title: Synthesis of oligonucleotides containing the Dewar valence isomer of the (6-4) photoproduct and their application to (6-4) photolyase studies.
abstract: The (6-4) photoproduct, which is a major UV light-induced lesion formed between adjacent pyrimidine bases, is isomerized to its Dewar valence isomer by exposure to longer wavelengths. We have synthesized a phosphoramidite building block of the Dewar photoproduct formed at the thymidylyl(3'-5')thymidine site, and incorporated it into oligonucleotides on a DNA synthesizer, aiming to use them for biological studies. An alternative activator, benzimidazolium triflate, gave better results, while by-products were detected at longer retention time in the ordinary synthesis. We characterized the synthetic oligonucleotides by UV conversion, nuclease digestion and mass spectrometry. Their use in the study of the (6-4) photolyase, a DNA repair enzyme, revealed its different recognition modes between the (6-4) photoproduct and the Dewar isomer.
authors.affiliation: Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan.
authors.forename: Junpei
authors.initials: J
authors.lastname: Yamamoto
authors.forename: Kenichi
authors.initials: K
authors.lastname: Hitomi
authors.forename: Takeshi
authors.initials: T
authors.lastname: Todo
authors.forename: Shigenori
authors.initials: S
authors.lastname: Iwai
mesh_terms: D002851:Chromatography, High Pressure Liquid; D004255:Deoxyribodipyrimidine Photo-Lyase / Q000378:metabolism*; D015226:Dinucleoside Phosphates / Q000737:chemistry; D006576:Heterocyclic Compounds, 4 or More Rings / Q000737:chemistry*; D009841:Oligonucleotides / Q000138:chemical synthesis / Q000737:chemistry* / Q000378:metabolism; D009943:Organophosphorus Compounds / Q000737:chemistry; D013237:Stereoisomerism; D013379:Substrate Specificity; D013936:Thymidine / Q000031:analogs & derivatives* / Q000737:chemistry; D014466:Ultraviolet Rays
chemical_list: D015226:Dinucleoside Phosphates; D006576:Heterocyclic Compounds, 4 or More Rings; D009841:Oligonucleotides; D009943:Organophosphorus Compounds; C434331:phosphoramidite; C017758:thymidylyl-(3'-5')-thymidine; D004255:Deoxyribodipyrimidine Photo-Lyase; D013936:Thymidine