title: Chemical synthesis and biochemical properties of oligonucleotides that contain the (5'S,5S,6S)-5',6-cyclo-5-hydroxy-5,6-dihydro-2'-deoxyuridine DNA lesion.
abstract: The first chemical synthesis of (5'S,5S,6S)-5',6-cyclo-5-hydroxy-5,6-dihydro-2'-deoxyuridine [(5'S,5S,6S)-cyclo-5-OH-dHdU], a radiation-induced decomposition product of 2'-deoxycytidine in aerated solution, is reported. Subsequently, 2'-deoxycytidine was incorporated into oligodeoxyribonucleotides with defined sequences by using an optimized system of protection that takes into account the reactivity and stability of the modified building blocks. After deprotection and purification, the chemical composition of the modified DNA fragments was assessed by enzymatic digestions and mass spectrometry measurements. The MS analyses confirmed the presence and integrity of the lesion within the synthesized DNA fragments. In vitro replication and repair studies showed that (5'S,5S,6S)-cyclo-5-OH-dHdU acts as a block for DNA polymerases when inserted into DNA oligomers and is not excised by any of the tested DNA N-glycosylases. Therefore, (5'S,5S,6S)-cyclo-5-OH-dHdU may represent a potential lethal lesion within the cell if it is not removed by the nucleotide excision repair machinery.
mesh_terms: D002851:Chromatography, High Pressure Liquid; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D004249:DNA Damage; D004260:DNA Repair / Q000502:physiology; D004259:DNA-Directed DNA Polymerase / Q000737:chemistry / Q000502:physiology; D003841:Deoxycytidine / Q000737:chemistry / Q000528:radiation effects; D003857:Deoxyuridine / Q000031:analogs & derivatives* / Q000138:chemical synthesis*; D004591:Electrophoresis, Polyacrylamide Gel; D008401:Gas Chromatography-Mass Spectrometry; D006867:Hydrolases / Q000494:pharmacology; D009691:Nucleic Acid Denaturation; D009841:Oligonucleotides / Q000138:chemical synthesis* / Q000378:metabolism; D009943:Organophosphorus Compounds / Q000138:chemical synthesis; D010880:Piperidines / Q000737:chemistry
chemical_list: C472107:5',6-cyclo-5-hydroxy-5,6-dihydro-2'-deoxyuridine; D009841:Oligonucleotides; D009943:Organophosphorus Compounds; D010880:Piperidines; C434331:phosphoramidite; D003841:Deoxycytidine; D004247:DNA; D004259:DNA-Directed DNA Polymerase; D006867:Hydrolases; D003857:Deoxyuridine