized with reference to Korean Unexamined Patent Application Publication No. 10-2021-0061265), and then a fluorescent material 6-FAM, commercially available as a reporter, were attached to label the 5′ end of each probe using a MerMade™ 48×DNA Synthesizer, thereby synthesizing a double-labeled probe.
Additionally, for a comparison experiment with a commercially-available quencher, double-labeled probes in which the 5′-end was labeled with VIC, HEX and Cal Flour® Orange 560 and the 3′ end was labeled with Compound 1 were synthesized in the same manner as described above.
In addition, a double-labeled probe in which the 3′ end was labeled with BHQ1 using BHQ1-CPG (synthesized with reference to Korena Unexamined Patent Application Publication No. 10-2021-0061265) instead of Compound 1-CPG to label the 3′ end with Black Hole Quencher® 1 (BHQ1, LGC Biosearch Technologies) instead of Compound 1 was synthesized.
The synthesized double-labeled probe was obtained by being separated from CPG, and then purified by RP-HPLC.
The types of the synthesized double-labeled probes are shown in Table 2 below.
The absorption/emission wavelength ranges of the 6-FAM, VIC, HEX and Cal Fluor® Orange 560, which were attached to the 5′ end to label are shown in Table 3 below, and the absorption spectra (PBS solvent) and molar extinction coefficients (E, Lmol−1 cm−1) of the quenchers, Compound 1 and BHQ1, attached to the 3′ end to label, are shown in Table 4 below.
To confirm the quenching properties of the double-labeled probes according to Examples 1-1 and 1-2, real-time PCR (Biorad, using CFX-96™) for BQCV plasmid DNA (100, 20 and 4 fg/ul) was repeatedly performed twice per concentration with the compositions listed in Table 5 below.
The real-time PCR results are shown in Table 6,
Referring to Table 6, and
To compare quenching properties of the quencher according to Compound 1 and the commercially-available quencher, BHQ1 quencher, real-time PCR for BQCV plasmid DNA (25 fg/μl) was repeatedly performed twice with the compositions shown in Table 7 below using the double-labeled probes according to Examples 1-1, 2, 3 and 4, and Comparative Examples 1 to 4 (Biorad, using CFX96™).
As quenchers for 6-FAM, VIC, HEX and Cal Fluor® Orange 560 reporters, the real-time PCR results using Compound 1 and BHQ1 are shown in Tables 8 to 11 and
Referring to Tables 8 to 11 and
From the results, when Compound 1, instead of BHQ1, was used as a quencher, relatively low Ct was shown, and it can be expected that the final amplified RFU value will be formed high.
In addition, considering a molecular diagnostic aspect, since the limit of detection (LoD) of Compound 1 is lower than that of a conventional, commercially-available quencher, when Compound 1 is used as a quencher of a double-labeled probe, even when target DNA or RNA in a sample is present at a relatively low concentration, it can be expected that Compound 1 may be more easily detected than the commercially-available quenching material.
Therefore, the quenchers defined herein may be applied to the conventional biomolecule labeling and detection field (e.g., a PCR experiment, etc.), or may sufficiently replace the conventional, commercially-available quenchers.
In the above, the embodiments of the present invention have been described, but it will be understood by those of ordinary skill in the art that the present invention may be changed and modified in various ways by addition, modification, or deletion of components without departing from the spirit of the present invention defined in the appended claims.
| Number | Date | Country | Kind |
|---|---|---|---|
| 10-2020-0171415 | Dec 2020 | KR | national |
| 10-2021-0172759 | Dec 2021 | KR | national |
This application is based on the PCT Application No. PCT/KR2021/018524, filed on Dec. 9, 2021, and claims the benefit of priority from Korean Patent Application No. 10-2020-0171415, filed on Dec. 9, 2020, and Korean Patent Application No. 10-2021-0172759, filed on Dec. 6, 2021, the disclosures of which are incorporated herein by reference in its entirety.
| Number | Date | Country | |
|---|---|---|---|
| Parent | PCT/KR2021/018524 | Dec 2021 | US |
| Child | 18332421 | US |
