Fundamentals of sequencing of difficult templates--an overview.
作者： Jan Kieleczawa
DOI:
关键词: Genetics 、 DNA metabolism 、 Base sequence 、 Sequence analysis 、 Computational biology 、 Biology 、 Sequence (medicine) 、 DNA sequencing 、 Dna genetics 、 Genome 、 Template
摘要: Despite enormous progress, the DNA sequencing of difficult regions, whether they are part complex genomes or individual constructs, still presents a significant challenge and may require many trials, brute-force, intervention very experienced sequencer (and sometimes all above). Very early on, it was realized that various types templates requires distinct treatments. To sequence through GC-rich addition DMSO, NP-40/Tween-20 detergents, mix (4:1) BD3.0:dGTP3.0 helpful. get long poly-A/T tails, one would be successful using tailored poly- A/T (V/B) N primers spanned pre-tail tail regions. A few years ago invitrogen introduced set additives proved to useful for different templates.
参考文章(23)
Dominic Esposito, William K. Gillette, James L. Hartley, Blocking oligonucleotides improve sequencing through inverted repeats. BioTechniques. ,vol. 35, pp. 914- 920 ,(2003) , 10.2144/03355BM02
Daniel C Ducat, Francisco J Herrera, Steven J Triezenberg, None, Overcoming obstacles in DNA sequencing of expression plasmids for short interfering RNAs. BioTechniques. ,vol. 34, pp. 1140- 1144 ,(2003) , 10.2144/03346BM04
Maria Sasvari-Szekely, Andras Guttman, Huba Kalasz, Arpad Gerstner, Sequencing difficult DNA templates using membrane-mediated loading with hot sample application. BioTechniques. ,vol. 28, pp. 628- 630 ,(2000)
John R. Nelson, Yuyang Christine Cai, Theresa L. Giesler, Joseph W. Farchaus, Shanmuuga T. Sundaram, Maria Ortiz-Rivera, Lou P. Hosta, Peter L. Hewitt, J. Anthony Mamone, C. Palaniappan, Carl W. Fuller, TempliPhi, ⌽29 DNA Polymerase Based Rolling Circle Amplification of Templates for DNA Sequencing BioTechniques. ,vol. 32, pp. 44- ,(2002) , 10.2144/JUN0208
S Tabor, C C Richardson, DNA sequence analysis with a modified bacteriophage T7 DNA polymerase. Effect of pyrophosphorolysis and metal ions. Journal of Biological Chemistry. ,vol. 265, pp. 8322- 8328 ,(1990) , 10.1016/S0021-9258(19)39075-1
Scott M. Hammond, Amy A. Caudy, Gregory J. Hannon, Post-transcriptional gene silencing by double-stranded RNA Nature Reviews Genetics. ,vol. 2, pp. 110- 119 ,(2001) , 10.1038/35052556
Haqqi T, Zhao X, Yadav Sp, Sequencing telomeric DNA template with short tandem repeats using dye terminator cycle sequencing. Journal of biomolecular techniques. ,vol. 11, pp. 111- 121 ,(2000)
Jan Kieleczawa, Simple modifications of the standard DNA sequencing protocol allow for sequencing through siRNA hairpins and other repeats. Journal of biomolecular techniques. ,vol. 16, pp. 220- 223 ,(2005)
J.E. Langan, L. Rowbottom, T. Liloglou, J.K. Field, J.M. Risk, Sequencing of difficult templates containing poly(A/T) tracts: closure of sequence gaps. BioTechniques. ,vol. 33, pp. 276- 280 ,(2002) , 10.2144/02332BM04
Frank B Dean, John R Nelson, Theresa L Giesler, Roger S Lasken, Rapid Amplification of Plasmid and Phage DNA Using Phi29 DNA Polymerase and Multiply-Primed Rolling Circle Amplification Genome Research. ,vol. 11, pp. 1095- 1099 ,(2001) , 10.1101/GR.180501