Molecular structure of deoxycytidyl-3'-methylphosphonate (RP) 5'-deoxyguanidine, d[Cp(CH3)G]. A neutral dinucleotide with Watson-Crick base pairing and a right handed helical twist.
The crystal structure of d[Cp(CH3)G] has been determined as part of a project to study the mechanism of the B----Z transition in DNA. The asymmetric unit contains two dinucleotides and the equivalent of 7.5 water molecules, partially disordered over 12 definable positions. The two symmetry-independent dinucleotides form a duplex with Watson-Crick base-pairing and a right-handed helical sense. Comparison with previously determined structures of the B and A conformation showed that this duplex is closer to B than to A but significantly different from B. It corresponds to a stretched out helix with a 4 A rise per base pair and a helical twist of 32 degrees. This structure may serve as a model for the bending of DNA in certain situations. The configuration at the methyl phosphonate is RP, and a mechanism, based on this assignment, is presented for the B----Z transition in DNA.
Han
F
F
Physical and Analytical Chemistry Research, Upjohn Company, Kalamazoo, MI 49001.
Watt
W
W
Duchamp
D J
DJ
Callahan
L
L
Kézdy
F J
FJ
Agarwal
K
K
D001482:Base Composition; D001483:Base Sequence; D055598:Chemical Phenomena; D002627:Chemistry, Physical; D015226:Dinucleoside Phosphates; D008958:Models, Molecular; D008969:Molecular Sequence Data; D015394:Molecular Structure; D009690:Nucleic Acid Conformation; D009943:Organophosphorus Compounds; D014961:X-Ray Diffraction
D015226:Dinucleoside Phosphates; D009943:Organophosphorus Compounds; C064054:deoxycytidyl-3'-methylphosphonate-5'-deoxyguanidine; C032627:methylphosphonic acid