Sequencing in the presence of Betaine: Improvement in sequencing of the localized repeat sequence regions

Journal of Biomolecular Techniques

Volumn 13, Issue 4, 2002, Pages 265-271

  Haqqi, T ^a   Zhao, X ^a   Panciu, A ^a   Yadav, S P ^a  

^a LERNER RESEARCH INSTITUTE   (United States)

Author keywords

Betaine; DNA secondary structure; DNA sequencing; Optimization of DNA sequencing; PCR; Repetitive elements

Indexed keywords

EID: 0242611363     PISSN: 15240215     EISSN: 19434731     Source Type: Journal    
DOI: None     Document Type: Article

References (22)

1. Mytelka DS, Chamberlin MJ. Analysis and suppression of DNA polymerase pauses associated with a trinucleotide consensus. Nucleic Acids Res 1996;24:2774-2781.
2. Fuller CW. Modified T7 DNA polymerase for DNA sequencing. Methods Enzymol 1992;216:329-354.
3. Hirao I, Nishimura Y, Tagawa YI, Watanabe K, Miura KI. Extraordinarily stable mini-hairpins: electrophoretical and thermal properties of the various sequence variants of g(GCGAAAGC) and their effect on DNA sequencing. Nucleic Acids Res 1992;20:3891-3896.
4. Barr PJ, Thayer RM, Laybourn P, Najarian RC, Seela F, Tolan DR. 7-Deaza-2'-deoxyguanosine-5'-triphosphate: enhanced resolution of M13 dideoxy sequencing. Bio-Techniques 1986;4:428-432.
5. Mizusawa S, Nishimura S, Seela F. Improvement of the dideoxy chain termination method of DNA sequencing by use of deoxy-7-deaza-guanosine triphosphate in place of dGTP. Nucleic Acids Res 1986;14:1319-1324.
6. Adams PS, Dolejsi MK, Grills G, et al. An analysis of techniques used to improve the accuracy of automated DNA sequencing of a GC-rich template: results from the 2nd ABRF DNA Sequence Research Group Study. 1999. Available online at http://www.abrg.org/index.cfm/group.show/DNASequencing.28.htm.
7. Sarkar G, Kapelner S, Sommer SS. Formamide can dramatically improve the specificity of PCR. Nucleic Acids Res 1990;18:7465.
8. Motz M, Paabo S, Kilger C. Improved cycle sequencing of GC-rich templates by a combination of nucleotide analogs. BioTechniques 2000;29:268-270.
9. Rees WA, Yager TD, Korte J, von Hippel PH. Betaine can eliminate the base pair composition dependence of DNA melting. Biochemistry 1993;32:137-144.
10. Henke W, Herdel K, Jung K, Schnorr D, Loening SA. Betaine improves the PCR amplification of GC-rich DNA sequences. Nucleic Acids Res 1997;25:3957-3958.
11. Shammas FV, Heikkila R, Osland A. Improvement of quantitative PCR reproducibility by betaine as determined by fluorescence-based method. BioTechniques 2001;30:950-954.
12. Zhao X, Haqqi T, Yadav SP. Sequencing telomeric DNA template with short tandem repeats using dye terminator cycle sequencing. J Biomol Tech 2000;11:111-121.
13. Chakrabarti R, Scutt CE. The enhancement of PCR amplification by low molecular-weight sulfones. Gene 2001;274:293-298.
14. Lilley K. Sequencing GC rich regions and hairpins. 1999. Available online at http://www.le.ac.uk/cmht/pnacl/frames/fdnaseq/GC.html.
15. Usdin K, Woodford J. CGG repeats associated with DNA instability and chromosome fragility from structures that block DNA synthesis in vitro. Nucleic Acids Res 1995;23:4202-4209.
16. +-free buffers eliminates a common cause of premature chain termination in PCR and PCR sequencing. Nucleic Acids Res 1995;23:539.
17. Thakar M, Bilenko A, Becktel WJ. Osmolyte mediation of T7 DNA polymerase and plasmid DNA stability. Biochemistry 1994;33:12255-12259.
18. Kornberg A, Baker T. DNA Replication, 2nd ed. New York: WH Freeman, 1992.
19. Krasilnikov AS, Panyutin GM, Samadashwily GM, Cox R, Lazurkin YS, Mirkin SM. Mechanisms of triplex caused polymerization arrest. Nucleic Acids Res 1997;25:1339-1346.
20. Weissensteiner T, Lanchbury JS. Strategy for controlling preferential amplification and avoiding false negatives in PCR typing. BioTechniques 1996;21:1102-1108.
21. Schroth GP, Ho PS. Occurrence of potential cruciform and H-DNA forming sequences in genomic DNA. Nucleic Acids Res 1995;23:1977-1983.
22. Brinton BT, Caddle MS, Heintz NH. Position and orientation- dependent effects of a eukaryotic Z-triplex DNA motif on episomal DNA replication in cos-7 cells. J Biol Chem 1991;266:5153-5161.