title: Base pair opening kinetics study of the aegPNA:DNA hydrid duplex containing a site-specific GNA-like chiral PNA monomer.
abstract: Peptide nucleic acids (PNA) are one of the most widely used synthetic DNA mimics where the four bases are attached to a N-(2-aminoethyl)glycine (aeg) backbone instead of the negative-charged phosphate backbone in DNA. We have developed a chimeric PNA (chiPNA), in which a chiral GNA-like γ(3)T monomer is incorporated into aegPNA backbone. The base pair opening kinetics of the aegPNA:DNA and chiPNA:DNA hybrid duplexes were studied by NMR hydrogen exchange experiments. This study revealed that the aegPNA:DNA hybrid is much more stable duplex and is less dynamic compared to DNA duplex, meaning that base pairs are opened and reclosed much more slowly. The site-specific incorporation of γ(3)T monomer in the aegPNA:DNA hybrid can destabilize a specific base pair and its neighbors, maintaining the thermal stabilities and dynamic properties of other base pairs. Our hydrogen exchange study firstly revealed the unique kinetic features of base pairs in the aegPNA:DNA and chiPNA:DNA hybrids, which will provide an insight into the development of methodology for specific DNA recognition using PNA fragments.
authors.affiliation: Department of Chemistry and RINS, Gyeongsang National University, Jinju, Gyeongnam 660-701, Molecular-Level Interface Research Center, Department of Chemistry, KAIST, Daejeon 305-701, Republic of Korea.
authors.forename: Yeo-Jin
authors.initials: YJ
authors.lastname: Seo
authors.forename: Jisoo
authors.initials: J
authors.lastname: Lim
authors.forename: Eun-Hae
authors.initials: EH
authors.lastname: Lee
authors.forename: Taedong
authors.initials: T
authors.lastname: Ok
authors.forename: Juyoung
authors.initials: J
authors.lastname: Yoon
authors.forename: Joon-Hwa
authors.initials: JH
authors.lastname: Lee
authors.forename: Hee-Seung
authors.initials: HS
authors.lastname: Lee
mesh_terms: D020029:Base Pairing; D004247:DNA / Q000737:chemistry*; D041961:Deuterium Exchange Measurement; D007700:Kinetics; D019906:Nuclear Magnetic Resonance, Biomolecular; D020135:Peptide Nucleic Acids / Q000737:chemistry*; D011522:Protons; D013696:Temperature; D013941:Thymine / Q000031:analogs & derivatives / Q000737:chemistry
chemical_list: D020135:Peptide Nucleic Acids; D011522:Protons; D004247:DNA; D013941:Thymine