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Sequencing of Difficult DNA Regions by SAM Sequencing

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PCR Protocols

Part of the book series: Methods in Molecular Biology ((MIMB,volume 687))

Abstract

Nucleotide analogues are used increasingly in medicine and biotechnology to effect DNA sequence change, principally via clastogenic and transcriptional effects. This article, however, discusses the use of mutagenic nucleotide analogues to improve the sequencing of recalcitrant and repetitive DNA motifs. Guidance in the technical and practical approaches that support use of this approach with different DNA sequencing technologies is provided, including for high-throughput technologies.

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References

  1. Voelkerding, K.V, Dames, S.A., and Durtschi, J.D. (2009) Next-generation sequencing: from basic research to diagnostics. Clin. Chem. 55, 641–58.

    Article  PubMed  CAS  Google Scholar 

  2. Mitchelson, K.R., Hawkes, D.B., Turakulov, R., and Men, A.E. (2007) Overview: developments in DNA sequencing. In: New High Throughput Technologies for DNA Sequencing and Genomics. Series: Perspectives in Bioanalysis (Ed., Mitchelson, K.R.), vol. 2, Elsevier, Amsterdam, pp. 3–44.

    Chapter  Google Scholar 

  3. Keith, J.M., Adams, P., Bryant, D., Mitchelson, K.R., Cochran, D.A.E., and Lala, G.H. (2003) Inferring an original sequence from erroneous copies: a Bayesian approach. In: Proceedings of the 1st Asia-Pacific Bioinformatics Conference (APBC2003) (Ed., Chen, Y.P.), vol. 19, Australian Computer Society, Adelaide, pp. 23–28.

    Google Scholar 

  4. Keith, J.M., Adams, P., Bryant, D., Mitchelson, K.R. Cochran, D.A.E., and Lala, G.H. (2003) Inferring an original sequence from erroneous copies: two approaches. Asia Pacific Biotech News 7, 107–14.

    Article  Google Scholar 

  5. Keith, J.M., Adams, P., Bryant, D., Cochran, D.A.E., Lala, G.H., and Mitchelson, K.R. (2004) Algorithms for sequencing via mutagenesis. Bioinformatics 20, 2401–10.

    Article  PubMed  CAS  Google Scholar 

  6. Keith, J.M., Adams, P., Bryant, D., Kroese, D.P., Mitchelson, K.R., Cochran, D.A.E., and Lala, G.L. (2002) A simulated annealing algorithm for finding consensus sequence. Bioinformatics 18, 1494–9.

    Article  PubMed  CAS  Google Scholar 

  7. Keith, J.M., Cochran, D.A.E., Lala, G.H., Adams, P., Bryant, D., and Mitchelson, K.R. (2004) Unlocking hidden genomic sequence. Nucleic Acids Res. 32, e35.

    Article  PubMed  Google Scholar 

  8. Cochran, D., Lala, G., Keith, J., Adams, P., Bryant, D., and Mitchelson, K. (2006) Sequencing by aligning mutated DNA fragments. In: The Frontiers of Biochip Technologies (Eds., Xing, W.L. and Cheng, J.), Springer, New York, pp. 231–45.

    Chapter  Google Scholar 

  9. Zaccolo, M., Williams, D.M., Brown, D.M., and Gherardi, E. (1996) An approach to random mutagenesis of DNA using mixtures of triphosphate derivatives of nucleoside analogues. J. Mol. Biol. 255, 589–603.

    Article  PubMed  CAS  Google Scholar 

  10. Yu, H., Eritja, R., Bloom, L.B., and Goodman, M.F. (1993) Ionization of bromouracil and fluorouracil stimulates base mispairing frequencies with guanine. J. Biol. Chem. 268, 15, 935–43.

    Google Scholar 

  11. Hill, F., Williams, D.M., Loakes, D., and Brown, D.M. (1998) Comparative mutagenicities of N6-methoxy-2,6-diaminopurine (dK) and N6-methoxyaminopurine 2′-deoxyribonucleosides (dZ) and their 5′-triphosphates. Nucleic Acids Res. 26, 1144–9.

    Article  PubMed  CAS  Google Scholar 

  12. Kamiya, H., Maki, H., and Kasai, H. (2000) Two DNA polymerases of Escherichia coli display distinct misinsertion specificities for 2-hydroxy-dATP during DNA synthesis. Biochemistry 39, 9508–13.

    Article  PubMed  CAS  Google Scholar 

  13. Suen, W., Spiro, T.G., Sowers, L.C., and Fresco, J.R. (1999) Identification by UV resonance Raman spectroscopy of an imino tautomer of 5-hydroxy-2′-deoxycytidine, a powerful base analog transition mutagen with a much higher unfavored tautomer frequency than that of the natural residue 2′-deoxycytidine. Proc. Natl. Acad. Sci. USA 96, 4500–5.

    Article  PubMed  CAS  Google Scholar 

  14. Ma, X., Ke, T., Mao, P., Jin, X., Ma, L., and He, G. (2008) The mutagenic properties of BrdUTP in a random mutagenesis process. Mol. Biol. Rep. 35, 663–7.

    Article  PubMed  CAS  Google Scholar 

  15. Keith, J.M., Hawkes, D.B., Carter, J.A., Cochran, D.A.E, Adams, P., Bryant, D.E., and Mitchelson, K.R. (2007) Sequencing aided by mutagenesis facilitates de novo sequencing of megabase DNA fragments by short length reads. In: New High Throughput Technologies for DNA Sequencing and Genomics. Series: Perspectives in Bioanalysis (Ed., Mitchelson, K.R.), vol. 2, Elsevier, Amsterdam, pp. 303–26.

    Chapter  Google Scholar 

  16. Dean, F.B., Nelson, J.R., Giesler, T.L., and Lasken, R.S. (2001) Rapid amplification of plasmid and phage DNA using Phi 29 DNA polymerase and multiply-primed rolling circle amplification. Genome Res. 11, 1095–9.

    Article  PubMed  CAS  Google Scholar 

  17. Nelson, J.R., Cai, Y.C., Giesler, T.L., Farchaus, J.W., Sundaram, S.T., Ortiz-Rivera, M., Hosta, L.P., Hewitt, P.L., Mamone, J.A., Palaniappan, C., and Fuller, C.W. (2002) TempliPhi, φ29 DNA polymerase based rolling circle amplification of templates for DNA sequencing. Biotechniques 32, S44–7.

    Google Scholar 

  18. Dean, F.B., Hosono, S., Fang, L., Wu, X., Faruqi, A.F., Bray-Ward, P., Sun, Z., Zong, Q., Du, Y., Du, J., Driscoll, M., Song, W., Kingsmore, S.F., Egholm, M., and Lasken, R.S. (2002) Comprehensive human genome amplification using multiple displacement amplification. Proc. Natl. Acad. Sci. USA 99, 5261–6.

    Article  PubMed  CAS  Google Scholar 

  19. Harismendy, O., Ng, P.C., Strausberg, R.L., Wang, X., Stockwell, T.B., Beeson, K.Y., Schork, N.J., Murray, S.S., Topol, E.J., Levy, S., and Frazer, K.A. (2009) Evaluation of next generation sequencing platforms for population targeted sequencing studies. Genome Biol. 10, R32.

    Article  PubMed  Google Scholar 

  20. Dohm, J.C., Lottaz, C., Borodina, T., and Himmelbauer, H. (2008) Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res. 36, e105.

    Article  PubMed  Google Scholar 

  21. Wicker, T., Schlagenhauf, E., Graner, A., Close, T.J., Keller, B., and Stein, N. (2006) 454 sequencing put to the test using the complex genome of barley. BMC Genomics 7, 275.

    Article  PubMed  Google Scholar 

  22. Schuerman, G.S., Van Meervelt, L., Loakes, D., Brown, D.M., Kong Thoo Lin, P., Moore, M.H., and Salisbury, S.A. (1998) A thymine-like base analogue forms wobble pairs with adenine in a Z-DNA duplex. J. Mol. Biol. 282, 1005–11.

    Article  PubMed  CAS  Google Scholar 

  23. Inoue, M., Kamiya, H., Fujikawa, K., Ootsuyama, Y., Murata-Kamiya, N., Osaki, T., Yasumoto, K., and Kasai, H. (1998) Induction of chromosomal gene mutations in Escherichia coli by direct incorporation of oxidatively damaged nucleotides. J. Biol. Chem. 273, 11069–74.

    Article  PubMed  CAS  Google Scholar 

  24. Negishi, K., Loakes, D., and Schaaper, R.M. (2002) Saturation of DNA mismatch repair and error catastrophe by a base analogue in Escherichia coli. Genetics 161, 1363–71.

    PubMed  CAS  Google Scholar 

  25. Nampalli, S. and Kumar, S. (2000) Efficient synthesis of 8-oxo-dGTP: a mutagenic nucleotide. Bioorg. Med. Chem. Lett. 10, 1677–9.

    Article  PubMed  CAS  Google Scholar 

  26. Hill, F., Loakes, D., and Brown, D.M. (1998) Polymerase recognition of synthetic oligodeoxyribonucleotides incorporating degenerate pyrimidine and purine bases. Proc. Natl. Acad. Sci. USA 95, 4258–63.

    Article  PubMed  CAS  Google Scholar 

  27. Driggers, P.H. and Beattie, K.L. (1988) Effect of pH on the base-mispairing properties of 5-bromouracil during DNA synthesis. Biochemistry 27, 1729–35.

    Article  PubMed  CAS  Google Scholar 

  28. Sowers, L.C., Fazakerley, G.V., Eritja, R., Kaplan, B.E., and Goodman, M.F. (1986) Base pairing and mutagenesis: observation of a protonated base pair between 2-aminopurine and cytosine in an oligonucleotide by proton NMR. Proc. Natl. Acad. Sci. USA 83, 5434–8.

    Article  PubMed  CAS  Google Scholar 

  29. Privat, E.J. and Sowers, L.C. (1996) A proposed mechanism for the mutagenicity of 5-formyluracil. Mutat. Res. 354, 151–6.

    Article  PubMed  Google Scholar 

  30. Hossain, M.T., Sunami, T., Tsunoda, M., Hikima, T., Chatake, T., Ueno, Y., Matsuda, A., and Takénaka, A. (2001) Crystallographic studies on damaged DNAs IV. N(4)-methoxycytosine shows a second face for Watson-Crick base-pairing, leading to purine transition mutagenesis. Nucleic Acids Res. 29, 3949–54.

    PubMed  CAS  Google Scholar 

  31. Janion, C. (1978) The efficiency and extent of mutagenic activity of some new mutagens of base-analogue type. Mutat. Res. 56, 225–34.

    Article  PubMed  CAS  Google Scholar 

  32. Purmal, A.A., Kow, Y.W., and Wallace, S.S. (1994) 5-Hydroxypyrimidine deoxynucleoside triphosphates are more efficiently incorporated into DNA by exonuclease-free Klenow fragment than 8-oxopurine deoxynucleoside triphosphates. Nucleic Acids Res. 22, 3930–5.

    Article  PubMed  CAS  Google Scholar 

  33. Purmal, A.A., Kow, Y.W., and Wallace, S.S. (1994) Major oxidative products of cytosine, 5-hydroxycytosine and 5-hydroxyuracil, exhibit sequence dependent mispairing in vivo. Nucleic Acids Res. 22, 72–8.

    Article  PubMed  CAS  Google Scholar 

  34. Loeb, L.A., Essigmann, J.M., Kazazi, F., Zhang, J., Rose, K.D., and Mullins, J.I. (1999) Lethal mutagenesis of HIV with mutagenic nucleoside analogs. Proc. Natl. Acad. Sci. USA 96, 1492–7.

    Article  PubMed  CAS  Google Scholar 

  35. Taniguchi, Y. and Kool, E.T. (2007) Nonpolar isosteres of damaged DNA bases: effective mimicry of mutagenic properties of 8-oxopurines. J. Am. Chem. Soc. 129, 8836–44.

    Article  PubMed  CAS  Google Scholar 

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Author information

Authors and Affiliations

  1. Medical Systems Biology Research Center, Tsinghua University, Beijing, China

    Keith R. Mitchelson

  2. CapitalBio Corporation: National Engineering Research Center for Beijing Biochip Technology, Beijing, China

    Keith R. Mitchelson

Authors
  1. Keith R. Mitchelson
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Editor information

Editors and Affiliations

  1. , Department of Pathology, The University of Melbourne, Corner of Grattan St & Royal Parade, Parkville, 3010, Victoria, Australia

    Daniel J. Park

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© 2011 Humana Press

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Mitchelson, K.R. (2011). Sequencing of Difficult DNA Regions by SAM Sequencing. In: Park, D. (eds) PCR Protocols. Methods in Molecular Biology, vol 687. Humana Press. https://doi.org/10.1007/978-1-60761-944-4_6

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  • DOI: https://doi.org/10.1007/978-1-60761-944-4_6

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  • Publisher Name: Humana Press

  • Print ISBN: 978-1-60761-943-7

  • Online ISBN: 978-1-60761-944-4

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