An uncommon nucleotide conformation shown by molecular structure of deoxyuridine-5'-phosphate and nucleic acid stereochemistry

Abstract

Crystal structure determinations of nucleic acid fragments have shown that several of the conformational features found in the monomeric building blocks are also manifested at the nucleic acid level. Stereochemical variations between thymine and uracil nucleotides are therefore of interest as they can provide a structural basis for some of the differences between the conformations of DNA and RNA. X-ray studies have so far not shown any major dissimilarities between these two nucleotide species although the sugar ring of deoxyribonucleotides is found to possess greater flexibility than that in ribonucleotides. We report here the molecular structure of deoxyuridine-5′-phosphate (dUMP-5′) which is not a common monomer unit of DNAs as it is replaced by its 5-methyl analogue deoxythymidine-5′-phosphate (dTMP-5′). The investigation was undertaken to help determine whether or not this implied a fundamental difference between the geometries of these two molecules.