PMID: 8604314Feb 15, 1996Paper

The thermal stability of DNA fragments with tandem mismatches at a d(CXYG).d(CY'X'G) site

Nucleic Acids Research
S H Ke, R M Wartell

Abstract

Temperature-Gradient Gel Electrophoresis (TGGE) was employed to determine the thermal stabilities of 28 DNA fragments, 373 bp long, with two adjacent mismatched base pairs, and eight DNAs with Watson-Crick base pairs at the same positions. Heteroduplex DNAs containing two adjacent mismatches were formed by melting and reannealing pairs of homologous 373 bp DNA fragments differing by two adjacent base pairs. Product DNAs were separated based on their thermal stability by parallel and perpendicular TGGE. The polyacrylamide gel contained 3.36 M urea and 19.2 % formamide to lower the DNA melting temperatures. The order of stability was determined in the sequence context d(CXYG).d(CY'X'G) where X.X' and Y.Y" represent the mismatched or Watson-Crick base pairs. The identity of the mismatched bases and their stacking interactions influence DNA stability. Mobility transition melting temperatures (T u) of the DNAs with adjacent mismatches were 1.0-3.6 degrees C (+/-0.2 degree C) lower than the homoduplex DNA with the d(CCAG).d(CTGG) sequence. Two adjacent G.A pairs, d(CGAG).d(CGAG), created a more stable DNA than DNAs with Watson-Crick A.T pairs at the same sites. The d(GA).d(GA) sequence is estimated to be 0.4 (+/-30%) kcal/mol more st...Continue Reading

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Citations

May 22, 2003·Journal of Molecular Biology·Ko-Hsin Chin, Shan-Ho Chou
May 21, 1998·Nucleic Acids Research·H T Allawi, J SantaLucia
May 9, 2003·Nucleic Acids Research·Shan-Ho ChouAndrew H-J Wang
May 5, 2007·Nucleic Acids Research·Anjana Sen, Peter E Nielsen
Sep 20, 2015·FEBS Letters·Pei Guo, Sik Lok Lam
Mar 31, 2007·IEEE Transactions on Nanobioscience·John A RoseAkira Suyama
Mar 19, 2014·Chemical Society Reviews·Anton GranzhanMarie-Paule Teulade-Fichou
Apr 18, 1997·Journal of Molecular Biology·S H ChouB R Reid

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