WHITE PAPERAptamers and Their PotenƟal ApplicaƟons atBase Pair BiotechnologiesIÄãÙʗç‘ã®ÊÄAptamer development has historic...
W«®ã› PƒÖ›Ù-Aptamers and Their PotenƟal ApplicaƟons at Base Pair Biotechnologies DʑçÛÄ㛗 AÖÖ½®‘ƒã®ÊÄÝ Ê¥ AÖãƒÃ›ÙÝ So fa...
W«®ã› PƒÖ›Ù-Aptamers and Their PotenƟal ApplicaƟons at Base Pair Biotechnologies DʑçÛÄ㛗 AÖÖ½®‘ƒã®ÊÄÝ Ê¥ AÖãƒÃ›ÙÝ CÊÄã®...
W«®ã› PƒÖ›Ù-Aptamers and Their PotenƟal ApplicaƟons at Base Pair Biotechnologies AÖãƒÃ›ÙÝ FÊÙ F½Êó CùãÊÛãÙù CÊÄã®Ä盗 Obt...
W«®ã› PƒÖ›Ù-Aptamers and Their PotenƟal ApplicaƟons at Base Pair Biotechnologies AÖãƒÃ›ÙÝ FÊÙ C«›Ã®‘ƒ½ S›ÄÝÊÙÝ Researchers...
W«®ã› PƒÖ›Ù-Aptamers and Their PotenƟal ApplicaƟons at Base Pair Biotechnologies AÖãƒÃ›ÙÝ FÊÙ C«›Ã®‘ƒ½ S›ÄÝÊÙÝ CÊÄã®Ä盗 F...
W«®ã› PƒÖ›Ù-Aptamers and Their PotenƟal ApplicaƟons at Base Pair Biotechnologies W«Ê½› C›½½ SELEX ¥ÊÙ AÖãƒÃ›ÙÝ In addition...
W«®ã› PƒÖ›Ù-Aptamers and Their PotenƟal ApplicaƟons at Base Pair Biotechnologies SçÃÃÙù Aptamers represent a promising fo...
W«®ã› PƒÖ›Ù-Aptamers and Their PotenƟal ApplicaƟons at Base Pair Biotechnologies REFERENCES CITED ConƟnued: 24. Liu J, Lu ...
W«®ã› PƒÖ›Ù-Aptamers and Their PotenƟal ApplicaƟons at Base Pair Biotechnologies REFERENCES CITED ConƟnued: 53. Neff CP, Z...
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White Paper Base Pair Biotechnologies Aptamer Applications


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Aptamers from Base Pair Biotechnologies in various assays, aptamers as antibody replacements

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White Paper Base Pair Biotechnologies Aptamer Applications

  1. 1. WHITE PAPERAptamers and Their PotenƟal ApplicaƟons atBase Pair BiotechnologiesIÄãÙʗç‘ã®ÊÄAptamer development has historically been limited to one-target at a time, Base Pair Biotechnologies has addressed thissevere limitation by successfully multiplexing the conventional aptamer selection process. Our platform technology is apatent pending approach to aptamer discovery that allows us to offer de novo aptamer discovery servicesat unprecedented speed and throughput. Our expertise in aptamer and related assay development allows us to supportour customers in a wide range of novel applications. This document gives background on aptamers, complimentary applica-tions, and Base Pair Biotechnologies approach and success with aptamer development.AÖãƒÃ›ÙÝAptamers are single-stranded DNA or RNA (ssDNA or ssRNA) molecules that can bind to pre-selected targets includingsmall molecules, proteins, and peptides among others with high affinity and specificity. These molecules can assume a varie-ty of shapes due to their propensity to form helices and single-stranded loops, explaining their versatility in binding to di-verse targets. They are used as sensors [1], and therapeutic tools [2], and to regulate cellular processes [3], as well as toguide drugs to their specific cellular targets [4-7]. Contrary to the actual genetic material, their specificity and characteris-tics are not directly determined by their primary sequence, but instead by their tertiary structure [8].Aptamers are generated from large random libraries by an iterative process oftencalled Systematic Evolution of Ligands by Exponential Enrichment (SELEX) [9, 10]. Theconventional SELEX technique in Figure 1 starts with a large library of random sin-gle stranded nucleotides or aptamers (ca. 1015 unique sequences). A typical librarywill contain a randomized region of ca. 40 nucleotides flanked by two constant re-gions for PCR priming. The library is exposed usually to a single target and thebound aptamers are partitioned and amplified for the next round. With eachround the stringency of the binding conditions is increased until the only remainingaptamers in the pool are highly specific for, and bind with high affinity to, the target.Once multiple rounds of SELEX are completed, the DNA sequences are usuallyidentified by conventional cloning and sequencing. Base Pair Biotechnologies hasaddressed the limitation of single target SELEX by successfully multiplexing the pro- Figure 1. Schematic of convention-cess. al, single-target DNA aptamer selec- tion. 8058 El Rio St., Houston, TX 77054 • basepairbio.com • info@basepairbio.com
  2. 2. W«®ã› PƒÖ›Ù-Aptamers and Their PotenƟal ApplicaƟons at Base Pair Biotechnologies DʑçÛÄ㛗 AÖÖ½®‘ƒã®ÊÄÝ Ê¥ AÖãƒÃ›ÙÝ So far, aptamers are best known as ligands to proteins, rivaling antibodies in both affinity and specificity [11-14], and the first aptamer-based therapeutics were recently FDA-approved (Macugen) [15-17]. More recently, however, aptamers have also been developed to bind small organic molecules and cellular toxins [18-26], viruses [27, 28], and even targets as small as heavy metal ions [29-33]. While aptamers are analogous to antibodies in their range of target recognition and variety of applications, they possess several key advantages over their protein counterparts [34]: Aptamers are self-refolding, single-chain, and redox-insensitive. They also lack the large hydrophobic cores of proteins and thus do not aggregate. They tolerate (or recover from) pH and temperatures that proteins do not. They are easier and more economical to produce (especially at the affinity reagent scale). In stark contrast to peptides, proteins and to some small chemicals aptamers are made through chemical synthesis, a process that is well defined, highly reproducible, sequence independent and can be readily and predictably scaled up. Their production does not depend on bacteria, cell cultures or animals. In contrast to antibodies, toxicity and low immunogenicity of particular antigens do not interfere with the aptamer se- lection. Further, using the technology proposed, highly custom or “orphaned” targets can be address rapidly and cheaply. They are capable of greater specificity and affinity than antibodies [35]. They can easily be modified chemically to yield improved, custom tailored properties. For instance, reporter and func- tional groups and PEG can easily be attached to the aptamer in a deterministic way. In fact, they can even be combined with antibodies [36, 37]. Similarly, their ADME properties can be readily tuned by conjugation to other groups (PEG, etc). Their small size leads to a high number of moles of target bound per gram, and they may have improved transport properties allowing cell specific targeting and improved tissue penetration [38-42]. They are much more stable at ambient temperature than antibodies yielding a much higher shelf life, and they can toler- ate transportation without any special requirements for cooling, eliminating the need for a continuous cold chain. The fact that, after selection, aptamers can be produced by chemical synthesis eliminates batch-to-batch variation which complicates production of therapeutic proteins [43] and the variability of diagnostic antibody reagents. Aptamers identified by SELEX can also be easily analyzed and manipulated to characterize the minimum sequence requirements for ap- tamer:target recognition. Sequences can be inspected for primary and secondary structure motifs [44-48], and single base perturbations of identified aptamers can be studied for the resulting affects on binding affinity. This sort of rational/directed optimization would be much more challenging using the antibody approach. Page 2 8058 El Rio St., Houston, TX 77054 • basepairbio.com • info@basepairbio.com
  3. 3. W«®ã› PƒÖ›Ù-Aptamers and Their PotenƟal ApplicaƟons at Base Pair Biotechnologies DʑçÛÄ㛗 AÖÖ½®‘ƒã®ÊÄÝ Ê¥ AÖãƒÃ›ÙÝ CÊÄã®Ä盗 In most applications, aptamers have been successfully employed as direct replacements for antibodies. Aptamer dot-blots [49] and aptamer-westerns [50, 51] are well supported in the literature. With respect to the integration of aptamers into biosensors, numerous publications support the feasibility of this approach. For instance, aptamers have been incorporated into lead sensors [30-32], drug sensors [24, 26], and estrogen measuring devices [52]. They can be used in single-target measuring devices or even in arrays [38], further extending their versatility. Recently, aptamers have also been used as chi- meric conjugates to siRNAs to improve delivery [53]. AÖãƒÃ›Ù R›Ý›ƒÙ‘« ƒÄ— D›ò›½ÊÖÛÄ㠃ã BƒÝ› Pƒ®Ù B®Ê㛑«Äʽʦ®›Ý The principal scientist at Base Pair Biotechnologies, Dr. Bill Jackson, has considerable experience in the development and novel application of nucleic acid aptamers, and these molecules have enjoyed recent increasing acceptance in both diagnostic and therapeutic settings. Besides multiple publications in 2010, Dr. Jackson authored a 200+ page market research report available from BCC Research LLC on the use of aptamers in both diagnostic and therapeutic applications [54]. In addition to the aptamer selection services Base Pair Biotechnologies maintains an active research program involving novel uses of aptamers. The PI and his colleagues have considerable experience in developing novel molecular diagnostics using a variety of analytical techniques including mass spectrometry [55-59] and DNA microarrays [56, 60]. More recently the PI has been involved in a variety of projects involving aptamers [61-64]. Recent funding has included an EPA SBIR Phase I pro- ject for aptamer-based detection of the cyanobacterial toxin, anatoxin-a, a project to develop aptamer-mimetics to proteins such as stem cell factor (SCF) to replace peptide agonists with inexpensive aptamers, and the aforementioned project to develop a platform for massively parallel SELEX. We have also developed recombinant techniques to express small foreign RNA’s (aptamers and siRNA) within the ribosome of E. coli [62-65]. Currently we are developing aptamer affinity reagents to high priority cancer biomarker proteins under Contract SBIR Phase I funding from the National Cancer Institute. AÖãƒÃ›ÙÝ FÊÙ F½Êó CùãÊÛãÙù In addition to validation of aptamers via SPR, we have successfully employed aptamers in fluorescence activated cell sorting (FACS) with collaborators at nearby M.D. Anderson Cancer Center (Houston, TX). Specifically, our collaborator has been using our aptamers to label and differentiate a panel of recombinant proteins expressed on desired T-cell subsets using flow cytometry. The availability of an inexpensive and efficacious alternative to monoclonal antibodies (mAbs) in this application is important as a method to produce cellular reagents to be used in compliance with current good manufacturing practice (cGMP). Page 3 8058 El Rio St., Houston, TX 77054 • basepairbio.com • info@basepairbio.com
  4. 4. W«®ã› PƒÖ›Ù-Aptamers and Their PotenƟal ApplicaƟons at Base Pair Biotechnologies AÖãƒÃ›ÙÝ FÊÙ F½Êó CùãÊÛãÙù CÊÄã®Ä盗 Obtaining monoclonal antibodies (mAbs) as reagents to validate the manufacture of cell-based therapeutics for clinical appli- cation is tedious, labor intensive and expensive as applied to generation of clinical-grade reagents. This is chiefly because of the concern of adventitious virus that may accompany the production of mAbs. Aptamer technology based on in vitro DNA synthesis will avoid this issue and greatly simplify and reduce the costs associated with producing materials for use in compli- ance with cGMP. Figure 2. Demonstration of the feasibility of FACS using fluores- cent aptamers selected against cell surface proteins. While some cross-reactivity is observed, screening and better selection of recombinant aptamer targets should alleviate these problems. Figure 2 above shows some of the preliminary fluorescence activated cell sorting (FACS) data utilizing our aptamers as re- placements to fluorescently labeled mAb reagents. Briefly, cells were first transfected with a defined membrane-bound in- terleukins (IL7, IL15, or IL21). Cells were then washed to remove serum and culture media and incubated at 37°C for 60 minutes with an aptamer developed to either IL-7, IL-15, or IL-21. Aptamers were synthesized with a 3’-biotin for facile labeling in situ with streptavidin-FITC conjugate. Following binding, aptamer-bound cells were washed once with PBS and then stained with streptavidin-FITC followed by an additional wash with PBS. Finally, cells were sorted by conventional FACS based on FITC fluorescence; cell counts to the right of the vertical blue line represent positive binding. As expected from an initial screen, there is some cross-reactivity of the tested aptamers. This is due to the use of a common recombi- nant Fc region for presenting these three cytokines on the cell surface. Nevertheless, some degree of specificity/ orthogonality of the aptamers is seen, and the experiment demonstrates that in principal, expensive mAbs could be replaced by aptamers for the FACS application. Page 4 8058 El Rio St., Houston, TX 77054 • basepairbio.com • info@basepairbio.com
  5. 5. W«®ã› PƒÖ›Ù-Aptamers and Their PotenƟal ApplicaƟons at Base Pair Biotechnologies AÖãƒÃ›ÙÝ FÊÙ C«›Ã®‘ƒ½ S›ÄÝÊÙÝ Researchers at Base Pair Biotechnologies have also employed aptamers in competitive sensing chemistries for detection of environmental and clinical analytes. For instance, a sensor for the thyroid hormone (small molecule), thyroxine (so-called “free-T4”) was developed. Figure 3 below depicts the modular, aptamer/quantum-dot-based sensing scheme employed. A QD Nanoshell B Immobilized analyte- analog Fluorescence Emission Aptamer with quencher dye analyte EX. hν EX. hν ~ 10 nm PEG coat- Figure 3. Schematic of Modular, Aptamer-based QD-FRET sensing chemistry (approximate scale). In a competitive-binding fluorescence resonance energy transfer (FRET) assay, quantum dots (QDs) are conjugated to an immobilized version of the intended analyte (T4 in the text exam- ple). Aptamers which bind T4 with high specificity are identified by in vitro selection or " ELEX" S . Panel (A): Aptamers synthesized with a terminal fluorophore for quenching of the QD are bound to immobilized T4. Panel (B) When free T4 in the sample is exposed to this reagent mixture, QD- quenching aptamers are released from the QDs resulting in a fluorescence signal proportional to the T4 concentration. To select a DNA aptamer to the molecule, thyroxine was covalently immobilized via its primary amine to a solid phase gel by standard chemistries. After 10 rounds of conventional (e.g. single-target) selection, individual aptamers were cloned and sequenced. Evolution of a unique sequence, characterized by a high GC content, as typical for known thyroxine aptamers [66] was clearly observed (sequence not shown). Page 5 8058 El Rio St., Houston, TX 77054 • basepairbio.com • info@basepairbio.com
  6. 6. W«®ã› PƒÖ›Ù-Aptamers and Their PotenƟal ApplicaƟons at Base Pair Biotechnologies AÖãƒÃ›ÙÝ FÊÙ C«›Ã®‘ƒ½ S›ÄÝÊÙÝ CÊÄã®Ä盗 Figure 4 shows the performance of the FRET-aptamer sensor which has been described in detail elsewhere [67]. The sensor was found non-responsive to several structurally similar chemicals and was thus, specific for the analyte. Base Pair Biotech- nologie’s parent company BioTex has considerable fluorescent biosensor expertise [67-70]. The fluorescence emitted from the sensor was measured in a portable, inexpensive Qubit™ fluorometer (Invitrogen). Thus, using a sensing cocktail that can be readily lyophilized and reconstituted by the sample, such an assay could be taken to the field or bedside for environ- mental or clinical point of care use. Figure 4. Quantitative detection of the small molecule thyroxine (T4) via FRET- aptamer detection. Insets show structure of T4 and portable (4.5 x 6.5 x 1.8 inch) Qubit™ fluorometer (Invitrogen) used to acquire data. This sort of sensing scheme can be readily devised for proteins as well. We have developed an analogous sensing chemistry using aptamers specific for insulin evolved at BioTex. Figure 5 below shows that result. These data demonstrate not only the ability of Base Pair Biotechnology scientists to select DNA aptamers to novel targets, but also the broad, modular ap- plicability of DNA aptamers in numerous applications. Figure 5. Response curve of quan- tum-dot-based sensor (Figure 4) to insulin as formulated with the insu- A B lin-specific aptamer #43 selected at BioTex. (Panel A) The increase in fluorescence with increasing insulin concentrations is due to FRET. The putative secondary structure of insulin-aptamer #43 is shown in panel B. Page 6 8058 El Rio St., Houston, TX 77054 • basepairbio.com • info@basepairbio.com
  7. 7. W«®ã› PƒÖ›Ù-Aptamers and Their PotenƟal ApplicaƟons at Base Pair Biotechnologies W«Ê½› C›½½ SELEX ¥ÊÙ AÖãƒÃ›ÙÝ In addition to selection of aptamers against purified targets, we also have significant experience in selection of aptamers against the surface of whole cells. Specifically, under NSF funding, we collaborated with a biotechnology company in an at- tempt to develop an inexpensive DNA aptamer mimetic for so-called stem cell factor (SCF or “kit ligand”). Recombinant SCF is a rather expensive, but commonly used reagent in stem cell culture. To achieve this goal, we enriched our random- ized DNA library for aptamers binding whole stem cells and then selectively displaced the desired aptamers from the c-Kit receptor using SCF itself. Although we were unable to evolve an agonist mimetic (to effect stem cell proliferation in cul- ture), did successfully develop a number of candidate c-Kit specific antagonists. We are currently quantifying their affinity. AÖãƒÃ›Ù ½ÊãÝ Ê¥ 2D ¦›½Ý ƒÄ— ELISA SçÝã®ãçã›Ý It has already been demonstrated that aptamers can perform well in a Western-blot application [50, 51]. Similarly they have functioned as direct replacements for antibody reporters in ELISAs and dot blots [49]. A number of aptamer conjuga- tion/functionalization schemes are likely accepted for this purpose. Most simply, aptamers can synthesized to contain either a 5’- or 3’-fluorphore of choice. Alternatively, as described in Preliminary Work, we have considerable experience in conju- gating aptamers to quantum dots with the advantage of higher quantum yield and larger Stokes’ shifts of fluorescence. Final- ly, for additional signal, aptamers can be synthesized with a 5’- or 3’-biotin and detected by a streptavidin/horseradish perox- idase conjugate (strep-HRP). Numerous commercial sources for both fluorescent and chromagenic HRP substrates are available. Such an approach is often referred to as an “ELONA” [71, 72] or aptamer-ELISA (“ELASA”) [73]. AÖãƒÃ›Ù-›ƒ— Öٛ‘®Ö®ãƒã®ÊÄ ÊÙ ›ÄÙ®‘«Ã›Äã As mentioned elsewhere, one of the attractions/advantages of aptamers is that they are readily synthesized with modifica- tions for conjugation, covalent coupling, fluorescent reporting, etc. Specifically, aptamers can be readily coupled to beads or nanoparticles by synthesizing them with a terminal biotin or amino-group. Such functionalized particles have been used to concentrate transcription factors [74], or, in the form of magnetic beads, have been employed to enrich bacterial pathogens [75] or cancer cells [76]. Similarly, it should be feasible to develop highly multiplexed bead-based assays such as Lu- minex/Magpix. IÃÃçÄÊ«®Ýãʑ«›Ã®ÝãÙù Employing aptamers in conventional histology and molecular imaging is another logical extension for their use in lieu of anti- bodies. In recent years, directly, or indirectly labeled aptamers have, for instance, been used to detect individual receptors [77] or to differentiate cancerous from non-cancerous cells [78]. Page 7 8058 El Rio St., Houston, TX 77054 • basepairbio.com • info@basepairbio.com
  8. 8. W«®ã› PƒÖ›Ù-Aptamers and Their PotenƟal ApplicaƟons at Base Pair Biotechnologies SçÃÃÙù Aptamers represent a promising form of synthetic, inexpensive affinity reagent which can be employed in numerous applica- tions. Despite their promise, however, they have generally only been developed or ‘evolved’ against a single target at a time. High costs for aptamer selection (as well as now-expiring intellectual property constraints) have until now hindered their more widespread use. Base Pair Biotechnologie’s novel approach to multiplex aptamer selection can inexpensively provide aptamer affinity reagents to a revolutionary breadth of targets. Finally, our team has the expertise to demonstrate and support our cus- tomers in a variety of novel aptamer-based application areas. REFERENCES CITED: 1. Holthoff EL, Bright FV: Molecularly templated materials in chemical sensing. Anal. Chim. Acta 2007, 594:147-161. 2. Kaur G, Roy I: Therapeutic applications of aptamers. Expert opinion on investigational drugs 2008, 17:43-60. 3. Toulme JJ, Di Primo C, Boucard D: Regulating eukaryotic gene expression with aptamers. FEBS letters 2004, 567:55-62. 4. Chu TC, Marks 3rd JW, Lavery LA, Faulkner S, Rosenblum MG, Ellington AD, Levy M: Aptamer:toxin conjugates that specifically target prostate tumor cells. Cancer Res. 2006, 66:5989-92. 5. Chu TC, Twu KY, Ellington AD, Levy M: Aptamer mediated siRNA delivery. Nucl. Acids Res. 2006, 34:e73-. 6. Chu TC, Shieh F, Lavery LA, Levy M, Richards-Kortum R, Korgel BA, Ellington AD: Labeling tumor cells with fluorescent nanocrystal-aptamer bioconjugates. Biosens Bioelectron. 2006, Feb 20. 7. Cao Z, Tong R, Mishra A, Xu W, Wong GCL, Cheng J, Lu Y: Reversible Cell-Specific Drug Delivery with Aptamer-Functionalized Liposomes. Angew. Chem. Int. Ed. 2009, 48:6494-6498. 8. Breaker RR: Natural and engineered nucleic acids as tools to explore biology. Nature 2004, 432:838-45. 9. Tuerk C, Gold L: Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 1990, 249:505-10. 10. Ellington AD, Szostak JW: In vitro selection of RNA molecules that bind specific ligands. Nature 1990, 346:818-22. 11. Tuerk C, MacDougal S, Gold L: RNA pseudoknots that inhibit human immunodeficiency virus type 1 reverse transcriptase. Proceedings of the National Academy of Sciences 1992, 89:6988-92. 12. Lee JF, Hesselberth JR, Meyers LA, Ellington AD: Aptamer Database. Nucleic Acids Res 2004, 32:D95-100. 13. Ruckman J, Green LS, Beeson J, Waugh S, Gillette WL, Henninger DD, Claesson-Welsh L, Janjic N: 2’-Fluoropyrimidine RNA-based Aptamers to the 165- Amino Acid Form of Vascular Endothelial Growth Factor (VEGF165), Inhibition Of Receptor Binding And Vegf-Induced Vascular Permeability Through Interactions Requiring The Exon 7-Encoded Domain. J Biol Chem 1998, 273:20556-7. 14. Jayasena SD: Aptamers: an emerging class of molecules that rival antibodies in diagnostics. Clin. Chem. 1999, 45:1628-1650. 15. Lee J-H, Canny MD, De Erkenez A, Krilleke D, Ng Y-S, Shima DT, Pardi A, Jucker F: A therapeutic aptamer inhibits angiogenesis by specifically targeting the heparin binding domain of VEGF165. Proc. Natl. Acad. Sci. 2005, 102:18902-18907. 16. Ng EWM, Shima DT, Calias P, Cunningham ET, Guyer DR, Adamis AP: Pegaptanib, a targeted anti-VEGF aptamer for ocular vascular disease. Nature Re- views Drug Discovery 2006, 5:123-132. 17. Siddiqui MAA, Keating GM: Pegaptanib: in exudative age-related macular degeneration. Drugs 2005, 65:1571-1577. 18. Sazani PL, Larralde R, Szostak JW: A Small Aptamer with Strong and Specific Recognition of the Triphosphate of ATP. J Am Chem Soc 2004, 126:8371. 19. Tang J, Breaker RR: Mechanism for allosteric inhibition of an ATP-sensitive ribozyme. Nucleic acids research 1998, 26:4214-21. 20. Yang Q, Goldstein IJ, Mei H-Y, Engelke DR: DNA ligands that bind tightly and selectively to cellobiose. Proc Natl Acad Sci U S A 1998, 95:5462-5467. 21,.Babendure JR, Adams SR, Tsien RY: Aptamers Switch on Fluorescence of Triphenylmethane Dyes. J Am Chem Soc 2003, 125:14716-7. 22. Hirao I, Yoshinari S, Yokoyama S, Endo Y, Ellington AD: In vitro selection of aptamers that bind to ribosome-inactivating toxins. Nucleic Acids Symp Ser 1997, 37:283-4. 23. Hirao I, Harada Y, Nojima T, Osawa Y, Masaki H, Yokoyama S: In Vitro Selection of RNA Aptamers that Bind to Colicin E3 and Structurally Resemble the Decoding Site of 16S Ribosomal RNA†. Biochemistry 2004, 43:3214-3221. Page 8 8058 El Rio St., Houston, TX 77054 • basepairbio.com • info@basepairbio.com
  9. 9. W«®ã› PƒÖ›Ù-Aptamers and Their PotenƟal ApplicaƟons at Base Pair Biotechnologies REFERENCES CITED ConƟnued: 24. Liu J, Lu Y: Fast Colorimetric Sensing of Adenosine and Cocaine Based on a General Sensor Design Involving Aptamers and Nanoparticles. An- gew. Chem., Int. Ed. 2006, 117:90-94. 25. Stojanovic MN, de Prada P, Landry DW: Aptamer-Based Folding Fluorescent Sensor for Cocaine. J Am Chem Soc 2001, 123:4928-4931. 26. Stojanovic MN, Landry DW: Aptamer-Based Colorimetric Probe for Cocaine. J Am Chem Soc 2002, 124:9678-9679. 27. Gopinath SCB, Misono TS, Kawasaki K, Mizuno T, Imai M, Odagiri T, Kumar PKR: An RNA aptamer that distinguishes between closely related human influenza viruses and inhibits haemagglutinin-mediated membrane fusion. J Gen Virol 2006, 87:479-87. 28. Gopinath SCB, Sakamaki Y, Kawasaki K, Kumar PKR: An Efficient RNA Aptamer against Human Influenza B Virus Hemagglutinin. Journal of Biochemistry 2006 139(5):837-846 2006, 139:837-46. 29. Liu J, Lu Y: A Colorimetric Lead Biosensor Using DNAzyme-Directed Assembly of Gold Nanoparticles. Journal of the American Chemical Society 2003, 125:6642-6643. 30. Chang I-H, Tulock J, Liu J, Kim W-S, Cannon Jr. D, Lu Y, Bohn P, Sweedler J, Cropek D: Miniaturized Lead Sensor Based on Lead-Specific DNAzyme in a Nanocapillary Interconnected Microfluidic Device. Environ. Sci. Technol. 2005, 39:3756. 31. Swearingen CB, Wernette DP, Cropek DM, Lu Y, Sweedler JV, Bohn PW: Immobilization of a Catalytic DNA Molecular Beacon on Au for Pb(II) Detec- tion. Anal. Chem. 2005, 77:442-8. 32. Wernette DP, Kim H-K, Liu J, Swearingen CB, Yue Z, Zavareh M, Ingram CW, Economy J, Shannon MA, Bohn PW, Lua Y: New Catalytic DNA Biosensors for Trace Contaminants in Water. 33. Wrzesinski J, Ciesiolka J: Characterization of structure and metal ions specificity of Co2+-binding RNA aptamers. Biochemistry 2005, 44:6257-68. 34. Stoltenburg R, Reinemann C, Strehlitz B: SELEX--a (r)evolutionary method to generate high-affinity nucleic acid ligands. Biomolecular engineering 2007, 24:381-403. 35. Jayasena SD: Aptamers: An Emerging Class of Molecules That Rival Antibodies in Diagnostics. Clinical Chemistry 1999, 45:1628–1650. 36. Ferreira CS, Papamichael K, Guilbault G, Schwarzacher T, Gariepy J, Missailidis S: DNA aptamers against the MUC1 tumour marker: design of aptamer- antibody sandwich ELISA for the early diagnosis of epithelial tumours. Analytical and bioanalytical chemistry 2008, 390:1039-50. 37. Burbulis I, Yamaguchi K, Yu R, Resnekov O, Brent R: Quantifying small numbers of antibodies with a “near-universal” protein-DNA chimera. Nature Methods 2007, 4:1011-3. 38. McCauley TG, Hamaguchi N, Stanton M: Aptamer-based biosensor arrays for detection and quantification of biological macromolecules. Analytical biochemistry 2003, 319:244-50. 39. Cao Z, Tong R, Mishra A, Xu W, Wong GCL, Cheng J, Lu Y: Reversible Cell-Specific Drug Delivery with Aptamer-Functionalized Liposomes. Angew. Chem. Int. Ed. 2009, 48:6494-6498. 40. De Rosa G, La Rotonda MI: Nano and Microtechnologies for the Delivery of Oligonucleotides with Gene Silencing Properties. Molecules 2009, 14:2801-2823. 41. Ferreira CSM, Cheung MC, Missailidis S, Bisland S, Gariepy J: Phototoxic aptamers selectively enter and kill epithelial cancer cells. Nucl. Acids Res. 2009, 37:866-876. 42. Yan AC, Levy M: Aptamers and aptamer targeted delivery. rnabiology 2009, 6:316-320. 43. Cload S, McCauley T, Keefe A, Healy J, Wilson C: Properties of Therapeutic Aptamers. In Aptamer Handbook, The. Wiley-VCH Verlag GmbH & Co. KGaA; 2006. 44. Mathews DH, Sabina J, Zuker M, Turner DH: Expanded Sequence Dependence of Thermodynamic Parameters Improves Prediction of RNA Sec- ondary Structure. J Mol Biol 1999, 288:911-40. 45. Markham NR, Zuker M: UNAFold: software for nucleic acid folding and hybridization. Methods Mol. Biol 2008, 453:3-31. 46. Zuker M: Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 2003, 31:3406-15. 47. Zuker M and S: Optimal computer folding of large RNA sequences using thermodymanics and auxiliary information. Nucleic Acids Res. 1981, 9:133- 148. 48. Hofacker IL: Vienna RNA secondary structure server. Nucleic Acids Res 2003, 31:3429-3431. 49. Zhu J, Li T, Hu J, Wang E: A novel dot-blot DNAzyme-linked aptamer assay for protein detection. Anal Bioanal Chem 2010, 397:2923-2927. 50. Tombelli S, Mascini M: Aptamers as molecular tools for bioanalytical methods. Curr. Opin. Mol. Ther 2009, 11:179-188. 51. Shin S, Kim I-H, Kang W, Yang JK, Hah SS: An alternative to Western blot analysis using RNA aptamer-functionalized quantum dots. Bioorg. Med. Chem. Lett 2010, 20:3322-3325. 52. Kim YS, Jung HS, Matsuura T, Lee HY, Kawai T, Gu MB: Electrochemical detection of 17beta-estradiol using DNA aptamer immobi- lized gold electrode chip. Biosensors & bioelectronics 2007, 22:2525-31. Page 9 8058 El Rio St., Houston, TX 77054 • basepairbio.com • info@basepairbio.com
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Joshi R, Janagama H, Dwivedi HP, Senthil Kumar TMA, Jaykus L-A, Schefers J, Sreevatsan S: Selection, characterization, and application of DNA aptamers for the capture and detection of Salmonella enterica serovars. Mol. Cell. Probes 2009, 23:20-28. 76. Smith JE, Medley CD, Tang Z, Shangguan D, Lofton C, Tan W: Aptamer-conjugated nanoparticles for the collection and detection of multiple cancer cells. Anal. Chem 2007, 79:3075-3082. 77. Chen Y, Munteanu AC, Huang Y-F, Phillips J, Zhu Z, Mavros M, Tan W: Mapping receptor density on live cells by using fluorescence correlation spectroscopy. Chemistry 2009, 15:5327-5336. 78. Chen HW, Medley CD, Sefah K, Shangguan D, Tang Z, Meng L, Smith JE, Tan W: Molecular recognition of small-cell lung cancer cells using aptamers. ChemMedChem 2008, 3:991-1001. Page 10 8058 El Rio St., Houston, TX 77054 • basepairbio.com • info@basepairbio.com