title: Flexibility and stabilization of HgII-mediated C:T and T:T base pairs in DNA duplex.
abstract: Owing to their great potentials in genetic code extension and the development of nucleic acid-based functional nanodevices, DNA duplexes containing HgII-mediated base pairs have been extensively studied during the past 60 years. However, structural basis underlying these base pairs remains poorly understood. Herein, we present five high-resolution crystal structures including one first-time reported C-HgII-T containing duplex, three T-HgII-T containing duplexes and one native duplex containing T-T pair without HgII. Our structures suggest that both C-T and T-T pairs are flexible in interacting with the HgII ion with various binding modes including N3-HgII-N3, N4-HgII-N3, O2-HgII-N3 and N3-HgII-O4. Our studies also reveal that the overall conformations of the C-HgII-T and T-HgII-T pairs are affected by their neighboring residues via the interactions with the solvent molecules or other metal ions, such as SrII. These results provide detailed insights into the interactions between HgII and nucleobases and the structural basis for the rational design of C-HgII-T or T-HgII-T containing DNA nanodevices in the future.
authors.affiliation: State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200433, China.|State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China.
authors.forename: Hehua
authors.initials: H
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200433, China.
authors.forename: Chen
authors.initials: C
authors.lastname: Cai
authors.affiliation: Department of Chemistry and The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA.
authors.forename: Phensinee
authors.initials: P
authors.lastname: Haruehanroengra
authors.affiliation: State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China.
authors.forename: Qingqing
authors.initials: Q
authors.lastname: Yao
authors.affiliation: State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200433, China.
authors.forename: Yiqing
authors.initials: Y
authors.lastname: Chen
authors.affiliation: State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200433, China.
authors.forename: Chun
authors.initials: C
authors.lastname: Yang
authors.affiliation: State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China.
authors.forename: Qiang
authors.initials: Q
authors.lastname: Luo
authors.affiliation: State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China.
authors.forename: Baixing
authors.initials: B
authors.lastname: Wu
authors.affiliation: State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200433, China.
authors.forename: Jixi
authors.initials: J
authors.lastname: Li
authors.affiliation: State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China.
authors.forename: Jinbiao
authors.initials: J
authors.lastname: Ma
authors.affiliation: Department of Chemistry and The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA.
authors.forename: Jia
authors.initials: J
authors.lastname: Sheng
authors.affiliation: State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200433, China.
authors.forename: Jianhua
authors.initials: J
authors.lastname: Gan
mesh_terms: D020029:Base Pairing; D003596:Cytosine / Q000737:chemistry*; D004247:DNA / Q000737:chemistry*; D008628:Mercury / Q000737:chemistry*; D008958:Models, Molecular; D012997:Solvents / Q000737:chemistry; D013324:Strontium / Q000737:chemistry; D013941:Thymine / Q000737:chemistry*
chemical_list: D012997:Solvents; D003596:Cytosine; D004247:DNA; D008628:Mercury; D013941:Thymine; D013324:Strontium