Selection of bead-displayed, PNA-encoded chemicals

Journal of Molecular Recognition

Volumn 23, Issue 5, 2010, Pages 414-422

  Gassmana, Natalie R ^a,b   Nellia, J Patrick ^a   Dutta, Samrat ^a   Kuhn, Adam ^a   Bonin, Keith ^a   Pianowski, Zbigniew ^c   Winssinger, Nicolas ^c   Guthold, Martin ^a,b   Macosko, Jed C ^a  

^a WAKE FOREST UNIVERSITY   (United States)

^b WAKE FOREST BAPTIST HEALTH   (United States)

^c UNIVERSITÉ DE STRASBOURG   (France)

Author keywords

Beads; DNA encoded chemicals; Drug discovery; Fluorescence; Micropipette; Microscopy; PNA encoded chemicals; Small molecule screening

Indexed keywords

FLUORESCENT DYE; PEPTIDE LIBRARY; PEPTIDE NUCLEIC ACID;

ARTICLE; CHEMISTRY; COMBINATORIAL CHEMISTRY; DRUG DEVELOPMENT; EVALUATION; INSTRUMENTATION; METHODOLOGY; NUCLEOTIDE SEQUENCE;

BASE SEQUENCE; COMBINATORIAL CHEMISTRY TECHNIQUES; DRUG DISCOVERY; FLUORESCENT DYES; PEPTIDE LIBRARY; PEPTIDE NUCLEIC ACIDS;

EID: 77956406798     PISSN: 09523499     EISSN: 10991352     Source Type: Journal    
DOI: 10.1002/jmr.1007     Document Type: Article

References (40)

1. Boder ET, Wittrup KD. 1997. Yeast surface display for screening combinatorial polypeptide libraries. Nat. Biotechnol. 15: 553-557.
2. Brenner S, Lerner RA. 1992. Encoded combinatorial chemistry. Proc. Natl. Acad. Sci. USA 89: 5381-5383.
3. Buller F, Mannocci L, Zhang YX, Dumelin CE, Scheuermann J, Neri D. 2008. Design and synthesis of a novel DNA-encoded chemical library using Diels-Alder cycloadditions. Bioorg. Med. Chem. Lett. 18: 5926-5931.
4. Chen JW, Iannone MA, Li MS, Taylor JD, Rivers P, Nelsen AJ, Slentz-Kesler KA, Roses A, Weiner MP. 2000. A microsphere-based assay for multiplexed single nucleotide polymorphism analysis using single base chain extension. Genome Res. 10: 549-557.
5. Childs-Disney JL, Wu ML, Pushechnikov A, Aminova O, Disney MD. 2007. A small molecule microarray platform to select RNA internal loopligand interactions. ACS Chem. Biol. 2: 745-754.
6. Clackson T, Hoogenboom HR, Griffiths AD, Winter G. 1991. Making antibody fragments using phage display libraries. Nature 352: 624-628.
7. Conrad RC, Baskerville S, Ellington AD. 1995. In vitro selection methodologies to probe RNA function and structure. Mol. Divers. 1: 69-78.
8. Debaene F, Da Silva JA, Pianowski Z, Duran FJ, Winssinger N. 2007. Expanding the scope of PNA-encoded libraries: divergent synthesis of libraries targeting cysteine, serine and metalloproteases as well as tyrosine phosphatases. Tetrahedron 63: 6577-6586.
9. Diehl F, Li M, He Y, Kinzler K, Vogelstein B, Dressman D. 2006. BEAMing: single-molecule PCR on microparticles in water-in-oil emulsions. Nat. Methods 3: 551-559.
10. Disney MD, Labuda LP, Paul DJ, Poplawski SG, Pushechnikov A, Tran T, Velagapudi SP, Wu M, Childs-Disney JL. 2008. Two-dimensional combinatorial screening identifies specific aminoglycoside - RNA internal loop partners. J. Am. Chem. Soc. 130: 11185-11194.
11. Fitzwater T, Polisky B. 1996. A SELEX primer. Comb. Chem. 267: 275-301.
12. Forst CV. 1998. Molecular evolution: a theory approaches experiments. J. Biotechnol. 64: 101-118.
13. Gartner Z, Kanan M, Liu D. 2002. Multistep small-molecule synthesis programmed by DNA templates. J. Am. Chem. Soc. 124: 10304-10306.
14. Gartner ZJ, Tse BN, Grubina R, Doyon JB, Snyder TM, Liu DR. 2004. DNA-templated organic synthesis and selection of a library of macrocycles. Science 305: 1601-1605.
15. Halpin DR, Harbury PB. 2004a. DNA display I. Sequence-encoded routing of DNA populations. PLoS Biol. 2: 1015-1021.
16. Halpin DR, Harbury PB. 2004b. DNA display II. Genetic manipulation of combinatorial chemistry libraries for small-molecule evolution. PLoS Biol. 2: 1022-1030.
17. Halpin DR, Lee JA, Wrenn SJ, Harbury PB. 2004. DNA display III. Solid-phase organic synthesis on unprotected DNA. PLoS Biol. 2: 1031-1038.
18. Harris JL, Winssinger N. 2005. PNA encoding (PNA1/4peptide nucleic acid): from solution-based libraries to organized microarrays. Chem. Eur. J. 11: 6792-6801.
19. Harris J, Mason DE, Li J, Burdick KW, Backes BJ, Chen T, Shipway A, Van Heeke G, Gough L, Ghaemmaghami A, Shakib F, Debaene F, Winssinger N. 2004. Activity profile of dust mite allergen extract using substrate libraries and functional proteomic microarrays. Chem. Biol. 11: 1361-1372.
20. Haupts U, Rudiger M, Ashman S, Turconi S, Bingham R, Wharton C, Hutchinson J, Carey C, Moore KJ, Pope AJ. 2003. Single-molecule detection technologies in miniaturized high-throughput screening: fluorescence intensity distribution analysis. J. Biomol. Screen. 8: 19-33.
21. Iannone MA, Taylor JD, Chen JW, Li MS, Rivers P, Slentz-Kesler KA, Weiner MP. 2000. Multiplexed single nucleotide polymorphism genotyping by oligonucleotide ligation and flow cytometry. Cytometry 39: 131-140.
22. Joo C, Ha T. 2008. Single-molecule FRET with total internal reflection microscopy. In Single-Molecule Techniques: A Laboratory Manual, Selvin P, Ha T (eds), 1st edn, Vol. 2. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York: 3-36.
23. Kapur R, Giuliano KA, Campana M, Adams T, Olson K, Jung D, Mrksich M, Vasudevan C, Taylor DL. 1999. Streamlining the drug discovery process by integrating miniaturization, high throughput screening, high content screening, and automation on the CellChip/sup TM/system. Biomed. Microdevices 2: 99-109.
24. Kim SK, Shin BC, Ott TA, Cha W, La IJ, Yoo MY. 2008. SELEX: combinatorial library methodology and applications. Biochip J. 2: 97-102.
25. Kleiner RE, Brudno Y, Birnbaum ME, Liu DR. 2008. DNA-templated polymerization of side-chain-functionalized peptide nucleic acid aldehydes. J. Am. Chem. Soc. 130: 4646-4659.
26. Li M, Diehl F, Dressman D, Vogelstein B, Kinzler K. 2006. BEAMing up for detection and quantification of rare sequence variants. Nat. Methods 3: 95-97.
27. Melkko S, Dumelin CE, Scheuermann J, Neri D. 2007a. Lead discovery by DNA-encoded chemical libraries. Drug Discov. Today 12: 465-471.
28. Melkko S, Zhang Y, Dumelin CE, Scheuermann J, Neri D. 2007b. Isolation of high-affinity trypsin inhibitors from a DNA-encoded chemical library. Angew. Chem. Int. Ed. 46: 4671-4674.
29. Mendonsa SD, Bowser MT. 2004. In vitro evolution of functional DNA using capillary electrophoresis. J. Am. Chem. Soc. 126: 20-21.
30. Nifli AP, Notas G, Mamoulaki M, Niniraki M, Ampartzaki V, Theodoropoulos PA, Kopnitsky MJ, Castanas E. 2006. Comparison of a multiplex, beadbased fluorescent assay and immunofluorescence methods for the detection of ANA and ANCA autoantibodies in human serum. J. Immunol. Methods 311: 189-197.
31. Peng L, Stephens B, Bonin K, Cubicciotti R, Guthold M. 2007. A combined atomic force/fluorescence microscopy technique to select aptamers in a single cycle from a small pool of random oligonucleotides. Microsc. Res. Tech. 70: 372-381.
32. Pianowski ZL, Winssinger N. 2008. Nucleic acid encoding to program selfassembly in chemical biology. Chem. Soc. Rev. 37: 1330-1336.
33. Shlyakhtenko LS, Yuan B, Emadi S, Lyubchenko YL, Sierks MR. 2007. Singlemolecule selection and recovery of structure-specific antibodies using atomic force microscopy. Nanomedicine 3: 192-197.
34. Silacci M, Brack S, Schirru G, Marlind J, Ettorre A, Merlo A, Viti F, Neri D. 2005. Design, construction, and characterization of a large synthetic human antibody phage display library. Proteomics 5: 2340-2350.
35. Smith GP. 1985. Filamentous fusion page - novel expression vectors that display cloned antigens on the virion surface. Science 228: 1315-1317.
36. Stoltenburg R, Reinemann C, Strehlitz B. 2007. SELEX-A (r) evolutionary method to generate high-affinity nucleic acid ligands. Biomol. Eng. 24: 381-403.
37. Sundberg SA. 2000. High-throughput and ultra-high-throughput screening: solution- and cell-based approaches. Curr. Opin. Biotechnol. 11: 47-53.
38. Urbina HD, Debaene F, Jost B, Bole-Feysot C, Mason DE, Kuzmic P, Harris JL, Winssinger N. 2006. Self-assembled small-molecule microarrays for protease screening and profiling. Chembiochem 7: 1790-1797.
39. Wrenn SJ, Harbury PB. 2007. Chemical evolution as a tool for molecular discovery. Annu. Rev. Biochem. 76: 331-349.
40. Yin J, Liu F, Schinke M, Daly C, Walsh CT. 2004. Phagemid encoded small molecules for high throughput screening of chemical libraries. J. Am. Chem. Soc. 126: 13570-13571.