title: C5-(1-propynyl)-2'-deoxy-pyrimidines enhance mismatch penalties of DNA:RNA duplex formation.
abstract: UV melting experiments show that C5-(1-propynyl)ation of seven pyrimidines to give a fully propynylated oligodeoxynucleotide (PrODN) heptamer increases the thermodynamic stability of six Watson-Crick paired DNA:RNA duplexes by 8.2 kcal/mol, on average, at 37 degrees C. About 2.5 kcal/mol of this enhancement is due to long-range cooperativity between the propynylated pyrimidines, Y(p)'s. On average, penalties for dU(p):rG, dC(p):rA, dU(p):rC, and dC(p):rC mismatches are enhanced by 2.9 kcal/mol in PrODN:RNA duplexes over those in unmodified duplexes. This results in penalties as large as 10 kcal/mol for a single mismatch. Removing a single propyne two base pairs away from a mismatch in a PrODN:RNA duplex eliminates the enhancement in specificity. Evidently, enhanced specificity is directly linked to long-range cooperativity between Y(p)'s. In most cases, the enhanced specificity is larger for internal than for terminal mismatches. PrODN:RNA duplexes are destabilized by full phosphorothioate backbone substitution to give S-PrODN:RNA duplexes. The S-PrODN:RNA duplexes retain enhanced mismatch penalties, however. These results provide insight for utilizing long-range cooperativity and enhanced specificity to improve nucleic acid based probe and drug design.
authors.affiliation: Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, USA.
authors.forename: T W
authors.initials: TW
authors.lastname: Barnes
authors.forename: D H
authors.initials: DH
authors.lastname: Turner
mesh_terms: D020137:Base Pair Mismatch; D004247:DNA / Q000737:chemistry*; D003841:Deoxycytidine / Q000737:chemistry; D003857:Deoxyuridine / Q000737:chemistry; D009692:Nucleic Acid Heteroduplexes / Q000737:chemistry*; D009693:Nucleic Acid Hybridization; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*; D011743:Pyrimidines / Q000737:chemistry*; D012313:RNA / Q000737:chemistry*; D013816:Thermodynamics; D013873:Thionucleotides / Q000737:chemistry
chemical_list: D009692:Nucleic Acid Heteroduplexes; D009838:Oligodeoxyribonucleotides; D011743:Pyrimidines; D013873:Thionucleotides; D003841:Deoxycytidine; D012313:RNA; D004247:DNA; D003857:Deoxyuridine