PMID: 8948641Nov 15, 1996Paper

Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes

Nucleic Acids Research
N SugimotoK Honda

Abstract

To improve the previous DNA/DNA nearest-neighbor parameters, thermodynamic parameters (deltaH degrees, deltaS degrees and deltaG degrees) of 50 DNA/DNA duplexes were measured. Enthalpy change of a helix initiation factor is also considered though the parameters reported recently did not contain the factor. A helix initiation factor for DNA/DNA duplex determined here was the same as that of RNA/RNA duplex (deltaG degrees(37) = 3.4 kcal/mol). The improved nearest-neighbor parameters reproduced not only these 50 experimental values used here but also 15 other experimental values obtained in different studies. Comparing deltaG degrees(37) values of DNA/DNA nearest-neighbor parameters obtained here with those of RNA/RNA and RNA/DNA, RNA/RNA duplex was generally the most stable of the three kinds of duplexes with the same nearest-neighbor sequences. Which is more stable between DNA/DNA and RNA/DNA duplexes is sequence dependent.

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Citations

Jan 1, 1997·Biopolymers·J SantaLucia, D H Turner
Jun 19, 2010·Analytical and Bioanalytical Chemistry·Sulayman A Oladepo, Glen R Loppnow
Sep 8, 2011·Analytical and Bioanalytical Chemistry·David BroylesSapna Deo
Feb 3, 2012·Analytical and Bioanalytical Chemistry·Carlos Briones, Miguel Moreno
Mar 14, 2007·Applied Microbiology and Biotechnology·Shoko IwaiHiroaki Furumai
Jan 27, 2012·Molecular Genetics and Genomics : MGG·Felix BormannChristine Sers
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Dec 18, 2001·Journal of Virological Methods·Chul Hyun JooYoo Kyum Kim
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Jun 20, 2002·European Journal of Biochemistry·Peng WuNaoki Sugimoto
Oct 18, 2008·The Journal of Biological Chemistry·Carrie M StithPeter M Burgers
Aug 20, 2004·Journal of Biomolecular Structure & Dynamics·Dierdre MurphyGareth Redmond
Dec 15, 2010·Journal of Biomolecular Structure & Dynamics·Yusen Zhang, Wei Chen
Mar 18, 2004·Oligonucleotides·Jean-Louis Mergny, Laurent Lacroix
Oct 27, 2004·Bioinformatics·Alejandro Panjkovich, Francisco Melo
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May 21, 1998·Nucleic Acids Research·H T Allawi, J SantaLucia
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Feb 13, 2003·Nucleic Acids Research·Wenonah A VercoutereMark Akeson
Jun 26, 2003·Nucleic Acids Research·S H ChenC A Hsiung
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Jun 28, 2005·Nucleic Acids Research·Alejandro PanjkovichFrancisco Melo
Jun 28, 2005·Nucleic Acids Research·Jakob FredslundJens Stougaard
Jul 29, 2005·Nucleic Acids Research·Kobe FlorquinYves Van de Peer
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Mar 11, 2006·Nucleic Acids Research·Miguel A Ramírez-RomeroGuillermo Dávila
Apr 25, 2007·Nucleic Acids Research·Warren A Kibbe

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