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Nucleic Acids Res. Nov 15, 1996; 24(22): 4501–4505.
PMCID: PMC146261

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

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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Selected References

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  • Breslauer KJ, Frank R, Blöcker H, Marky LA. Predicting DNA duplex stability from the base sequence. Proc Natl Acad Sci U S A. 1986 Jun;83(11):3746–3750. [PMC free article] [PubMed]
  • Freier SM, Kierzek R, Jaeger JA, Sugimoto N, Caruthers MH, Neilson T, Turner DH. Improved free-energy parameters for predictions of RNA duplex stability. Proc Natl Acad Sci U S A. 1986 Dec;83(24):9373–9377. [PMC free article] [PubMed]
  • Tinoco I, Jr, Uhlenbeck OC, Levine MD. Estimation of secondary structure in ribonucleic acids. Nature. 1971 Apr 9;230(5293):362–367. [PubMed]
  • Sugimoto N, Nakano S, Katoh M, Matsumura A, Nakamuta H, Ohmichi T, Yoneyama M, Sasaki M. Thermodynamic parameters to predict stability of RNA/DNA hybrid duplexes. Biochemistry. 1995 Sep 5;34(35):11211–11216. [PubMed]
  • LeCuyer KA, Crothers DM. The Leptomonas collosoma spliced leader RNA can switch between two alternate structural forms. Biochemistry. 1993 May 25;32(20):5301–5311. [PubMed]
  • Connell GJ, Yarus M. RNAs with dual specificity and dual RNAs with similar specificity. Science. 1994 May 20;264(5162):1137–1141. [PubMed]
  • Hall KB, McLaughlin LW. Thermodynamic and structural properties of pentamer DNA.DNA, RNA.RNA, and DNA.RNA duplexes of identical sequence. Biochemistry. 1991 Nov 5;30(44):10606–10613. [PubMed]
  • SantaLucia J, Jr, Allawi HT, Seneviratne PA. Improved nearest-neighbor parameters for predicting DNA duplex stability. Biochemistry. 1996 Mar 19;35(11):3555–3562. [PubMed]
  • Kierzek R, Caruthers MH, Longfellow CE, Swinton D, Turner DH, Freier SM. Polymer-supported RNA synthesis and its application to test the nearest-neighbor model for duplex stability. Biochemistry. 1986 Dec 2;25(24):7840–7846. [PubMed]
  • Sugimoto N, Kierzek R, Freier SM, Turner DH. Energetics of internal GU mismatches in ribooligonucleotide helixes. Biochemistry. 1986 Sep 23;25(19):5755–5759. [PubMed]
  • Petersheim M, Turner DH. Base-stacking and base-pairing contributions to helix stability: thermodynamics of double-helix formation with CCGG, CCGGp, CCGGAp, ACCGGp, CCGGUp, and ACCGGUp. Biochemistry. 1983 Jan 18;22(2):256–263. [PubMed]
  • Ratmeyer L, Vinayak R, Zhong YY, Zon G, Wilson WD. Sequence specific thermodynamic and structural properties for DNA.RNA duplexes. Biochemistry. 1994 May 3;33(17):5298–5304. [PubMed]
  • Marky LA, Breslauer KJ. Calculating thermodynamic data for transitions of any molecularity from equilibrium melting curves. Biopolymers. 1987 Sep;26(9):1601–1620. [PubMed]
  • Zieba K, Chu TM, Kupke DW, Marky LA. Differential hydration of dA.dT base pairing and dA and dT bulges in deoxyoligonucleotides. Biochemistry. 1991 Aug 13;30(32):8018–8026. [PubMed]

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