Patent Application
20140200337
1. Field of the Invention
The present invention pertains to the field of nucleic acid (especially DNA) ligand-based diagnostics and prophylaxis or passive “immunity” (i.e., binding and blocking infectious agents from infecting or progressing throughout the body). In particular, the application relates to single-stranded deoxyribonucleic acid (“DNA”) and ribonucleic acid (“RNA”) ligand sequences, whether individual or linked together to form longer multiple binding site “receptors,” that specifically target and bind to arthropod-borne bacteria and viruses (arboviruses). Such arthropod-borne bacteria include the Rickettsia genus that can cause typhus or spotted fevers and deadly hemorrhagic fevers or other lethal diseases such as Crimean-Congo Hemorrhagic Fever (“CCHF”) viruses, Chikungunya (“CHIK”) viruses, Dengue viruses, and West Nile Viruses (“WNV”) or parasites such as various species of Leishmania. The arthropod vectors can include mosquitoes, ticks, lice, mites, midges, fleas, flies and sandflies.
These individual or linked DNA ligand (aptamer) sequences represent valuable target analyte-responsive components of diagnostic devices or biosensors. A biosensor can be defined as any device that employs a biologically-derived molecule as the sensing component and transduces a target analyte binding event into a detectable physical signal (including, but not limited to, changes in light intensity, absorbance, emission, wavelength, color, electrical conduction, electrical resistance, or other electrical properties, etc). Once bonded with the target, these DNA ligand sequences can be used to qualitatively determine the presence of target analyte, as well as to quantify the target analyte amount, in a sample using a broad variety of assay types and diagnostic or sensor platforms including, but not limited to: affinity-based lateral flow test strips, enzyme-linked (“ELISA-like”) microplate assays, membrane blotting, surface plasmon resonance (“SPR”), surface acoustic wave (“SAW”) or surface transverse wave (“STW”) sensors, magnetic bead (“MB”)-based capture, plastic-adherent sandwich assays, electrochemiluminescence (“ECL”), radioisotopic, fluorescence intensity assays including quantum dot (“QD”) or other fluorescent nanoparticle (“NP”)-based assays, fluorescence lifetime, and fluorescence polarization (“FP”) assays.
The invention includes general DNA ligand or aptamer-based methods of detection and quantification of these arthropod-borne diseases or related pathogens in homogenized or chemically (chaotrope or detergent)-extracted arthropods or animal or human body fluids such as whole blood, plasma, serum, sputum or saliva, interstitial, synovial, or cerebrospinal fluid aspirates, mucus, and urine or solid biopsy samples.
In addition, these DNA ligand sequences are valuable in competitive displacement assays which are not solely dependent on affinity or avidity to produce sensitive detection. Such assays would include competitive displacement fluorescence or Förster resonance energy transfer (“FRET”) assays or DNA ligand “beacon” FRET assays. Each of these types of assays and detection platforms has different applications in either central laboratories or as a component of portable detectors to identify infected arthropods (homogenates or extracts) or human or animal body fluids.
It has been established that aptamers can replace antibodies in lateral flow or chromatographic test strip assay formats and may enhance detection sensitivity by virtue of higher affinity versus comparable antibodies. Such test strips or dipsticks represent rapid, inexpensive and convenient visual detection formats. The user can add various human body fluids or arthropod homogenates or extracts (proteins removed from arthropod guts by low levels of detergents or chaotropes including guanidinium or metal salts) and obtain a positive or negative result by visualizing a red colloidal gold-aptamer conjugate line. Use of fluorescent nanoparticle (“FNP”)- or quantum dot (“QD”)-DNA aptamer conjugates on the test line of a lateral flow test strip in combination with a handheld UV penlight or common laser pointer to illuminate the fluorescent test and control lines appears to confer even greater sensitivity to the assay.
These individual or linked DNA ligand (concatamer-like aptamer) sequences represent valuable target analyte-responsive components of diagnostic devices or “biosensors.” A biosensor is defined as any sensor device that employs a biologically-derived molecule as the sensing component and transduces a target analyte binding event into a detectable physical signal, including, but not limited to, changes in light intensity, absorbance, transmittance, refraction (Surface Plasmon Resonance or SPR), wavelength, color, agglutination of cells or particles, fluorescence intensity, fluorescence lifetime, fluorescence polarization or anisotropy, fluorescence correlation spectroscopy (“FCS”), fluorescence or Förster resonance energy transfer (FRET; nonradiative dipole-dipole coupling of fluorophores or fluorophores and quenchers), upconverting phosphor (anti-Stokes shifts), two-photon interaction phenomena, Raman spectroscopy or surface-enhanced Raman spectroscopy (“SERS”), electrical conduction, electrical resistance or other electrical properties, mass, photon or radioactive particle emissions, etc.
Once bonded with the target, these DNA ligand sequences can be used to qualitatively determine the presence of analyte, as well as to quantify or semi-quantify the target analyte amount in a sample using a broad variety of assay types and diagnostic or sensor platforms including, but not limited to, affinity-based lateral flow test strips, membrane blotting, surface plasmon resonance (“SPR”), surface acoustic waveguides (“SAW”) or surface transverse waveguides (“STW”) devices, magnetic bead (“MB”)-based capture, plastic-adherent sandwich assays (“PASA”), chemiluminescence (“CL”), electrochemiluminescence (“ECL”), radioisotopic, fluorescence intensity, including quantum dot (“QD”) or other fluorescent nanoparticle (“FNP”) of dye-based, fluorescence lifetime, and fluorescence polarization (“FP”) assays, or enzyme-linked (“ELISA-like”) microplate assays.
Finally, since envelope- or capsid-protruding spike proteins on viral surfaces control binding to and invasion of host cells, the DNA ligands may have prophylactic or therapeutic value by simply binding or coating the viral spike proteins to prevent attachment to host cell surfaces and inhibiting virus entry into host cells. The prophylactic effect has been demonstrated for H5N1 influenza virus with similar DNA ligand or aptamer sequences that coated the H5N1 viruses and prevented or severely inhibited invasion of host cells and slowed or stopped subsequent viral replication.
2. Background Information
The DNA ligand sequences listed herein were derived by iterative cycles of affinity-based selection of DNA ligands from a randomized library using rickettsial or leishmanial surface molecules (cold 1.5M MgCl2-extracted outer membrane proteins; OMPs), recombinant surface proteins or synthetic peptide epitopes derived from the known amino acid sequences of viral envelope protein spikes or other surface epitopes as defined in Table 1. After affinity-based selection, the DNA ligands were subjected to polymerase chain reaction (“PCR”) amplification followed by cloning and traditional Sanger dideoxynucleotide DNA sequencing. The utility of many of the sequences in ELISA-like plate assays as well as fluorescence (intensity) assays have been used and verified as illustrated by Tables 2-7 and
Some of the sequences function more effectively in affinity-based (ELISA-like, lateral flow strips, or fluorescence intensity) assays, while other DNA ligand sequences against the same pathogen targets have functioned better in competitive FRET assays). Therefore, all of the listed sequences have potential utility in some assay format for use in one or more tests or types of sensors for arthropod-borne pathogens and their therapy or prevention.
Arthropod-borne pathogens can present serious threats to human health in the form of alphaviruses or flaviviruses (arboviruses) that can cause encephalitis or hemorrhagic fevers or shock syndromes and death. Similarly, untreated rickettsial infections can lead to serious cases of spotted fevers or typhus with significant mortality. Finally, visceral and non-visceral leishmaniasis are serious conditions which are difficult to treat and can be fatal. All of these diseases are transferred to man by arthropod vectors (flying or other insects including mosquitoes, fleas, mites, midges, ticks, lice, flies and sandflies).
Rapid, accurate, and ultrasensitive detection of arthropod-borne diseases aids physicians by supplying key diagnostic information in the early phases of infection. This in turn allows administration of the proper antibiotic or anti-viral agent to treat these potentially deadly diseases before they become life-threatening. Current methods of detection such as lateral flow immunochromatographic test strips, although rapid, are not very sensitive and miss early stage disease detection or rely on detection of antibodies against the disease agent which may take weeks to emerge in the patient's serum. The same is true for many slower and more tedious ELISA tests which are somewhat more sensitive than lateral flow test strips, but often rely on detection of antibodies slowly made by the patient against the infectious pathogen over a period of weeks to months. In addition, there are no truly effective therapies for some of the arboviruses.
The DNA ligands disclosed herein can potentially and directly detect many arthropod-borne pathogenic microbes with greater sensitivity and speed than conventional antibodies. These same DNA ligands or aptamers may also have value as high affinity and highly specific binding agents against arboviruses, rickettsia and parasites to block or slow disease progression.
The present invention provides specific DNA sequence information for nucleic acid ligands selected and amplified from randomized pools to bind arthropod-borne pathogenic rickettsia, arboviruses and parasites in a variety of assay formats and sensor or diagnostic platforms. In addition, the DNA ligands may bind and slow or block infection and inhibit disease progression due to these pathogens, thereby functioning as prophylactics or therapeutics in vivo.
There is no single preferred embodiment for use of the DNA ligand sequences in assay or biosensor formats identified herein. Rather, as is the case with monoclonal antibodies, the sequences are useful to varying extents in a variety of assay formats and sensors or diagnostic devices chosen from the following non-comprehensive and non-exclusive list: lateral flow or chromatographic test strips or “dipsticks,” ELISA-like enzyme-linked microplate assays, magnetic bead-based capture assays, ECL or other chemiluminescence assays, radioisotopic assays and a variety of fluorescence assays including, but not limited to, fluorescence intensity or spectrofluorometry, lifetime, fluorescence polarization (“FP”) and fluorescence resonance energy transfer (“FRET”) assays (both end-labeled beacons and competitive FRET), SAW and STW-based detection, SPR.
Referring to the figures,
As nature, immunology, and
Linear linkage by chemical synthesis is quite facile, if one already knows the aptamer DNA sequences or shorter (approximately 5-10 base) binding site sequences to be linked. One can simply design one long sequence to incorporate the desired aptamers or binding sites with repetitive poly-adenine (A), poly-cytosine (C), poly-guanine (G), poly-thymine (T), poly-uridine (U), or other intervening sequences that are unlikely to bind the target epitopes. The length of the composite aptamer construct will be limited by current chemical synthesis technology to about 200 bases. However, cellular biosynthesis or enzymatic synthesis by polymerase chain reaction or asymmetric PCR (producing predominately single-stranded ss-DNA from a template) would not be so limited and should produce aptamer constructs up to 2,000 bases before the Taq polymerase or other thermostable DNA polymerase falls off the template DNA. The 2 kilobase Taq polymerase limit is the basis for the well-known Random Amplification of Polymorphic DNA (“RAPD”) method of DNA or genetic “fingerprint” analyses in which primers greater than 2 kilobases apart fail to produce a PCR product or amplicon, because Taq becomes disengaged from the template DNA before traveling 2,000 bases. In this way, lengthy aptamer constructs of less than 2 kilobases could be made from complementary DNA templates that would enable binding of different epitopes that are distal on the surface of relatively large objects such as viruses and whole bacteria, rickettsia, or eukaryotic parasites and other cells. Again, poly-A, C, G, T, or U or other linker nucleotide segments (similar to the concept of genetic “introns”) could be designed into the cDNA template to produce the resultant nascent strand to ligate aptamers or aptamer binding sites together into one contiguous linear chain with intervening linkers as shown in
For 2-D or 3-D linked aptamer structures a variety of linker chemistries are available, but the preferred embodiment is probably addition of a UniLink™ primary amine group somewhere in the mid-section of a larger multi-aptamer construct followed by covalent linkage and branching of two or more such multi-aptamer constructs by means of bifunctional linkers such as low levels (≦1%) of glutaraldehyde, carbodiimides, sulfo-EGS, sulfo-SMCC or other such bifunctional linkers familiar to those skilled in conjugate chemistry. This strategy would result in larger flower-like or dendrimer-like 2-D or 3-D structures consisting of two or more lengthy multi-aptamer structures.
Table 2 illustrates diversity of affinities for several different CCHF envelope peptide epitopes using two methods (0.1M bicarbonate buffer at pH 8.5 or N-oxy-succinimide-coated microwells) to immobilize the peptides and then carry out a traditional ELISA-like assay with 100 μL of 5′biotinylated DNA ligands for one hour at room temperature (RT, followed by a wash step, addition of 100 μL of 1:2,000 dilution of streptavidin-peroxidase (1 mg/mL stock) for 30 minutes at RT, three more wash steps and finally treatment with one-step ABTS substrate for 10 minutes at RT and reading of absorbance at 405 nm on a microplate reader. Tables 2 and 5-7 show ELISA-like rankings of the various top 3 to 10 DNA ligands by SEQ ID NOs for each of the general arthropod disease categories.
The highest ranking or highest affinity DNA ligands register the highest absorbance at 405 nm values and can be used in other types of affinity-based assays besides the ELISA-formatted assays. The highest affinity or highest ranking CCHF DNA ligands such as CCHF1-9F and CCHF3-6R also yielded very high affinity constants of greater 108 to 4.23×1011 by surface plasmon resonance (SPR) using a Biacore X-100 sensor as documented in Tables 3 and 4. The same or similar ELISA-like methods were used to screen and rank DNA ligand affinities against cognate arboviral, rickettsial and Leishmania targets as shown in Tables 5-7. Table 8 chronicles all of the actual candidate DNA ligand nucleotide sequences and corresponding SEQ ID NOs for all of the arthropod-borne pathogen-binding DNA ligands.
4.23 × 1011
1.48 × 1010
R. parkeri
R. rickettsii
R. typhi
R. belli
R. conorii
R. parkeri
R. rickettsii
R. typhi
The DNA ligand sequences have repeatedly been reduced to practice and used to detect low levels of CCHF viral envelope epitopes in neat buffer or animal sera as shown in
Similarly sensitive plastic-adherent sandwich fluorescence assay results for two species of rickettsia cells with LLOD or about 75 cells are shown in
Aptamer-based LF test strips are assembled much like traditional immunochromatographic strips by combining a Whatman GB002 sample pad, a Whatman Standard 17 conjugate pad, Millipore High Flow 240 analytical membrane (for slower migration and greatest sensitivity) and a Whatman 470 wicking or absorbent applied to a pressure sensitive sticky laminate backing. The sample pad is soaked in 0.05M Tris-HCl (pH 8.03) with 0.15 mM NaCl and 0.25% Triton X-100 for 30 minutes followed by air drying of the sample pad strip at 37° C. for several hours until completely dry. The components are assembled with the sample pad overlapping the conjugate pad and both the conjugate pad and wicking pads overlapping onto the nitrocellulose analytical membrane at each end of the analytical membrane as shown in
The streptavidin-colloidal gold for use in conjugates was obtained from DCN at 10 O.D. units per mL and 100 μL of this reagent was added to 100 μL of each 5′-biotinylated aptamer (1.3 to 1.5 mg/mL). Similarly, 100 μL of each 5′-biotin aptamer were added to 100 μL of simple streptavidin at (0.5 mL, Sigma Chemical Co.) and reagents were gently mixed at RT (20-25° C.) for 30 minutes. Any unbound aptamers were removed by use of sterile 30 kD molecular weight cut off spin columns which were centrifuged at 5,000×g for 10 minutes. The retentate was resuspended or rehydrated in 100 μL of sterile 1× BB and used in LF test strip experiments. The capture lines or “dots” (droplets) were laid down as 1 μL droplets a few millimeters from the conjugate pad on Millipore High Flow (HF) 240 nitrocellulose analytical membranes, sometimes in series, and air dried prior to baking in a UV oven for 15 minutes. The conjugate pads were loaded with 10-15 μL of colloidal gold-streptavidin-biotin-aptamer conjugates and target analytes were added in 100 μL of 1× BB at the indicated amounts in each figure. All colloidal gold LF tests were conducted and evaluated after 5 minutes of run time to enable the HF 240 membranes time to fully develop.
DNA aptamer-quantum dot and aptamer-fluorescent nanoparticle (FluoSpheres™; “FS” from Invitrogen) conjugates were initially adhering rather tightly to glass fiber conjugate pads and not releasing well or not migrating as far as unconjugated particles, but these obstacles were overcome by switching to a larger porosity HighFlow (“HF”) 75 analytical membrane and 40 nm streptavidin-FS to obtain the successful proof-of-concept data shown in
Although the invention and DNA ligand sequences listed in Table 8 have been described with reference to specific embodiments, this description is not meant to be construed in a limited sense. Various modifications of the disclosed embodiments, as well as alternative embodiments of the inventions will become apparent to persons skilled in the art upon reference to the description of the invention. It is, therefore, contemplated that the appended claims will cover such modifications that fall within the scope of the invention.
This application claims the benefit of the filing date of Provisional U.S. Application Ser. No. 61/401,731, filed on Aug. 18, 2010, entitled “Methods and Compositions of DNA Ligands for Arthropod-borne Pathogen Detection and Prophylaxis or Therapy”, and Non-Provisional U.S. patent application Ser. No. 13/199,082, filed Aug. 18, 2011, entitled “Methods and Compositions of DNA Ligands for Arthropod-borne Pathogen Detection and Prophylaxis or Therapy”, the entire disclosures of which are hereby incorporated by reference into the present disclosure, to include the Sequence Listing previously submitted with the subject application(s).
| Number | Date | Country | |
|---|---|---|---|
| Parent | 13199082 | Aug 2011 | US |
| Child | 14177962 | US |
