Chemical and enzymatic synthesis of DNA and RNA containing selenium for X-ray crystallography using multiwavelength anomalous dispersion

A novel approach has been developed to synthesize DNA and RNA oligonucleotides containing selenium for structure determination by X-ray crystallography using Multiwavelength Anomalous Diffraction (MAD). The impetus for the project has been based on a challenging aspect in the field of nucleic acid X-ray crystallography: the elucidation of the three-dimensional structures of DNA and RNA molecules is hampered by the difficulty to create suitable heavy atom derivatives for crystallographic phasing. To address this problem, a chemical and an enzymatic approach have been investigated to introduce the selenium functionality into both DNA and RNA covalently. In the chemical approach, the solid phase synthesis via the phosphoramidite chemistry was utilized to synthesize relatively short oligonucleotides. To this end, synthetic procedures were designed to incorporate the selenium functionality at either the 5'- or 2 '-positions of thymidine and uridine phosphoramidites. These phosphoramidite derivatives were then utilized to introduce selenium at specific sites in selected DNA and RNA oligonucleotides. In all cases, the selenium functional group is presented in the form of methyl selenide in order to confer superior stabilities to the corresponding products. Similarly, insight into the enzymatic synthesis of phosphoroselenoate DNA and RNA has been achieved via the synthesis of nucleoside triphosphates harboring selenium at the alpha-phosphate, in which selenium replaces one of the non-bridging oxygen atoms. The synthesis of these nucleoside triphosphate analogs was performed via a phosphite intermediate that was oxidized with 3H-1,2-benzothiaselenol-3-one. This enzymatic strategy was of particular interest because, in contrast to the solid phase approach, it facilitated the synthesis of long DNA and RNA molecules using the Klenow DNA polymerase and the T7 RNA polymerase, respectively. The presence of selenium in the phosphoroselenoate DNA and RNA were confirmed using selenium-enhanced resistance to enzymatic digestion. The data demonstrated the practicability of the chemical and enzymatic approaches to introduce the selenium functionality into DNA and RNA as a scatter center for MAD phasing in nucleic acid X-ray crystallography. The development and maturity of this selenium derivatization method should significantly advance the field of nucleic acid structure analysis, biomedicine, and genomic research.