Aptameric enzyme subunit for homogeneous DNA sensing

Biotechnology Letters

Volumn 30, Issue 2, 2008, Pages 243-252

  Ikebukuro, Kazunori ^a   Yoshida, Wataru ^a   Sode, Koji ^a  

^a TOKYO UNIVERSITY OF AGRICULTURE AND TECHNOLOGY   (Japan)

Author keywords

Aptameric enzyme subunit; Enzyme inhibiting aptamer; Homogeneous DNA sensing

Indexed keywords

DNA SEQUENCES; ENZYME INHIBITION; MOLECULAR STRUCTURE;

APTAMERIC ENZYME SUBUNIT; ENZYME INHIBITING APTAMERS; HOMOGENEOUS DNA SENSING;

ENZYME ACTIVITY;

APTAMER; DNA; PROTEIN SUBUNIT; THROMBIN;

ARTICLE; CHEMISTRY; DRUG ANTAGONISM; GENETIC PROCEDURES; GENETICS; HUMAN; METABOLISM; MOLECULAR GENETICS; NUCLEIC ACID HYBRIDIZATION; NUCLEOTIDE SEQUENCE;

APTAMERS, NUCLEOTIDE; BASE SEQUENCE; BIOSENSING TECHNIQUES; DNA; HUMANS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID HYBRIDIZATION; PROTEIN SUBUNITS; THROMBIN;

EID: 37549010223     PISSN: 01415492     EISSN: 15736776     Source Type: Journal    
DOI: 10.1007/s10529-007-9526-z     Document Type: Article

References (27)

1. 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
2. Dapic V, Abdomerovic V, Marrington R, Peberdy J, Rodger A, Trent JO, Bates PJ (2003) Biophysical and biological properties of quadruplex oligodeoxyribonucleotides. Nucleic Acids Res 31:2097-2107
3. Ellington AD, Szostak JW (1990) In vitro selection of RNA molecules that bind specific ligands. Nature 346:818-822
4. Fouchier RA, Bestebroer TM, Herfst S, Van Der Kemp L, Rimmelzwaan GF, Osterhaus AD (2000) Detection of influenza A viruses from different species by PCR amplification of conserved sequences in the matrix gene. J Clin Microbiol 38:4096-4101
5. Galan JE, Curtiss R (1990) Expression of Salmonella typhimurium genes required for invasion is regulated by changes in DNA supercoiling. Infect Immun 58:1879-1885
6. Ho HA, Boissinot M, Bergeron MG, Corbeil G, Dore K, Boudreau D, Leclerc M (2002) Angew. Chem., Int. Ed. Colorimetric and Fluorometric Detection of Nucleic Acids Using Cationic Polythiophene Derivatives. 114:1618-1621
7. Ikebukuro K, Okumura Y, Sumikura K, Karube I (2005) A novel method of screening thrombin-inhibiting DNA aptamers using an evolution-mimicking algorithm. Nucleic Acids Res 33:e108
8. Isacsson J, Cao H, Ohlsson L, Nordgren S, Svanvik N, Westman G, Kubista M, Sjoback R, Sehlstedt U (2000) Rapid and specific detection of PCR products using light-up probes. Mol Cell Probes 14:321-328
9. Kuryavyi V, Majumdar A, Shallop A, Chernichenko N, Skripkin E, Jones R, Patel DJ (2001) A double chain reversal loop and two diagonal loops define the architecture of a unimolecular DNA quadruplex containing a pair of stacked G(syn)-G(syn)-G(anti)-G(anti) tetrads flanked by a G-(T-T) Triad and a T-T-T triple. J Mol Biol 310:181-194
10. Li Q, Luan G, Guo Q, Liang J (2002) A new class of homogeneous nucleic acid probes based on specific displacement hybridization. Nucleic Acids Res 30:E5
11. 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 U. S. A. 90:3745-3749
12. Marra MA et al (2003) The Genome sequence of the SARS-associated coronavirus. Science 300:1399-1404
13. Masuko M, Ohtani H, Ebata K, Shimadzu A (1998) Optimization of excimer-forming two-probe nucleic acid hybridization method with pyrene as a fluorophore. Nucleic Acids Res 26:5409-5416
14. Pavlov V, Shlyahovsky B, Willner I (2005) Fluorescence detection of DNA by the catalytic activation of an aptamer/thrombin complex. J Am Chem Soc 127:6522-6523
15. Rota PA et al (2003) Characterization of a novel coronavirus associated with severe acute respiratory syndrome. Science 300:1394-1399
16. Saghatelian A, Guckian KM, Thayer DA, Ghadiri MR (2003) DNA detection and signal amplification via an engineered allosteric enzyme. J Am Chem Soc 125:344-345
17. Schultze P, Macaya RF, Feigon J (1994) Three-dimensional solution structure of the thrombin-binding DNA aptamer d(GGTTGGTGTGGTTGG). J Mol Biol 235:1532-1547
18. Smirnov I, Shafer RH (2000) Effect of loop sequence and size on DNA aptamer stability. Biochemistry 39:1462-1468
19. Stojanovic MN, de Prada P, Landry DW (2001) Catalytic molecular beacons. Chembiochem 2:411-415
20. Tian Y, He Y, Mao C (2006) Cascade signal amplification for DNA detection. Chembiochem 7:1862-1864
21. Tuerk C, Gold L (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249:505-510
22. Tyagi S, Kramer FR (1996) Molecular beacons: probes that fluoresce upon hybridization. Nat Biotechnol 14:303-308
23. Wang DY, Sen D (2001) A novel mode of regulation of an RNA-cleaving DNAzyme by effectors that bind to both enzyme and substrate. J Mol Biol 310:723-734
24. Xiao Y, Pavlov V, Niazov T, Dishon A, Kotler M, Willner I (2004) Catalytic beacons for the detection of DNA and telomerase activity. J Am Chem Soc 126:7430-7431
25. Yoshida W, Sode K, Ikebukuro K (2006a) Aptameric enzyme subunit for biosensing based on enzymatic activity measurement. Anal Chem 78:3296-3303
26. Yoshida W, Sode K, Ikebukuro K (2006b) Homogeneous DNA sensing using enzyme-inhibiting DNA aptamers. Biochem Biophys Res Commun 348:245-252
27. Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31:3406-3415