Determination of the reopening temperature of a DNA hairpin structure in vitro

European Journal of Biochemistry

Volumn 271, Issue 18, 2004, Pages 3665-3670

  Pan, Xuefeng ^a  

^a INSTITUTE OF MICROBIOLOGY   (China)

Author keywords

DNA hairpin; Non B DNA secondary structure; Primer extension; Reopening temperature; Tm

Indexed keywords

AGAROSE; DNA; DOUBLE STRANDED DNA; OLIGONUCLEOTIDE;

ARTICLE; CONTROLLED STUDY; DENATURATION; DNA SEQUENCE; DNA STRUCTURE; DNA TEMPLATE; INCUBATION TIME; NONHUMAN; PRIORITY JOURNAL; RENATURATION; TEMPERATURE; THERMAL ANALYSIS;

BASE PAIRING; BASE SEQUENCE; DNA PRIMERS; DNA, BACTERIAL; ESCHERICHIA COLI; HYDROGEN BONDING; NUCLEIC ACID CONFORMATION; POLYMERASE CHAIN REACTION; TEMPERATURE; TEMPLATES, GENETIC; THERMODYNAMICS;

EID: 4544266120     PISSN: 00142956     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1432-1033.2004.04301.x     Document Type: Article

References (39)

1. Dai, X. & Rothman-Denes, L.B. (1999) DNA structure and transcription. Curr. Opin. Microbiol. 2, 126-130.
2. Wolffe, A.P. & Kurumizaka, H. (1998) The nucleosome: a powerful regulator of transcription. Prog. Nucleic Acid Res. Mol. Biol. 61, 379-422.
3. Balagurumoorthy, P., Brahmachari, S.K., Mohanty, D., Bansal, M. & Sasisekharan, V. (1992) Hairpin and parallel quartet structures for telomeric sequences. Nucleic Acids Res. 20, 4061-4067.
4. Balagurumoorthy, P. & Brahmachari, S.K. (1994) Structure and stability of human telomeric sequence. J. Biol. Chem. 269, 21858-21869.
5. del Solar, G., Giraldo, R., Ruiz-Echevarria, M.J., Espinosa, M. & Diaz-Orejas, R. (1998) Replication and control of circular bacterial plasmids. Microbiol. Mol. Biol. Rev. 62, 434-464.
6. Wang, Y.-H., Gellibolian, R., Shimizu, M., Wells, R.D. & Griffith, J.D. (1996) Long CCG triplet repeat blocks exclude nucleosomes: a possible mechanism for the nature of fragile sites in chromosomes. J. Mol. Biol. 263, 511-516.
7. Leach, D.R. (1994) Long DNA palindromes, cruciform structures, genetic instability and secondary structure repair. Bioessays 16, 893-900.
8. Holde, K.V. & Zlatanova, J. (1994) Unusual DNA structures, chromatin and transcription. Bioessays 16, 59-68.
9. Mitas, M. (1997) Trinucleotide repeats associated with human disease. Nucleic Acids Res. 259, 2245-2253.
10. McMurray, C.T. (1999) DNA secondary structure: a common and causative factor for expansion in human disease. Proc. Natl Acad. Sci. USA 96, 1823-1825.
11. Sinden, R.R. (1999) Trinucleotide repeats biological implications of the DNA structures associated with disease-causing triplet repeat. Am. J. Hum. Genet. 64, 346-353.
12. Sinden, R.R., Potaman, V.N., Oussatcheva, E.A., Pearson, C.E., Lyubchenko, Y.L. & Shlyakhtenko, L.S. (2002) Triplet repeat DNA structures and human genetic disease: dynamic mutations from dynamic DNA. J. Biosci. 27 (Suppl 1), 53-65.
13. Pearson, C.E. & Sinden, R.R. (1998) Trinucleotide repeat DNA structures: dynamic mutations from dynamic DNA. Curr. Opin. Struct. Biol. 8, 321-330.
14. Moore, H., Greenwell, P.W., Liu, C.-P., Arnheim, N. & Petes, T. (1999) Triplet repeats form secondary structures that escape DNA repair in Yeast. Proc. Natl Acad. Sci. USA 96, 1504-1509.
15. Sastry, S.S. & Hoffman, P.L. (1995) The influence of RNA and DNA template structures during transcript elongation by RNA polymerases. Biochem. Biophys. Res. Commun. 211, 106-114.
16. Rychlink, W. & Rhoads, R.E. (1989) A computer program for choosing optimal oligonucleotides for filter hybridization, sequencing and in vitro amplification of DNA. Nucleic Acids Res. 17, 8543-8551.
17. Zhang, Z., Huang, K., Zhang, Y., Liu, N. & Yang, K. (1994) Interference by complex structures of target DNA with specific PCR amplification. Appl. Biochem. Biotechnol. 44, 15-20.
18. Sambrook, J., Fritsch, E.F. & Maniatis, T. (1989) Molecular Cloning: A laboratory Manual, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
19. Canceil, D. & Ehrlich, S.D. (1996) Copy-choice recombination mediated by DNA polymerase III holoenzyme from Escherichia coli. Proc. Natl Acad. Sci. USA 93, 6647-6652.
20. Canceill, D., Viguera, E. & Ehrlich, S.D. (1999) Replication slippage of different DNA polymerases is inversely related to their strand displacement efficiency. J. Biol. Chem. 274, 27481-27490.
21. Viguera, E., Canceill, D. & Ehrlich, S.D. (2001) Replication slippage involves DNA polymerase pausing and dissociation. EMBO J. 20, 2587-2595.
22. Gacy, A.M. & McMurray, C.T. (1998) Influence of hairpins on template reannealing at trinucleotide repeats duplexes: a model for slipped DNA. Biochemistry 37, 9426-9434.
23. Mizukoshi, T., Tanaka, T., Arai, K., Kohda, D. & Masai, H. (2003) A critical role of the 3′ terminus of nascent DNA chains in recognition of stalled replication forks. J. Biol. Chem. 278, 42234-42239.
24. Cox, M.M., Goodman, M.F., Kreuzer, K.N., Sherratt, D.J., Sandler, S.J. & Marians, K.J. (2000) The importance of repairing stalled replication forks. Nature 484, 37-41.
25. SantaLucia, J. Jr (1998) A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Natl Acad. Sci. USA 95, 1460-1465.
26. Kunkel, T.A. (1995) Oligonucleotide-directed mutagenesis without phenotype selection. In Short Protocol in Molecular Biology (Ausubel, F.M., Brent, R., Kingston, R.E., Moore, D.D., Seidman, J.G., Smith, J.A. & Struhl, K., eds) 3rd edn. pp. 8.2-8.5, John Wiley & Sons Inc., New York, NY.
27. Li, D., Huang, H., Li, X. & Li, X. (2003) Hairpin formation in DNA computation presents limits for large NP-complete problems. Biosystems 72, 203-207.
28. Vallone, P.M., Paner, T.M., Hilario, J., Lane, M.J., Faldasz, B.D. & Benight, A.S. (1999) Melting studies of short DNA hairpins: influence of loop sequence and adjoining base pair identity on hairpin thermodynamic stability. Biopolymers 50, 425-442.
29. Moody, E.M. & Bevilacqua, P.C. (2003) Thermodynamic coupling of the loop and stem in unusually stable DNA hairpins closed by CG base pairs. J. Am. Chem. Soc. 125, 2032-2033.
30. Davis, T.M., McFail-Isom, L., Keane, E. & Williams, L.D. (1998) Melting of a DNA hairpin without hyperchromism. Biochemistry 37, 6975-6978.
31. Larsen, O.F., van Stokkum, I.H., Gobets, B., van Grondelle, R. & van Amerongen, H. (2001) Probing the structure and dynamics of a DNA hairpin by ultrafast quenching and fluorescence depolarization. Biophys. J. 81, 1115-1126.
32. Kushon, S.A., Jordan, J.P., Seifert, J.L., Nielsen, H., Nielsen, P.E. & Armitage, B.A. (2001) Effect of secondary structure on the thermodynamics and kinetics of PNA hybridization to DNA hairpins. J. Am. Chem. Soc. 123, 10805-10813.
33. Smirnov, I. & Shafer, R.H. (2000) Effect of loop sequence and size on DNA aptamer stability. Biochemistry 39, 1462-1468.
34. Tung, C.S. (1997) A computational approach to modeling nucleic acid hairpin structures. Biophys. J. 72, 876-885.
35. Rentzeperis, D., Alessi, K. & Marky, L.A. (1993) Thermodynamics of DNA hairpins: contribution of loop size to hairpin stability and ethidium binding. Nucleic Acids Res. 21, 2683-2689.
36. Yuckenberg, P.D., Witney, F., Geisselsoder, J. & McMclary, J. (1999) Site-directed in vitro mutagenesis using uracil-containing DNA and phagemid vectors. In Site-Directed Mutagenesis - a Laboratory Manual (McPherson, M.J., ed.), pp. 27-47. Oxford University Press, Oxford.
37. Chen, H.-J., Pan, X., Zhang, G., Zhang, Y., Liu, N. & Yang, K. (2001) Site-directed mutagenesis at disulfide bond Cys206-Cys210 of prochymosin (chymosin). Chin. J. Biotechnol. 17, 7-10.
38. Pan, X. (2004) Two-triplet CGA Repeats Impede DNA Replication in bacteriophage M13 in Escherichia coli. Microbiol. Res. 159, 97-102.
39. Zuker, M. (2003) Mfold web server for nucleic acids folding and hybridization prediction. Nucleic Acids Res. 31, 3406-3415.