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Flexibility and stabilization of HgII-mediated C:T and T:T base pairs in DNA duplex.

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Liu H, Cai C, Haruehanroengra P, Yao Q, Chen Y, Yang C, Luo Q, Wu B, Li J, Ma J, Sheng J, Gan J
OpenAccess logo Nucleic Acids Res 45 2910-2918 (2017)
Related entries: 5gsk, 5wsq, 5wsr, 5wss

Cited: 15 times
EuropePMC logo PMID: 27998930

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.

Articles - 5wsp mentioned but not cited (2)

  1. Flexibility and stabilization of HgII-mediated C:T and T:T base pairs in DNA duplex. Liu H, Cai C, Haruehanroengra P, Yao Q, Chen Y, Yang C, Luo Q, Wu B, Li J, Ma J, Sheng J, Gan J. Nucleic Acids Res 45 2910-2918 (2017)
  2. Structural variability of CG-rich DNA 18-mers accommodating double T-T mismatches. Kolenko P, Svoboda J, Černý J, Charnavets T, Schneider B. Acta Crystallogr D Struct Biol 76 1233-1243 (2020)


Reviews citing this publication (1)

  1. A survey of recent unusual high-resolution DNA structures provoked by mismatches, repeats and ligand binding. Satange R, Chang CK, Hou MH. Nucleic Acids Res 46 6416-6434 (2018)

Articles citing this publication (12)

  1. Crystal structure of a DNA duplex containing four Ag(i) ions in consecutive dinuclear Ag(i)-mediated base pairs: 4-thiothymine-2Ag(i)-4-thiothymine. Kondo J, Sugawara T, Saneyoshi H, Ono A. Chem Commun (Camb) 53 11747-11750 (2017)
  2. Concerted dynamics of metallo-base pairs in an A/B-form helical transition. Schmidt OP, Jurt S, Johannsen S, Karimi A, Sigel RKO, Luedtke NW. Nat Commun 10 4818 (2019)
  3. Concomitant Site-Specific Incorporation of Silver(I) and Mercury(II) Ions into a DNA Duplex. Jash B, Müller J. Chemistry 24 10636-10640 (2018)
  4. HgII binds to C-T mismatches with high affinity. Schmidt OP, Benz AS, Mata G, Luedtke NW. Nucleic Acids Res 46 6470-6479 (2018)
  5. 2'-O,4'-C-Methylene-Bridged Nucleic Acids Stabilize Metal-Mediated Base Pairing in a DNA Duplex. Nakagawa O, Fujii A, Kishimoto Y, Nakatsuji Y, Nozaki N, Obika S. Chembiochem 19 2372-2379 (2018)
  6. Chiral-at-Metal Silver-Mediated Base Pairs: Metal-Centred Chirality versus DNA Helical Chirality. Lefringhausen N, Seiffert V, Erbacher C, Karst U, Müller J. Chemistry 29 e202202630 (2023)
  7. Highly sensitive and selective mercury sensor based on mismatched base pairing with dioxT. Han JH, Hirashima S, Park S, Sugiyama H. Chem Commun (Camb) 55 10245-10248 (2019)
  8. Stable Hg(II)-mediated base pairs with a phenanthroline-derived nucleobase surrogate in antiparallel-stranded DNA. Jash B, Müller J. J Biol Inorg Chem 25 647-654 (2020)
  9. Synthesis and Enzymatic Incorporation of a Responsive Ribonucleoside Probe That Enables Quantitative Detection of Metallo-Base Pairs. Manna S, Srivatsan SG. Org Lett 21 4646-4650 (2019)
  10. "Metal-modified base pairs" vs. "metal-mediated pairs of bases": not just a semantic issue! Lippert B. J Biol Inorg Chem 27 215-219 (2022)
  11. Crystal structures and identification of novel Cd2+-specific DNA aptamer. Liu H, Gao Y, Mathivanan J, Armour-Garb Z, Shao Z, Zhang Y, Zhao X, Shao Q, Zhang W, Yang J, Cao C, Li H, Sheng J, Gan J. Nucleic Acids Res 51 4625-4636 (2023)
  12. Multistage dynamics of Hg2+-DNA interactions: a single-molecule study. Liu KT, Ran SY. Phys Chem Chem Phys 21 2919-2928 (2019)


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