Improved nearest-neighbor parameters for predicting DNA duplex stability.

by: J SantaLucia, HT Allawi, PA Seneviratne

Biochemistry, Vol. 35, No. 11. (19 March 1996), pp. 3555-3562.

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DOI, American Chem. Soc. Publications, Pubmed, Hubmed

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Abstract

Thermodynamic data were determined from UV absorbance vs temperature profiles of 23 oligonucleotides. These data were combined with data from the literature for 21 sequences to derive improved parameters for the 10 Watson-Crick nearest neighbors. The observed trend in nearest-neighbor stabilities at 37 degrees C is GC > CG > GG > GA approximately GT approximately CA > CT > AA > AT > TA (where only the top strand is shown for each nearest neighbor). This trend suggests that both sequence and base composition are important determinants of DNA duplex stability. On average, the improved parameters predict deltaG degrees(37), deltaH degrees, deltaS degrees, and T(m) within 4%, 7%, 8%, and 2 degrees C, respectively. The parameters are optimized for the prediction of oligonucleotides dissolved in 1 M NaC1.

@article{citeulike:100059, abstract = {Thermodynamic data were determined from UV absorbance vs temperature profiles of 23 oligonucleotides. These data were combined with data from the literature for 21 sequences to derive improved parameters for the 10 Watson-Crick nearest neighbors. The observed trend in nearest-neighbor stabilities at 37 degrees C is GC > CG > GG > GA approximately GT approximately CA > CT > AA > AT > TA (where only the top strand is shown for each nearest neighbor). This trend suggests that both sequence and base composition are important determinants of DNA duplex stability. On average, the improved parameters predict deltaG degrees(37), deltaH degrees, deltaS degrees, and T(m) within 4\%, 7\%, 8\%, and 2 degrees C, respectively. The parameters are optimized for the prediction of oligonucleotides dissolved in 1 M NaC1.}, address = {Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA.}, author = {SantaLucia, J. and Allawi, H. T. and Seneviratne, P. A. }, citeulike-article-id = {100059}, doi = {10.1021/bi951907q}, issn = {0006-2960}, journal = {Biochemistry}, keywords = {array, probe}, month = {March}, number = {11}, pages = {3555--3562}, posted-at = {2008-02-18 14:57:55}, priority = {2}, title = {Improved nearest-neighbor parameters for predicting DNA duplex stability.}, url = {http://dx.doi.org/10.1021/bi951907q}, volume = {35}, year = {1996} }

RIS record

TY - JOUR ID - citeulike:100059 L3 - citeulike-article-id:100059 TI - Improved nearest-neighbor parameters for predicting DNA duplex stability. JF - Biochemistry VL - 35 IS - 11 SP - 3555 EP - 3562 AD - Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA. SN - 0006-2960 N2 - Thermodynamic data were determined from UV absorbance vs temperature profiles of 23 oligonucleotides. These data were combined with data from the literature for 21 sequences to derive improved parameters for the 10 Watson-Crick nearest neighbors. The observed trend in nearest-neighbor stabilities at 37 degrees C is GC > CG > GG > GA approximately GT approximately CA > CT > AA > AT > TA (where only the top strand is shown for each nearest neighbor). This trend suggests that both sequence and base composition are important determinants of DNA duplex stability. On average, the improved parameters predict deltaG degrees(37), deltaH degrees, deltaS degrees, and T(m) within 4%, 7%, 8%, and 2 degrees C, respectively. The parameters are optimized for the prediction of oligonucleotides dissolved in 1 M NaC1. KW - array KW - probe AU - SantaLucia, J AU - Allawi, HT AU - Seneviratne, PA PY - 1996/03/19/ UR - http://dx.doi.org/10.1021/bi951907q ER -

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