title: Novel internucleotide 3'-NH-P(CH3)(O)-O-5' linkage. Oligo(deoxyribonucleoside methanephosphonamidates); synthesis, structure and hybridization properties.
abstract: Diastereomeric dithymidine methanephosphonamidates (TnpmT) were synthesized by reaction of 3'-amino-3'-deoxythymidine with 3'- O -acetylthymidin-5-yl-methanephosphonochloridate. Separated dinucleotide TnpmT(fast) and TnpmT(slow) diastereomers were used as building blocks to prepare chimeric dodecathy-midylates, possessing one to four modified linkages, by means of phosphoramidite automated solid phase synthesis. As expected, the methanephosphonamidate internucleotide linkage is resistant to nuclease P1, snake venom PDE and 3'-exonuclease from human plasma. Degradation of dodecathymidylates possessing modified internucleotide linkages in alternate positions proved the 'hopping' properties of 3'-exonuclease. Oligo(deoxyribonucleotide methanephosphonamidates) were tested for their binding affinity to complementary oligomers in thermal denaturation experiments. All the oligomers showed lower binding affinity to DNA and RNA targets, however, oligomers originating from the TnpmT(fast) dimeric unit exhibited better hybridization properties than their diastereomeric TnpmT(slow) counterparts. A lowering of T m of approximately 2.4 degrees C (1.0-1.8 degrees C) was observed for each introduced TnpmT(fast) modification and 6.0 degrees C (4.2-5.0 degrees C) for each TnpmT(slow) modification in duplexes of modified dodecathymidylates with dA12(A12) oligomers. The oligo(deoxyribonucleoside methanephosphonamidate) designated F4, possessing four modified methanephosphonate linkages originating from the TnpmT(fast) diastereomeric unit, exhibits a tendency for triplex formation, as was demonstrated in thermal denaturation experiments with the d(A21C4T21) hairpin oligomer.
authors.affiliation: Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lódz, Poland. bnawrot@lodz.pdi.net
authors.forename: B
authors.initials: B
authors.lastname: Nawrot
authors.forename: M
authors.initials: M
authors.lastname: Boczkowska
authors.forename: M
authors.initials: M
authors.lastname: Wójcik
authors.forename: M
authors.initials: M
authors.lastname: Sochacki
authors.forename: S
authors.initials: S
authors.lastname: Kazmierski
authors.forename: W J
authors.initials: WJ
authors.lastname: Stec
mesh_terms: D000818:Animals; D002236:Carbohydrate Conformation; D002241:Carbohydrates / Q000737:chemistry; D005092:Exonucleases / Q000378:metabolism; D006801:Humans; D009690:Nucleic Acid Conformation; D009693:Nucleic Acid Hybridization; D009711:Nucleotides; D009838:Oligodeoxyribonucleotides / Q000138:chemical synthesis / Q000737:chemistry* / Q000302:isolation & purification; D013936:Thymidine
chemical_list: D002241:Carbohydrates; D009711:Nucleotides; D009838:Oligodeoxyribonucleotides; D005092:Exonucleases; C022650:spleen exonuclease; D013936:Thymidine