Synthesis and characterization of a [3-15N]-labeled cis-syn thymine dimer-containing DNA duplex.
Cis-syn thymine dimers are the major photoproducts of DNA and are the principal cause of mutations induced by sunlight. To better understand the nature of base pairing with cis-syn thymine dimers, we have synthesized a decamer oligodeoxynucleotide (ODN) containing a cis-syn thymine dimer labeled at the N3 of both T's with 15N by two efficient routes from [3-15N]-thymidine phosphoramidite. In the postsynthetic irradiation route, an ODN containing an adjacent pair of [3-15N]-labeled T's was irradiated and the cis-syn dimer-containing ODN isolated by HPLC. In the mixed building block route, a mixture of cis-syn and trans-syn dimer-containing ODNs was synthesized from a mixture of [3-15N]-labeled thymine dimer phosphoramidites after which the cis-syn dimer-containing ODN was isolated by HPLC. The N3-nitrogen and imino proton signals of an (15)N-labeled thymine dimer-containing decamer duplex were assigned by 2D 1H-15N heterocorrelated HSQC NMR spectroscopy, and the 15N-1H coupling constant was found to be 1.8 Hz greater for the 5'-T than for the 3'-T. The larger coupling constant is indicative of weaker H-bonding that is consistent with the more distorted nature of the 5'-base pair found in solution state NMR and crystallographic structures.
Department of Chemistry, Washington University, St. Louis, Missouri 63130, USA.
Hussam M
HM
Bdour
Jeff Lung-Fa
JL
Kao
John-Stephen
JS
Taylor
D000577:Amides; D020029:Base Pairing; D004247:DNA / Q000737:chemistry*; D019281:Dimerization; D006860:Hydrogen Bonding; D007536:Isomerism; D009682:Magnetic Resonance Spectroscopy; D009154:Mutation; D009587:Nitrogen Isotopes; D009838:Oligodeoxyribonucleotides / Q000138:chemical synthesis* / Q000737:chemistry; D010756:Phosphoric Acids; D013941:Thymine / Q000737:chemistry*
D000577:Amides; D009587:Nitrogen Isotopes; D009838:Oligodeoxyribonucleotides; D010756:Phosphoric Acids; D004247:DNA; C011067:phosphoramidic acid; D013941:Thymine