Structure of a Dinucleotide: Thymidylyl-(5'→3')-Thymidylate-5' (pTpT)

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Science  14 Dec 1973:
Vol. 182, Issue 4117, pp. 1142-1143
DOI: 10.1126/science.182.4117.1142


The crystal and molecular structure of the naturally occurring deoxyribose dinucleotide sodium thymidylyl-(5'→3')-thymidylate-5' has been determined by x-ray diffraction. There are four molecules of dinucleotide and 52 water molecules in an orthorhombic unit cell of dimensions (in angstroms) a = 16.06, b = 15.13, c = 15.65, space group P21212. There is a very high degree of conformational consistency between the two halves of the molecule when the dinucleotide is viewed as the combination of two 5'-mononucleotides. The planes of the two thymines are not parallel, but are tilted 38° with respect to each other. An extensive system of hydrogen bonding exists involving the bases, waters, phosphates, and sodiums; no base-base hydrogen bonding occurs. The dinucleotide structural parameters should be of assistance in interpreting DNA fiber diagrams in terms of possible structures.