NMR studies on the dynamic features of Dcm sequences containing T: G mismatch

Abstract

Using nuclear magnetic resonance experiments, dynamic motion of base pair opening reaction occurring in DNA duplexes can be studied by observing hydrogen exchange of imino protons in guanine and thymine residues. Base catalyzed dynamics experiments provides opening/closing rate of the base pair and thus, equilibrium constant for base pair opening. In $\It{E. coli}$, very-short patch (VSP) repair system is major pathway for removal of the $T\cdotG$ mismatches in dcm target sequences. In the VSP repair pathway, the very-short patch repair (vsr) endonuclease selectively recognizes a $T\cdotG$ mismatch in dcm target sequences and hydrolyzes the 5`` phosphate group of mismatched thymine. The hydrogen exchange NMR studies here revealed that the $T5\cdotG18$ mismatch in the dcm target sequence significantly stabilizes own base pair but destabilizes the two neighboring $G4\cdotC19$ and $A6\cdotT17$ base pairs compare to other $T\cdotG$ 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.