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Spatial configurations of polynucleotide chains. III. Polydeoxyribonucleotides
Author(s) -
Olson Wilma K.,
Flory Paul J.
Publication year - 1972
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.1972.360110104
Subject(s) - deoxyribose , chemistry , polynucleotide , ribose , hydrogen bond , residue (chemistry) , stereochemistry , alkane stereochemistry , crystallography , amino acid residue , nucleic acid , molecule , crystal structure , enzyme , peptide sequence , organic chemistry , biochemistry , gene
The virtual bond scheme set forth in preceding papers for treating the average properties of polyriboadenylic acid (poly rA) is here applied to the calculation of the unperturbed mean‐square end‐to‐end distance of polydeoxyriboadenylic acid (poly dA). The modifications in structure and in charge distribution resulting from the replacement of the hydroxyl group at C 2′ in the ribose residue by hydrogen in deoxyribose produce only minor modifications in the conformational energies associated with the poly dA chain as compared to those found for poly rA. The main difference is manifested in the energy associated with rotations about the C 3′ –O 3′ bond of the deoxyribose residue in the C 2′ ‐endo conformation; accessible rotations are confined to the range between 0° and 30° relative to the trans conformation, whereas in the ribose unit the accessible regions comprise two ranges centered at approximately 35° and 85°. The characteristic ratio 〈 r 2 〉0/ n l 2 calculated on the basis of the conformational energy estimates is ≈9 for the poly dA chain with all deoxyribose residues in the C 3′ ‐endo conformation and ≈21 with all residues in the C 2′ ‐endo form. Satisfactory agreement is achieved between the theoretical values and experimental results on apurinic acid by treating the poly dA chain as a random copolymer of C 3′ ‐endo and C 2′ ‐endo conformational isomers present in a ratio of ∼1 to 9.