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.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Voelkerding, K.V, Dames, S.A., and Durtschi, J.D. (2009) Next-generation sequencing: from basic research to diagnostics. Clin. Chem. 55, 641–58.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Nampalli, S. and Kumar, S. (2000) Efficient synthesis of 8-oxo-dGTP: a mutagenic nucleotide. Bioorg. Med. Chem. Lett. 10, 1677–9.
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.
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.
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.
Privat, E.J. and Sowers, L.C. (1996) A proposed mechanism for the mutagenicity of 5-formyluracil. Mutat. Res. 354, 151–6.
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.
Janion, C. (1978) The efficiency and extent of mutagenic activity of some new mutagens of base-analogue type. Mutat. Res. 56, 225–34.
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.
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.
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.
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.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2011 Humana Press
About this protocol
Cite this protocol
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
Download citation
DOI: https://doi.org/10.1007/978-1-60761-944-4_6
Published:
Publisher Name: Humana Press
Print ISBN: 978-1-60761-943-7
Online ISBN: 978-1-60761-944-4
eBook Packages: Springer Protocols