[Structure of the B-form of DNA using the homopolymer poly(dA) . poly(dT) as an example. Refinement in accordance with x-ray and energy criteria].
The refinement of the B-form DNA structure was made using homopolymer poly(dA) (dT) as a model system. In the course of refinement 9 conformational and 22 independent experimental parameters (20 intensities of reflections and 2 helical parameters) were used. After the goal-function, including R-factor, helical and conformational parameters, was optimised, the structures with the values of potential energy and R-factor close correspondingly to the optimal values were selected. "The best" conformations obtained according to energy criteria have the value of an axial projection per one nucleotide pair of about 2,9 A that is equal to the corresponding value in the recently discovered relaxed form of DNA in solution. The most probable conformations according to combine energy and structural criteria have better value of the R-factor in comparison with those derived on the basis of X-ray only, although they are slightly less satisfactory according to the energy criteria. The conformation of DNA which have the values of an axial projection per one nucleotide pair--3,29 A; of the angle of rotation of neighboring nucleotide pair relative each other--36 degrees and of the angle of nucleotide pair with an axis of the helix -13,7 degrees seems to be the most accurate description of the doublehelical structure of poly(dA) . poly(dT). The atomic coordinates of the new model may be used in analysis of stereochemistry of the complexes of nucleic acids with polypeptide and proteins, that is in consideration of the problem of protein-nucleic acid recognition.
D004247:DNA; D008956:Models, Chemical; D009690:Nucleic Acid Conformation; D011067:Poly dA-dT; D011089:Polydeoxyribonucleotides; D013816:Thermodynamics; D014961:X-Ray Diffraction
D011089:Polydeoxyribonucleotides; D011067:Poly dA-dT; D004247:DNA
Struktura B-formy DNK na primere gomopolimera poly(dA) . poly(dT). Utochnenie po rentgenograficheskim i énergeticheskim kriteriiam.