Startseite Spontaneous DNA-DNA interaction of homologous duplexes and factors affecting the result of heteroduplex formation
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Spontaneous DNA-DNA interaction of homologous duplexes and factors affecting the result of heteroduplex formation

  • Anna A. Neschastnova , Victoria K. Gasanova , Vladimir I. Popenko , Andreana Lambrinakos , Gennady A. Belitsky , Richard G.H. Cotton und Marianna G. Yakubovskaya
Veröffentlicht/Copyright: 17. März 2006
Biological Chemistry
Aus der Zeitschrift Band 387 Heft 3

Abstract

Mutation detection and mismatch repair investigations based on heteroduplex formation require a linear DNA structure. DNA branching, described previously under physiological conditions, has been analysed in the heteroduplex formation process. Symmetrical χ-structures were detected after heteroduplex formation by gel electrophoresis and electron microscopy. Buffer composition, DNA concentration and duplex end-sequences influence DNA branching. Duplexes with homologous central regions but non-complementary ends do not form hybrid heteroduplexes or hybrid Holliday junctions. Our results explain the requirements for efficient heteroduplex formation, which were previously determined empirically: special solution composition, optimal DNA concentration and GC clamps. This provides the theoretical background for further optimisation of the procedure.

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References

Agirre, X., Garcia-Delgado, M., Calasanz, M.J., Larrayoz, M.J., Novo, F.J., and Vizmanos, J.L. (2002). Exon concatenation to increase the efficiency of mutation screening by DGGE. Biotechniques32, 1068–1070.10.2144/02325rr01Suche in Google Scholar

Babon, J.J., McKenzie, M., and Cotton, R.G. (1999). Mutation detection using fluorescent enzyme mismatch cleavage with T4 endonuclease VII. Electrophoresis20, 1162–1170.10.1002/(SICI)1522-2683(19990101)20:6<1162::AID-ELPS1162>3.0.CO;2-YSuche in Google Scholar

Belotserkovskii, B.P. and Johnston, B.H. (1996). Polypropylene tube surfaces may induce denaturation and multimerization of DNA. Science271, 222–223.10.1126/science.271.5246.222Suche in Google Scholar

Cotton, R.G.H. (1997). Mutation detection (Oxford, UK: Oxford University Press).Suche in Google Scholar

Cotton, R.G.H. and Campbell, R.D. (1989). Chemical reactivity of matched cytosine and thymine bases near mismatched and unmatched bases in a heteroduplex between DNA strands with multiple differences. Nucleic Acids Res.17, 4223–4233.10.1093/nar/17.11.4223Suche in Google Scholar

Davis, R.W. and Hyman, R.W. (1971). A study in evolution: the DNA base sequence homology between coliphages T7 and T3. J. Mol. Biol.62, 287–301.10.1016/0022-2836(71)90428-1Suche in Google Scholar

Doktycz, M.J., Morris, M.D., Dormady, S.J., Beattie, K.L., and Jacobson, K.B. (1995). Optical melting of 128 octamer DNA duplexes. Effect of base pair location and nearest neighbors on thermal stability. J. Biol. Chem.270, 8439–8445.10.1074/jbc.270.15.8439Suche in Google Scholar

Drake, J.W. (1966). Heteroduplex heterozygotes in bacteriophage T4 involving mutations of various dimensions. Proc. Natl. Acad. Sci. USA55, 506–512.10.1073/pnas.55.3.506Suche in Google Scholar

Duguid, J.G. and Bloomfield, V.A. (1995). Aggregation of melted DNA by divalent metal ion-mediated cross-linking. Biophys. J.69, 2642–2648.10.1016/S0006-3495(95)80134-7Suche in Google Scholar

Escary, J.L., Cecillon, M., Maciazek, J., Lathrop, M., Tournier-Lasserve, E., and Joutel, A. (2000). Evaluation of DHPLC analysis in mutational scanning of Notch3, a gene with a high G-C content. Hum. Mutat.16, 518–526.10.1002/1098-1004(200012)16:6<518::AID-HUMU9>3.0.CO;2-QSuche in Google Scholar

Gaillard, C. and Strauss, F. (1994). Association of poly-(CA)poly(TG) DNA fragments into four-stranded complexes bound by HMG1 and 2. Science264, 433–436.10.1126/science.8153633Suche in Google Scholar

Gaillard, C., Flavin, M., Woisard, A. and Strauss, F. (1999). Association of double-stranded DNA fragments into multistranded DNA structures. Biopolymers50, 679–689.10.1002/(SICI)1097-0282(199912)50:7<679::AID-BIP1>3.0.CO;2-3Suche in Google Scholar

Hatcher, S.L.S., Lambert, Q.T., Teplitz, R.L., and Carlson, J.R. (1993). Heteroduplex formation: a potential source of genotyping error from PCR products. Prenatal Diagn.13, 171–177.10.1002/pd.1970130304Suche in Google Scholar

Jakovcic, S., Casey, J., and Rabinowitz, M. (1975). Sequence homology between mitochondrial DNAs of different eukaryotes. Biochemistry14, 2043–2050.10.1021/bi00681a002Suche in Google Scholar

Lu, M., Guo, Q., Marky, L.A., Seeman, N.C., and Kallenbach, N.R. (1992). Thermodynamics of DNA branching. J. Mol. Biol.223, 781–789.10.1016/0022-2836(92)90989-WSuche in Google Scholar

Mandel'shtam, M.I., Golubkov, V.I., Lamber, E.P., Shapiro, I.M., Brezhneva, T.V., Semiglazov, V.F., Lipovetskii, B.M., Hanson, K.P., and Gaitskhoki, V.S. (2001). Search for frequently encountered mutations in genes predisposing to breast cancer. Genetika37, 1681–1686.Suche in Google Scholar

Markina, V.K., Danilova, O.A., Neschastnova, A.A., Belitsky, G.A., and Yakubovskaya, M.G. (2002). The role of duplex ends in the spontaneous interaction of homologous linear DNA fragments. Mol. Biol. (Moscow)36, 862–867.Suche in Google Scholar

McDonnel, M.W., Simon, M.N., and Studier, F.W. (1976). Analysis of restriction fragments of T7 DNA and determination of molecular weights by electrophoresis in neutral and alkaline gels. J. Mol. Biol.110, 119–146.Suche in Google Scholar

Neschastnova, A.A., Markina, V.K., Popenko, V.I., Danilova, O.A., Sidorov, R.A., Belitsky, G.A., and Yakubovskaya, M.G. (2002). Mechanism of spontaneous DNA-DNA interaction of homologous linear duplexes. Biochemistry41, 7795–7801.10.1021/bi015959tSuche in Google Scholar

Panyutin, I.G. and Hsieh, P. (1994). The kinetics of spontaneous DNA branch migration. Proc. Natl. Acad. Sci. USA91, 2021–2025.10.1073/pnas.91.6.2021Suche in Google Scholar

Rebischung, C., Gerard, J.P., Gayet, J., Thomas, G., Hamelin, R., and Laurent-Puig, P. (2002). Prognostic value of P53 mutations in rectal carcinoma. Int. J. Cancer100, 131–135.10.1002/ijc.10480Suche in Google Scholar

Rickert, A.M., Ballvora, A., Matzner, U., Klemm, M., and Gebhardt, C. (2005). Quantitative genotyping of single-nucleotide polymorphisms by allele-specific oligonucleotide hybridization on DNA microarrays. Biotechnol. Appl. Biochem.42, 93–96.Suche in Google Scholar

Roberts, E., Deeble, V.J., Woods, C.G., and Taylor, G.R. (1997). Potassium permanganate and tetraethylammonium chloride are a safe and effective substitute for osmium tetroxide in solid-phase fluorescent chemical cleavage of mismatch. Nucleic Acids Res.25, 3377–3380.10.1093/nar/25.16.3377Suche in Google Scholar

Roger, M. (1972). Evidence for conversion of heteroduplex transforming DNAs to homoduplexes by recipient pneumococcal cells (DNA strand resolution-DNA repair-bacterial transformation-genetic recombination). Proc. Natl. Acad. Sci. USA69, 466–470.10.1073/pnas.69.2.466Suche in Google Scholar

Saenger, W. (1984). Principles of Nucleic Acid Structure (New York, USA: Springer).10.1007/978-1-4612-5190-3Suche in Google Scholar

Tessitore, A., Di Rocco, Z.C., Cannita, K., Ricevuto, E., Toniato, E., Tosi, M., Ficorella, C., Frati, L., Gulino, A., Marchetti, P., and Martinotti, S. (2002). High sensitivity of detection of TP53 somatic mutations by fluorescence-assisted mismatch analysis. Genes Chromosomes Cancer35, 86–91.10.1002/gcc.10102Suche in Google Scholar

Tian, H. and Landers, J.P. (2002). Hydroxyethylcellulose as an effective polymer network for DNA analysis in uncoated glass microchips: optimization and application to mutation detection via heteroduplex analysis. Anal. Biochem.309, 212–223.10.1016/S0003-2697(02)00297-XSuche in Google Scholar

van Den Bosch, B.J., de Coo, R.F., Scholte, H.R., Nijland, J.G., van Den Bogaard, R., de Visser, M., de Die-Smulders, C.E., and Smeets, H.J. (2000). Mutation analysis of the entire mitochondrial genome using denaturing high performance liquid chromatography. Nucleic Acids Res.28, E89.10.1093/nar/28.20.e89Suche in Google Scholar PubMed PubMed Central

Wagner, T., Stoppa-Lyonnet, D., Fleischmann, E., Muhr, D., Sandberg, T., Caux, V., Moeslinger, R., Langbauer, G., Borg, A., and Oefner, P. (1999). Denaturing high-performance liquid chromatography detects reliably BRCA1 and BRCA2 mutations. Genomics62, 369–376.10.1006/geno.1999.6026Suche in Google Scholar PubMed

Wallace, A.J. (2002). SSCP/heteroduplex analysis. Methods Mol. Biol.187, 151–163.10.1385/1-59259-273-2:151Suche in Google Scholar

Yakubovskaya, M.G., Neschastnova, A.A., Popenko, V.I., Lipatova, Z.V., and Belitsky, G.A. (1999). Holliday junctions are formed in concentrated solutions of purified products of DNA amplification. Biochemistry (Moscow)64, 1310–1314.Suche in Google Scholar

Yakubovskaya, M.G., Neschastnova, A.A., Humphrey, K.E., Babon, J.J., Popenko, V.I., Smith, M.J., Lambrinakos, A., Lipatova, Z.V., Dobrovolskaia, M.A., Cappai, R., et al. (2001). Interaction of linear homologous DNA duplexes via Holliday junction formation. Eur. J. Biochem.268, 7–14.10.1046/j.1432-1327.2001.01861.xSuche in Google Scholar PubMed

Published Online: 2006-03-17
Published in Print: 2006-03-01

©2006 by Walter de Gruyter Berlin New York

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