title: Base pair opening kinetics and dynamics in the DNA duplexes that specifically recognized by very short patch repair protein (Vsr).
abstract: In Escherichia coli, the very short patch (VSP) repair system is a major pathway for removal of T.G mismatches in Dcm target sequences. In the VSP repair pathway, the very short patch repair (Vsr) endonuclease selectively recognizes a T.G mismatch in Dcm target sequences and hydrolyzes the 5'-phosphate group of the mismatched thymine. The hydrogen exchange NMR studies here revealed that the T5.G18 mismatch in the Dcm target sequence significantly stabilizes own base pair but destabilizes the two neighboring G4.C19 and A6.T17 base pairs compare to other T.G mismatches. These unusual patterns of base pair stability in the Dcm target sequence can explain how the Vsr endonuclease specifically recognizes the mismatched Dcm target sequence and intercalates into the DNA.
authors.affiliation: Department of Chemistry, KAIST, Daejeon 305-701, Republic of Korea.
authors.forename: Sung Jae
authors.initials: SJ
authors.lastname: Cho
authors.forename: Jongchul
authors.initials: J
authors.lastname: Bang
authors.forename: Joon-Hwa
authors.initials: JH
authors.lastname: Lee
authors.forename: Byong-Seok
authors.initials: BS
authors.lastname: Choi
mesh_terms: D020029:Base Pairing; D001483:Base Sequence; D053843:DNA Mismatch Repair / Q000502:physiology*; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D004706:Endodeoxyribonucleases / Q000378:metabolism*; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000378:metabolism*; D007700:Kinetics; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D013816:Thermodynamics
chemical_list: D004269:DNA, Bacterial; D029968:Escherichia coli Proteins; D004706:Endodeoxyribonucleases; C071421:vsr endonuclease