Abstract
The dissociation kinetics of 19 base paired oligonucleotide-DNA duplex containing a various single mismatched base pair are studied on dried agarose gels. The kinetics of the dissociation are first order under our experimental conditions. The incorporation of a single mismatched base pair destabilizes the DNA duplexes to some extent, the amount depending on the nature of the mismatched base pair. G-T and G-A mismatches slightly destabilize a duplex, while A-A, T-T, C-T and C-A mismatches significantly destabilize it. The activation energy for the overall dissociation processes for these oligonucleotide-DNA duplexes containing 19 base pairs is 52 +/- 2 Kcal mol-1 as determined from the slope of Arrhenius plot.
Full text
PDF














Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Aboul-ela F., Koh D., Tinoco I., Jr, Martin F. H. Base-base mismatches. Thermodynamics of double helix formation for dCA3XA3G + dCT3YT3G (X, Y = A,C,G,T). Nucleic Acids Res. 1985 Jul 11;13(13):4811–4824. doi: 10.1093/nar/13.13.4811. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Conner B. J., Reyes A. A., Morin C., Itakura K., Teplitz R. L., Wallace R. B. Detection of sickle cell beta S-globin allele by hybridization with synthetic oligonucleotides. Proc Natl Acad Sci U S A. 1983 Jan;80(1):278–282. doi: 10.1073/pnas.80.1.278. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Freier S. M., Albergo D. D., Turner D. H. Solvent effects on the dynamics of (dG-dC)3. Biopolymers. 1983 Apr;22(4):1107–1131. doi: 10.1002/bip.360220408. [DOI] [PubMed] [Google Scholar]
- Gillam S., Waterman K., Smith M. The base-pairing specificity of cellulose-pdT9. Nucleic Acids Res. 1975 May;2(5):625–634. doi: 10.1093/nar/2.5.625. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Gotoh O., Tagashira Y. Locations of frequently opening regions on natural DNAs and their relation to functional loci. Biopolymers. 1981 May;20(5):1043–1058. doi: 10.1002/bip.1981.360200514. [DOI] [PubMed] [Google Scholar]
- Kan L. S., Chandrasegaran S., Pulford S. M., Miller P. S. Detection of a guanine X adenine base pair in a decadeoxyribonucleotide by proton magnetic resonance spectroscopy. Proc Natl Acad Sci U S A. 1983 Jul;80(14):4263–4265. doi: 10.1073/pnas.80.14.4263. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kidd V. J., Wallace R. B., Itakura K., Woo S. L. alpha 1-antitrypsin deficiency detection by direct analysis of the mutation in the gene. Nature. 1983 Jul 21;304(5923):230–234. doi: 10.1038/304230a0. [DOI] [PubMed] [Google Scholar]
- Marky L. A., Breslauer K. J. Calorimetric determination of base-stacking enthalpies in double-helical DNA molecules. Biopolymers. 1982 Nov;21(11):2185–2194. doi: 10.1002/bip.360211107. [DOI] [PubMed] [Google Scholar]
- Patel D. J., Ikuta S., Kozlowski S., Itakura K. Sequence dependence of hydrogen exchange kinetics in DNA duplexes at the individual base pair level in solution. Proc Natl Acad Sci U S A. 1983 Apr;80(8):2184–2188. doi: 10.1073/pnas.80.8.2184. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Patel D. J., Kozlowski S. A., Ikuta S., Itakura K. Deoxyguanosine-deoxyadenosine pairing in the d(C-G-A-G-A-A-T-T-C-G-C-G) duplex: conformation and dynamics at and adjacent to the dG X dA mismatch site. Biochemistry. 1984 Jul 3;23(14):3207–3217. doi: 10.1021/bi00309a015. [DOI] [PubMed] [Google Scholar]
- Patel D. J., Kozlowski S. A., Marky L. A., Rice J. A., Broka C., Dallas J., Itakura K., Breslauer K. J. Structure, dynamics, and energetics of deoxyguanosine . thymidine wobble base pair formation in the self-complementary d(CGTGAATTCGCG) duplex in solution. Biochemistry. 1982 Feb 2;21(3):437–444. doi: 10.1021/bi00532a003. [DOI] [PubMed] [Google Scholar]
- Patel D. J., Kozlowski S. A., Marky L. A., Rice J. A., Broka C., Itakura K., Breslauer K. J. Extra adenosine stacks into the self-complementary d(CGCAGAATTCGCG) duplex in solution. Biochemistry. 1982 Feb 2;21(3):445–451. doi: 10.1021/bi00532a004. [DOI] [PubMed] [Google Scholar]
- Pirastu M., Kan Y. W., Cao A., Conner B. J., Teplitz R. L., Wallace R. B. Prenatal diagnosis of beta-thalassemia. Detection of a single nucleotide mutation in DNA. N Engl J Med. 1983 Aug 4;309(5):284–287. doi: 10.1056/NEJM198308043090506. [DOI] [PubMed] [Google Scholar]
- Schulze D. H., Pease L. R., Obata Y., Nathenson S. G., Reyes A. A., Ikuta S., Wallace R. B. Identification of the cloned gene for the murine transplantation antigen H-2Kb by hybridization with synthetic oligonucleotides. Mol Cell Biol. 1983 Apr;3(4):750–755. doi: 10.1128/mcb.3.4.750. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Southern E. M. Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol. 1975 Nov 5;98(3):503–517. doi: 10.1016/s0022-2836(75)80083-0. [DOI] [PubMed] [Google Scholar]
- Suggs S. V., Wallace R. B., Hirose T., Kawashima E. H., Itakura K. Use of synthetic oligonucleotides as hybridization probes: isolation of cloned cDNA sequences for human beta 2-microglobulin. Proc Natl Acad Sci U S A. 1981 Nov;78(11):6613–6617. doi: 10.1073/pnas.78.11.6613. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Ullrich A., Gray A., Berman C., Dull T. J. Human beta-nerve growth factor gene sequence highly homologous to that of mouse. Nature. 1983 Jun 30;303(5920):821–825. doi: 10.1038/303821a0. [DOI] [PubMed] [Google Scholar]
- Wallace R. B., Johnson M. J., Hirose T., Miyake T., Kawashima E. H., Itakura K. The use of synthetic oligonucleotides as hybridization probes. II. Hybridization of oligonucleotides of mixed sequence to rabbit beta-globin DNA. Nucleic Acids Res. 1981 Feb 25;9(4):879–894. doi: 10.1093/nar/9.4.879. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Wallace R. B., Schold M., Johnson M. J., Dembek P., Itakura K. Oligonucleotide directed mutagenesis of the human beta-globin gene: a general method for producing specific point mutations in cloned DNA. Nucleic Acids Res. 1981 Aug 11;9(15):3647–3656. doi: 10.1093/nar/9.15.3647. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Wallace R. B., Shaffer J., Murphy R. F., Bonner J., Hirose T., Itakura K. Hybridization of synthetic oligodeoxyribonucleotides to phi chi 174 DNA: the effect of single base pair mismatch. Nucleic Acids Res. 1979 Aug 10;6(11):3543–3557. doi: 10.1093/nar/6.11.3543. [DOI] [PMC free article] [PubMed] [Google Scholar]