Biomaterial Database

B-A transition in DNA. 1983

V I Ivanov, and Krylov DYu, and E E Minyat, and L E Minchenkova

Institute of Molecular Biology, Academy of Sciences of the USSR, Moscow.

The B-A transition is characterized by two main physical parameters which might be biologically important: the cooperativity length and free energy difference between the B and A states under physiological conditions. Earlier these values were determined by us in an experiment over the B-A shift in water-non-electrolyte solutions in the presence of small molecules ("ties") affecting the B-A equilibrium. Now we report a new method of determining the cooperativity length which utilizes a phase diagram (B,A, coil). The coordinates are the fraction of non-electrolytes and temperature. Application of the Ising model for joint description of the B-A and helix-coil transitions makes possible to find the cooperativity length using the known thermodynamic parameters of the DNA melting and the appearance of the phase diagram near the triple point (A,B,coil). The value thus found (approximately 10(1) base pairs) is in accord with the values obtained with ties. In the new method the junctions between the A and B segments actually play the role of ties, stabilizing the double-stranded state. A considerable effect of the melting curve widening within the B-A transition range was discovered. A possible explanation suggests the presence of the A-philic sequences in the natural DNA. The A-phility of the oligo G oligo C sequence was estimated from the B-A transition curves of the synthetic decanucleotide duplexes.

UI	MeSH Term	Description	Entries
D008956	Models, Chemical	Theoretical representations that simulate the behavior or activity of chemical processes or phenomena; includes the use of mathematical equations, computers, and other electronic equipment.	Chemical Models,Chemical Model,Model, Chemical
D008962	Models, Theoretical	Theoretical representations that simulate the behavior or activity of systems, processes, or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.	Experimental Model,Experimental Models,Mathematical Model,Model, Experimental,Models (Theoretical),Models, Experimental,Models, Theoretic,Theoretical Study,Mathematical Models,Model (Theoretical),Model, Mathematical,Model, Theoretical,Models, Mathematical,Studies, Theoretical,Study, Theoretical,Theoretical Model,Theoretical Models,Theoretical Studies
D009690	Nucleic Acid Conformation	The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.	DNA Conformation,RNA Conformation,Conformation, DNA,Conformation, Nucleic Acid,Conformation, RNA,Conformations, DNA,Conformations, Nucleic Acid,Conformations, RNA,DNA Conformations,Nucleic Acid Conformations,RNA Conformations
D004247	DNA	A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).	DNA, Double-Stranded,Deoxyribonucleic Acid,ds-DNA,DNA, Double Stranded,Double-Stranded DNA,ds DNA
D001483	Base Sequence	The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.	DNA Sequence,Nucleotide Sequence,RNA Sequence,DNA Sequences,Base Sequences,Nucleotide Sequences,RNA Sequences,Sequence, Base,Sequence, DNA,Sequence, Nucleotide,Sequence, RNA,Sequences, Base,Sequences, DNA,Sequences, Nucleotide,Sequences, RNA