Production of single-stranded DNAs by self-cleavage of rolling-circle amplification products

BioTechniques

Volumn 54, Issue 6, 2013, Pages 337-343

  Gu, Hongzhou ^a,b   Breaker, Ronald R ^a,b  

^a YALE UNIVERSITY   (United States)

^b HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

Deoxyribozymes; Rolling circle amplification; Self hydrolysis; Single stranded DNA ladder

Indexed keywords

DEOXYRIBOZYME; OLIGONUCLEOTIDE; PRIMER DNA; SINGLE STRANDED DNA;

AGAR GEL ELECTROPHORESIS; ARTICLE; DNA SYNTHESIS; DNA TEMPLATE; GENE AMPLIFICATION; HYDROLYSIS; NUCLEOTIDE SEQUENCE; ULTRAVIOLET RADIATION;

DNA, CATALYTIC; DNA, SINGLE-STRANDED; ELECTROPHORESIS, AGAR GEL; NUCLEIC ACID AMPLIFICATION TECHNIQUES; NUCLEIC ACID CONFORMATION; RNA;

EID: 84878998108     PISSN: 07366205     EISSN: 19409818     Source Type: Journal    
DOI: 10.2144/000114009     Document Type: Article

References (18)

1. Breaker, R.R. 1997. DNA enzymes. Nat. Biotechnol. 15:427-431.
2. Schlosser, K. and Y. Li. 2009. Biologically inspired synthetic enzymes made from DNA. Chem. Biol. 16:311-322.
3. Silverman, S.K. 2009. Deoxyribozymes: selection design and serendipity in the development of DNA catalysts. Acc. Chem. Res. 42:1521-1531.
4. Todd, A.V., C.J. Fuery, H.L. Impey, T.L. Applegate, and M.A. Haughton. 2000. DzyNA-PCR: use of DNAzymes to detect and quantify nucleic acid sequences in a real-time fluorescent format. Clin. Chem. 46:625-630.
5. Liu, J. and Y. Lu. 2006. Fluorescent DNAzyme biosensors for metal ions based on catalytic molecular beacons. Methods Mol. Biol. 335:275-288.
6. Silverman, S.K. 2008. Catalytic DNA (deoxyribozymes) for synthetic applications-current abilities and future prospects. Chem. Commun. (Camb.) 14:3467-3485.
7. Carmi, N., L.A. Shultz, and R.R. Breaker. 1996. In vitro selection of self-cleaving DNAs. Chem. Biol. 3:1039-1046.
8. Sheppard, T.L., P. Ordoukhanian, and G.F. Joyce. 2000. A DNA enzyme with N-glycosylase activity. Proc. Natl. Acad. Sci. USA 97:7802-7807.
9. Chandra, M., A. Sachdeva, and S.K. Silverman. 2009. DNA-catalyzed sequence-specific hydrolysis of DNA. Nat. Chem. Biol. 5:718-720.
10. Xiao, Y., R.J. Wehrmann, N.A. Ibrahim, and S.K. Silverman. 2012. Establishing broad generality of DNA catalysts for site-specific hydrolysis of single-stranded DNA. Nucleic Acids Res. 40:1778-1786.
11. Xiao, Y., M. Chandra, and S.K. Silverman. 2010. Functional compromises among pH tolerance, site specificity, and sequence tolerance for a DNA-hydrolyzing deoxyribozyme. Biochemistry 49:9630-9637.
12. Dokukin, V. and S.K. Silverman. 2012. Lanthanide ions as required cofactors for DNA catalysts. Chem. Sci. 3:1707-1714.
13. Gu, H., K. Furukawa, Z. Weinberg, D.F. Berenson, and R.R. Breaker. Small, highly-active DNAs that hydrolyze DNA. J. Am. Chem. Soc. (In press)
14. Liu, D., S.L. Daubendiek, M.A. Zillman, K. Ryan, and E.T. Kool. 1996. Rolling circle DNA synthesis: small circular oligonucleotides as efficient templates for DNA polymerases. J. Am. Chem. Soc. 118:1587-1594.
15. Lizardi, P.M., X. Huang, Z. Zhu, P. Bray-Ward, D.C. Thomas, and D.C. Ward. 1998. Mutation detection and single-molecule counting using isothermal rolling-circle amplification. Nat. Genet. 19:225-232.
16. Stougaard, M., S. Juul, F.F. Andersen, and B.R. Knudsen. 2011. Strategies for highly sensitive biomarker detection by rolling circle amplification of signals from nucleic acid composed sensors. Integr. Biol. (Camb). 3:982-992.
17. Asiello, P.J. and A. Baeumner. 2011. Miniaturized isothermal nucleic acid amplification, a review. Lab Chip 11:1420-1430.
18. Blondal, T., A. Thorisdottir, U. Unnsteinsdottir, S. Hjorleifsdottir, A. Ævarsson, S. Ernstsson, O.H. Fridjonsson, S. Skirnisdottir, et al. 2005. Isolation and characterization of a thermostable RNA ligase 1 from a Thermus scotoductus bacteriophage TS2126 with good single-stranded DNA ligation properties. Nucleic Acids Res. 33:135-142.