Selection-by-function: Efficient enrichment of cathepsin E inhibitors from a DNA library

Journal of Molecular Recognition

Volumn 20, Issue 1, 2007, Pages 58-68

  Naimuddin, Mohammed ^a,d,e   Kitamura, Koichirou ^a   Kinoshita, Yasunori ^b   Honda Takahashi, Yoko ^a   Murakami, Marina ^b   Ito, Masato ^b   Yamamoto, Kenji ^c   Hanada, Kazunori ^a   Husimi, Yuzuru ^a,b   Nishigaki, Koichi ^a,b  

^a JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^b SAITAMA UNIVERSITY   (Japan)

^c KYUSHU UNIVERSITY   (Japan)

^d Saitama Industrial Technology Center   (Japan)

^e NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

Author keywords

Activity based selection; Aptamers; Directed evolution; Inhibitors; Proteases; Substrate function link

Indexed keywords

CATHEPSIN D; CATHEPSIN E; DNA; PEPTIDE APTAMER; PROTEINASE INHIBITOR;

AMINO ACID SEQUENCE; ANIMAL; ARTICLE; CHEMISTRY; COMBINATORIAL CHEMISTRY; CONFORMATION; DRUG ANTAGONISM; ENZYME SPECIFICITY; GENE LIBRARY; GENETICS; KINETICS; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; RAT;

AMINO ACID SEQUENCE; ANIMALS; APTAMERS, PEPTIDE; BASE SEQUENCE; CATHEPSIN D; CATHEPSIN E; DNA; GENE LIBRARY; KINETICS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PROTEASE INHIBITORS; RATS; SELEX APTAMER TECHNIQUE; SUBSTRATE SPECIFICITY;

EID: 33846547053     PISSN: 09523499     EISSN: 10991352     Source Type: Journal    
DOI: 10.1002/jmr.812     Document Type: Article

References (41)

1. Bennett K, Levine T, Ellis JS, Peanasky RJ, Samloff IM, Kay J, Chain BM. 1992. Antigen processing for presentation by class II major histocompattbility complex requires cleavage by cathepsin E. Eur. J. Immunol. 22: 1519-1524.
2. Bock LC, Griffin LC, Latham JA, Vermaas EH, Toole JJ. 1992. Selection of single-stranded DNA molecules that bind and inhibit human thrombin. Nature 355: 564-566.
3. Brody EN, Gold L. 2000. Aptamers as therapeutic and diagnostic agents. J. Biotechnol. 74: 5-13.
4. Ellington AD, Szostak JW. 1990. In vitro selection of RNA molecules that bind specific ligands. Nature 346: 818-822.
5. Ellington AD, Szostak JW. 1992. Selection In vitro of single stranded DNA molecules that fold into specific ligand-binding structures. Nature 355: 850-852.
6. Famulok M, Mayer G. 1999. Aptamers as tools in molecular biology and immunology. Curr. Top. Microbiol. Immunol. 243: 123-136.
7. Famulok M, Mayer G, Blind M. 2000. Nucleic acid aptamer-From selection in vitro to applications in vivo. Acc. Chem. Res. 33: 591-599.
8. Gold L, Polisky B, Uhlenbeck O, Yarus M. 1995. Diversity of oligonucleotide functions. Annu. Rev. Biochem. 64: 763-797.
9. Gueron M, Leroy JL. 2000. The i-motif in nucleic acids. Curr Opin Struct Biol. 10: 326-331.
10. Hartig JS, Kool ET. 2004. Small circular DNAs for synthesis of the human telomere repeat: varied sizes, structures and telomere-encoding activities. Nucleic Acids Res. 32: e152.
11. Hermann T, Patel DJ. 2000. Adaptive recognition by nucleic acid aptamers. Science 287: 820-825.
12. Jayasena SD. 1999. Aptamers: an emerging class of molecules that rival antibodies in diagnostics. Clin. Chem. 45: 1628-1650.
13. Jarosch F, Buchner K, Klussmann S. 2006. In vitro selection using a dual RNA library that allows primerless selection. Nucleic Acids Res. 34: e86.
14. Kageyama T. 1995. Procathepsin E and cathepsin E. In Methods in Enzymology, Vol. 248 , Barett AJ (ed.). Academic Press: New York; 120-136.
15. Khati M, Schuman M, Ibrahim J, Sattentau Q, Gordon S, James W. 2003. Neutralization of infectivity of diverse R5 clinical isolates of human immunodeficiency virus type 1 by gp120-binding 2′F-RNA aptamers. J. Virol. 77: 12692-12698.
16. King DJ, Ventura DA, Brasier AR, Gorenstein DG. 1998. Novel combinatorial selection of phosphorothioate oligonucleotide aptamers. Biochemistry 37: 16489-16493.
17. Kitamura K, Kinoshita Y, Narasaki S, Nemoto N, Husimi Y, Nishigaki K. 2002. Construction of block-shuffled libraries of DNA for evolutionary protein engineering: Y-ligation-based block shuffling. Protein Eng. 15: 843-853.
18. Latham JA, Johnson R, Toole JJ. 1994. The application of a modified nucleotide in aptamer selection: novel thrombin aptamers containing 5-(1-pentynyl)-2′-deoxyuridine. Nucleic Acids Res. 22: 2817-2822.
19. Leroy JL, Gueron M, Mergny JL, Helene C. 1994. Intramolecular folding of a fragment of the cytosine-rich strand of telomeric DNA into an i-motif. Nucleic Acids Res. 22: 1600-1606.
20. Liu J, Tsukuba T, Okamoto K, Ohishi M, Yamamoto K. 2002. Mutational analysis of residues in two consensus motifs in the active sites of cathepsin E. E. J. Biochem. 132: 493-499.
21. Macaya RF, Schultze P, Smith FW, Roe JA, Feigon J. 1993. Thrombin-binding DNA aptamer forms a unimolecular quadruplex structure in solution. Proc. Natl Acad. Sci. USA 90: 3745-3749.
22. Martell RE, Nevins JR, Sullenger BA. 2002. Optimizing aptamer activity for gene therapy applications using expression cassette SELEX. Mol. Ther. 6: 30-34.
23. Mazumder A, Neamati N, Ojwang JO, Sunder S, Rando RF, Pommier Y. 1996. Inhibition of the human immunodeficiency virus Type 1 integrase by guanosine quartet structures. Biochemistry 35: 13762-13771.
24. Miyoshi D, Matsumura S, Nakano S, Sugimoto N. 2004. Duplex dissociation of telomere DNAs induced by molecular crowding. J. Am. Chem. Soc. 126: 165-169.
25. Mochizuki K, Oguro A, Ohtsu T, Sonenberg N, Nakamura Y. 2005. High affinity RNA for mammalian initiation factor 4E interferes with mRNA-cap binding and inhibits translation. RNA 11: 77-89.
26. Nishigaki K, Saito A, Hasegawa T, Naimuddin M. 2000. Whole genome sequence-enabled prediction of sequences performed for random PCR products of Escherichia coli. Nucleic Acids Res. 28: 1879-1884.
27. Nishioku T, Hashimoto K, Yamashita K, Liou SY, Kagamiishi Y, Maegawa H, Katsube N, Peters C, von Figura K, Saftig P, Katunuma N, Yamamoto K, Nakanishi H. 2002. Involvement of cathepsin E in exogenous antigen processing in primary cultured murine microglia. J. Biol. Chem. 277: 4816-4822.
28. Okamoto K, Yu H, Misumi Y, Ikehara Y, Yamamoto K. 1995. Isolation and sequencing of two cDNA clones encoding rat spleen cathepsin E and analysis of the activation of purified procathepsin E. Arch. Biochem. Biophys. 322: 103-111.
29. Phan AT, Mergny JL. 2002. Human telomeric DNA: G-quadruplex, i-motif and Watson-Crick double helix. Nucleic Acids Res. 30: 4618-4625.
30. Pileur F, Andreola ML, Dausse E, Michel J, Moreau S, Yamada H, Gaidamakov SA, Crouch RJ, Toulme JJ, Cazenave C 2003. Selective inhibitory DNA aptamers of the human RNase H1. Nucleic Acids Res. 31: 5776-5788.
31. Rhie A, Kirby L, Sayer N, Wellesley R, Disterer P, Sylvester I, Gill A, Hope J, James W, Tahiri-Alaoui A. 2003. Characterization of 2′-fluoro-RNA aptamers that bind preferentially to disease-associated conformations of prion protein and inhibit conversion. J. Biol. Chem. 278: 39697-39705.
32. Steger G. 1994. Thermal denaturation of double-stranded nucleic acids: prediction of temperatures critical for gradient gel electrophoresis and polymerase chain reaction. Nucleic Acids Res. 22: 2760-2768.
33. Takeda M, Ueno E, Kato Y, Yamamoto K. 1986. Isolation, and catalytic and immunochemical properties of cathepsin D-like acid proteinase from rat erythrocytes. J. Biochem. 100: 1269-1277.
34. Tsukuba T, Okamoto K, Yasuda Y, Morikawa W, Nakanishi H, Yamamoto K. 2000. New functional aspects of cathepsin D and cathepsin E. Mol. Cells 10: 601-611.
35. Tsukuba T, Okamoto K, Okamoto Y, Yanagawa M, Kohmura K, Yasuda Y, Uchi H, Nakahara T, Furue M, Nakayama K, Kadowaki T, Yamamoto K, Nakayama KI. 2003. Association of cathepsin E deficiency with development of atopic dermatitis. J. Biochem. 134: 893-902.
36. Tuerk C, Gold L. 1990. Systematic evolution of ligands by exponential enrichments: RNA ligands to bacteriophage T4 DNA polymerase. Science 249: 505-510.
37. Ulrich H, Martins AH, Pesquero JB. 2004. RNA and DNA aptamers in cytomics analysis. Cytometry A 59: 220-231.
38. Vater A, Jarosch F, Buchner K, Klussmann S. 2003. Short bioactive spiegelmers to migraine-associated calcitonin gene-related peptide rapidly identified by a novel approach: tailored-SELEX. Nucleic Acids Res. 31: e130.
39. Wyatt JR, Vickers TA, Roberson JL, Buckheit RW, Klimkait T, DeBaets E, Davis PW, Rayner B, Imbach JL, Ecker DJ. 1994. Combinatorially selected guanosine-quartet structure is a potent inhibitor of human immunodeficiency virus envelope-mediated cell fusion. Proc. Natl. Acad. Sci. USA 91: 1356-1360.
40. Yasuda Y, Kageyama T, Akamine A, Shibata M, Kominami E, Uchiyama Y, Yamamoto K. 1999. Characterization of new fluorogenic substrates for the rapid and sensitive assay of cathepsin E and cathepsin D. J. Biochem. 125: 1137-1143.
41. Zuker M. 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31: 3406-3415.