Premelting thermal fluctuational base pair opening probability of poly(dA). poly(dT) as predicted by the modified self-consistent phonon theory
Journal Article
·
· Biopolymers; (United States)
- Department of Physics, Purdue University, West Lafayette, Indiana (USA)
We employ a mean field, modified, self-consistent phonon theory to evaluate the single base-pair opening rate and the probability of a base pair in the amino proton exchangeable state for the homopolymer poly(dA).poly(dT) at temperatures below the helix-coil transition region. Our calculated premelting single base-pair opening probabilities are in general agreement with several available experimental estimates from amino proton exchange and formaldehyde-induced DNA melting measurements. These calculated opening probabilities, however, are in disagreement with the prediction of the helix-coil transition theory. Possible reasons for the differences are discussed, especially the possible different definition of a meaningful open state in the premelting region. The premelting open state of the modified self-consistent phonon approximation theory seems to be appropriate to describe a solvent-accessible open configuration that is sufficient to facilitate important chemical reactions such as imino proton exchange and formaldehyde reaction with the bases. This can be compared with the completely unstacked open state of the helix-coil transition theory originally defined in the helix-coil transition region. We propose that the amino proton exchangeable state is different from the open state associated with melting and only involves the breaking of the amino interbase H bond. The agreement between the calculated and experimentally estimated probability of a base pair in the amino proton exchangeable state seems to support this hypothesis.
- OSTI ID:
- 5395216
- Journal Information:
- Biopolymers; (United States), Journal Name: Biopolymers; (United States) Vol. 31:2; ISSN BIPMA; ISSN 0006-3525
- Country of Publication:
- United States
- Language:
- English
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Tue Jun 03 00:00:00 EDT 1986
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·
OSTI ID:5127466
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 x 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)
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Thu Dec 31 23:00:00 EST 1981
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OSTI ID:5809105
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OSTI ID:6342643
Related Subjects
560300* -- Chemicals Metabolism & Toxicology
63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTANT EFFECTS ON LIVING ORGS. AND BIOL. MAT.
ALDEHYDES
BARYONS
BIOLOGICAL EFFECTS
CHEMICAL BONDS
CONFIGURATION
DNA
ELEMENTARY PARTICLES
FERMIONS
FORMALDEHYDE
HADRONS
HELICAL CONFIGURATION
ION EXCHANGE
MOLECULAR STRUCTURE
NUCLEIC ACID DENATURATION
NUCLEIC ACIDS
NUCLEONS
ORGANIC COMPOUNDS
PROBABILITY
PROTONS
THERMODYNAMICS
63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTANT EFFECTS ON LIVING ORGS. AND BIOL. MAT.
ALDEHYDES
BARYONS
BIOLOGICAL EFFECTS
CHEMICAL BONDS
CONFIGURATION
DNA
ELEMENTARY PARTICLES
FERMIONS
FORMALDEHYDE
HADRONS
HELICAL CONFIGURATION
ION EXCHANGE
MOLECULAR STRUCTURE
NUCLEIC ACID DENATURATION
NUCLEIC ACIDS
NUCLEONS
ORGANIC COMPOUNDS
PROBABILITY
PROTONS
THERMODYNAMICS