Home LiteratureArticle Details
PMID: 4022774 Published · ppublish English Journal Article Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S.

Base-base mismatches. Thermodynamics of double helix formation for dCA3XA3G + dCT3YT3G (X, Y = A,C,G,T).

Nucleic acids research ·Vol. 13 ·No. 13 ·1985-07-11 ·Pages 4811-24

Aboul-ela F, Koh D, Tinoco I, Martin FH

Abstract

Thermodynamic parameters for double strand formation have been measured for the sixteen double helices of the sequence dCA3XA3G.dCT3YT3G, with each of the bases A, C, G and T at the positions labelled X and Y. The results are analyzed in terms of nearest-neighbors and are compared with thermodynamic parameters for RNA secondary structure. At room temperature the sequence (Formula: see text) is more stable than (Formula: see text) and is similar in stability to (Formula: see text) and (Formula: see text) are least stable. At higher temperatures the sequences containing a G.C base pair become more stable than those containing only A.T. All molecules containing mismatches are destabilized with respect to those with only Watson-Crick pairing, but there is a wide range of destabilization. At room temperature the most stable mismatches are those containing guanine (G.T, G.G, G.A); the least stable contain cytosine (C.A, C.C). At higher temperatures pyrimidine-pyrimidine mismatches become the least stable.

MeSH Terms
Base Composition Base Sequence DNA Hydrogen Bonding Nucleic Acid Conformation Thermodynamics
Chemicals
DNA
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Aboul-ela F
Koh D
Tinoco I
Martin F H
References (30)
30 references, click to expand
  1. Structural and energetic consequences of noncomplementary base oppositions in nucleic acid helices.
    Prog Nucleic Acid Res Mol Biol. 1975;15(0):185-218 PMID: 1094495
  2. The structure of helical 5'-guanosine monophosphate.
    J Mol Biol. 1975 Feb 25;92(2):171-9 PMID: 1142422
  3. Synthesis and thermal melting behavior of oligomer-polymer complexes containing defined lengths of mismatched dA-dG and dG-dG nucleotides.
    Biochemistry. 1977 May 31;16(11):2367-74 PMID: 301042
  4. Base pairing structure in the poly d(G-T) double helix: wobble base pairs.
    Nucleic Acids Res. 1978 Jun;5(6):1955-70 PMID: 673842
  5. Globin mRNA sequences: analysis of base pairing and evolutionary implications.
    Cold Spring Harb Symp Quant Biol. 1978;42 Pt 2:985-1002 PMID: 277330
  6. Local destabilisation of a DNA double helix by a T--T wobble pair.
    Nature. 1979 Sep 20;281(5728):235-6 PMID: 481593
  7. Hybridization of synthetic oligodeoxyribonucleotides to phi chi 174 DNA: the effect of single base pair mismatch.
    Nucleic Acids Res. 1979 Aug 10;6(11):3543-57 PMID: 158748
  8. Prediction of pairing schemes in RNA molecules-loop contributions and energy of wobble and non-wobble pairs.
    Biochimie. 1979;61(10):1133-50 PMID: 394764
  9. Sequence dependence of the helical repeat of DNA in solution.
    Nature. 1981 Jul 23;292(5821):375-8 PMID: 6265793
  10. Sequence-dependent helical periodicity of DNA.
    Nature. 1981 Jul 23;292(5821):378-80 PMID: 6265794
  11. Helical periodicity of DNA, Poly(dA) . poly(dT) and poly(dA-dT). poly(dA-dT) in solution.
    Eur J Biochem. 1981 Aug;118(2):215-22 PMID: 7285918
  12. Structure of a B-DNA dodecamer. II. Influence of base sequence on helix structure.
    J Mol Biol. 1981 Jul 15;149(4):761-86 PMID: 6273591
  13. DNA and RNA oligomer thermodynamics: the effect of mismatched bases on double-helix stability.
    Biopolymers. 1981 Dec;20(12):2509-31 PMID: 7326358
  14. Premelting and melting transitions in the d(CGCGAATTCGCG) self-complementary duplex in solution.
    Biochemistry. 1982 Feb 2;21(3):428-36 PMID: 7066294
  15. 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):437-44 PMID: 7066295
  16. Extra adenosine stacks into the self-complementary d(CGCAGAATTCGCG) duplex in solution.
    Biochemistry. 1982 Feb 2;21(3):445-51 PMID: 7066296
  17. Calorimetric determination of base-stacking enthalpies in double-helical DNA molecules.
    Biopolymers. 1982 Nov;21(11):2185-94 PMID: 7171732
  18. Kinetics for exchange of imino protons in the d(C-G-C-G-A-A-T-T-C-G-C-G) double helix and in two similar helices that contain a G . T base pair, d(C-G-T-G-A-A-T-T-C-G-C-G), and an extra adenine, d(C-G-C-A-G-A-A-T-T-C-G-C-G).
    Biochemistry. 1982 Dec 7;21(25):6567-74 PMID: 6295469
  19. Heteronomous DNA.
    Nucleic Acids Res. 1983 Jun 25;11(12):4141-55 PMID: 6866768
  20. 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):4263-5 PMID: 6576336
  21. The effect of single base-pair mismatches on the duplex stability of d(T-A-T-T-A-A-T-A-T-C-A-A-G-T-T-G) . d(C-A-A-C-T-T-G-A-T-A-T-T-A-A-T-A).
    Eur J Biochem. 1984 Feb 15;139(1):19-27 PMID: 6698006
  22. The locus of sequence-directed and protein-induced DNA bending.
    Nature. 1984 Apr 5-11;308(5959):509-13 PMID: 6323997
  23. 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):3207-17 PMID: 6466638
  24. Deoxyadenosine-deoxycytidine pairing in the d(C-G-C-G-A-A-T-T-C-A-C-G) duplex: conformation and dynamics at and adjacent to the dA X dC mismatch site.
    Biochemistry. 1984 Jul 3;23(14):3218-26 PMID: 6331846
  25. Molecular-mechanical studies of the mismatched base analogs of d(CGCGAATTCGCG)2:d(CGTGAATTCGCG)2, d(CGAGAATTCGCG)2, d(CGCGAATTCACG)2, d(CGCGAATTCTCG)2, and d(CGCAGAATTCGCG).d(CGCGAATTCGCG).
    Biopolymers. 1984 Dec;23(12):2901-29 PMID: 6525406
  26. Thermodynamic studies of RNA stability.
    J Biomol Struct Dyn. 1984 Mar;1(5):1229-42 PMID: 6086053
  27. Self-complementary oligoribonucleotides: adenylic acid-uridylic acid block copolymers.
    J Mol Biol. 1971 Apr 28;57(2):201-15 PMID: 5579619
  28. Free energy of imperfect nucleic acid helices. 3. Small internal loops resulting from mismatches.
    J Mol Biol. 1973 Aug 5;78(2):301-19 PMID: 4747633
  29. Improved estimation of secondary structure in ribonucleic acids.
    Nat New Biol. 1973 Nov 14;246(150):40-1 PMID: 4519026
  30. Stability of ribonucleic acid double-stranded helices.
    J Mol Biol. 1974 Jul 15;86(4):843-53 PMID: 4427357
Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
0305-1048
DOI
10.1093/nar/13.13.4811
Published
1985-07-11
Pages
4811-24
Language
English
Region
England
NLM ID
0411011
PMCID
PMC321828
Subset
IM
Grants
NIGMS NIH HHS · GM10840 · United States
External Links
PubMed source DOI: 10.1093/nar/13.13.4811 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2