Effects of metal ions on thermal stabilities of DNA duplexes containing homo- and heterochiral mismatched base pairs: comparison of internal and terminal substitutions

References

• (a) Clever, G. H.; Kaul, C.; Carell, T. DNA–Metal Base Pairs. Angew. Chem. Int. Ed. 2007, 46, 6226–6236.
   PubMed Web of Science ®Google Scholar
  (b) Takezawa, Y.; Shionoya, M. Metal-Mediated DNA Base Pairing: Alternatives to Hydrogen-Bonded Watson–Crick Base Pairs. Acc. Chem. Res. 2012, 45, 2066–2076.
   PubMed Web of Science ®Google Scholar
  (c) Biswarup, J.; Müller, J. Metal-Mediated Base Pairs: From Characterization to Application. Chem. Eur. J. 2017, 23, 17166–17178.
   PubMed Web of Science ®Google Scholar
  (d) Takezawa, Y.; Müller, J.; Shionoya, M. Artificial DNA Base Pairing Mediated by Diverse Metal Ions. Chem. Lett. 2017, 46, 622–633.
   Web of Science ®Google Scholar
  (e) Müller, J. Nucleic Acid Duplexes with Metal-Mediated Base Pairs and Their Structures. Coordination Chem. Rev. 2019, 393, 37–47.
   Web of Science ®Google Scholar
  (f) Tanaka, K.; Shionoya, M. Synthesis of a Novel Nucleoside for Alternative DNA Base Pairing through Metal Complexation. J. Org. Chem. 1999, 64, 5002–5003.
   Web of Science ®Google Scholar
  (g) Atwell, S.; Meggers, E.; Spraggon, G.; Schultz, P. G. Structure of a Copper- Mediated Base Pair in DNA. J. Am. Chem. Soc. 2001, 123, 12364–12367.
   PubMed Web of Science ®Google Scholar
  (h) Switzer, C.; Shinha, S.; Kim, P. H.; Heuberger, B. D. A Purine-like Nickel(II) Base Pair for DNA. Angew. Chem. Int. Ed. 2005, 44, 1529–1532.
   PubMed Web of Science ®Google Scholar
  (i) Tanaka, K.; Yamada, Y.; Shionoya, M. Formation of Silver(I)-Mediated DNA Duplex and Triplex through an Alternative Base Pair of Pyridine Nucleobases. J. Am. Chem. Soc. 2002, 124, 8802–8803.
   PubMed Web of Science ®Google Scholar
  (j) Takezawa, Y.; Maeda, W.; Tanaka, K.; Shionoya, M. Discrete Self-Assembly of Iron(III) Ions inside Triple-Stranded Artificial DNA. Angew. Chem. Int. Ed. 2009, 48, 1081–1084.
   PubMed Web of Science ®Google Scholar
  (k) Clever, G. H.; Carell, T. Controlled Stacking of 10 Transition-Metal Ions inside a DNA Duplex. Angew. Chem. Int. Ed. 2007, 46, 250–253.
   PubMed Web of Science ®Google Scholar
  (l) Johannsen, S.; Megger, N.; Böhme, D.; Sigel, R. K. O.; Müller, J. Solution Structure of a DNA Double Helix with Consecutive Metal-Mediated Base Pairs. Nat. Chem. 2010, 2, 229–234.
   PubMed Web of Science ®Google Scholar
  (m) Takezawa, Y.; Nishiyama, K.; Mashima, T.; Katahira, M.; Shionoya, M. Bifacial Base-Pairing Behaviors of 5-Hydroxyuracil DNA Bases through Hydrogen Bonding and Metal Coordination. Chem. Eur. J. 2015, 21, 14713–14716.
   PubMed Web of Science ®Google Scholar
  (n) Sinha, I.; Fonsecaguerra, C.; Müller, J. A Highly Stabilizing Silver(I)-Mediated Base Pair in Parallel-Stranded DNA. Angew. Chem. Int. Ed. 2015, 54, 3603–3606.
   PubMed Web of Science ®Google Scholar
  (o) Santamaria-Diaz, N.; Méndez-Arriaga, J. M.; Salas, J. M.; Galindo, M. A. Highly Stable Double-Stranded DNA Containing Sequential Silver(I)-Mediated 7-Deazaadenine/Thymine Watson–Crick Base Pairs. Angew. Chem. Int. Ed. 2016, 55, 6170–6174.
   PubMed Web of Science ®Google Scholar
  (p) Nakagawa, O.; Fujii, A.; Kishimoto, Y.; Nakatsuji, Y.; Nozaki, N.; Obika, S. 2′-O,4′-C-Methylene-Bridged Nucleic Acids Stabilize Metal-Mediated Base Pairing in a DNA Duplex. ChemBioChem 2018, 19, 2372–2379.
   PubMed Web of Science ®Google Scholar
  (q) Jash, B.; Müller, J. Stable Copper(I)-Mediated Base Pairing in DNA. Angew. Chem. Int. Ed. 2018, 57, 9524–9527.
   PubMed Web of Science ®Google Scholar
  (r) Jash, B.; Müller, J. A Stable Zinc(II)-Mediated Base Pair in a Parallel-Stranded DNA Duplex. J. Inorg. Biochem. 2018, 186, 301–306. DOI: 10.1016/j.jinorgbio.2018.07.002.
   PubMed Web of Science ®Google Scholar
• (a) Freeman, R.; Finder, T.; Willner, I. Multiplexed Analysis of Hg2+ and Ag + Ions by Nucleic Acid Functionalized CdSe/ZnS Quantum Dots and Their Use for Logic Gate Operations. Angew. Chem. Int. Ed. 2009, 48, 7818–7821.
   PubMed Web of Science ®Google Scholar
  (b) Park, K. S.; Jung, C.; Park, H. G. “Illusionary” Polymerase Activity Triggered by Metal Ions: Use for Molecular Logic-Gate Operations. Angew. Chem. Int. Ed. 2010, 49, 9757–9760.
   PubMed Web of Science ®Google Scholar
  (c) Pei, H.; Liang, L.; Yao, G.; Li, J.; Huang, Q.; Fan, C. Reconfigurable Three-Dimensional DNA Nanostructures for the Construction of Intracellular Logic Sensors. Angew. Chem. Int. Ed. 2012, 51, 9020–9024.
   PubMed Web of Science ®Google Scholar
  (d) Kanayama, N.; Takarada, T.; Fujita, M.; Maeda, M. DNA Terminal Breathing Regulated by Metal Ions for Colloidal Logic Gates. Chem. Eur. J. 2013, 19, 10794–10798.
   PubMed Web of Science ®Google Scholar
  (e) Bi, S.; Ji, B.; Zhang, Z.; Zhu, J.-J. Metal Ions Triggered Ligase Activity for Rolling Circle Amplification and its Application in Molecular Logic Gate Operations. Chem. Sci. 2013, 4, 1858–1863.
   Web of Science ®Google Scholar
  (f) Ma, D.-L.; Lin, S.; Lu, L.; Wang, M.; Hu, C.; Liu, L.-J.; Ren, K.; Leung, C.-H. G-Quadruplex-Based Logic Gates for HgII and AgI Ions Employing a Luminescent Iridium(III) Complex and Extension of Metal-Mediated Base Pairs by Polymerase. J. Mater. Chem. B 2015, 3, 4780–4785.
   PubMed Web of Science ®Google Scholar
  (g) Gao, W.; Zhang, L.; Liang, R.-P.; Qiu, J.-D. Metal-Ion-Triggered Exonuclease III Activity for the Construction of DNA Colorimetric Logic Gates. Chem. Eur. J. 2015, 21, 15272–15279.
   PubMed Web of Science ®Google Scholar
  (h) Park, K. S.; Lee, C. Y.; Park, H. G. Metal Ion Triggers for Reversible Switching of DNA Polymerase. Chem. Commun. 2016, 52, 4868–4871.
   PubMed Web of Science ®Google Scholar
  (i) Cheng, N.; Zhu, P.; Xu, Y.; Huang, K.; Luo, Y.; Yang, Z.; Xu, W. High-Sensitivity Assay for Hg (II) and Ag (I) Ion Detection: A New Class of Droplet Digital PCR Logic Gates for an Intelligent DNA Calculator. Biosens. Bioelectron. 2016, 84, 1–6.
   PubMed Web of Science ®Google Scholar
• (a) Tanaka, K.; Tengeiji, A.; Kato, T.; Toyama, N.; Sionoya, M. A Discrete Self- Assembled Metal Array in Artificial DNA. Science 2003, 299, 1212–1213.
   PubMed Web of Science ®Google Scholar
  (b) Tanaka, K.; Clever, G. H.; Takezawa, Y.; Yamada, Y.; Kaul, C.; Shionoya, M.; Carell, T. Programmable Self-Assembly of Metal Ions Inside Artificial DNA Duplexes. Nat. Nanotechnol. 2006, 1, 190–194.
   PubMed Web of Science ®Google Scholar
  (c) Liu, S.; Clever, G. H.; Takezawa, Y.; Kaneko, M.; Tanaka, K.; Guo, X.; Shionoya, M. Direct Conductance Measurement of Individual Metallo-DNA Duplexes within Single-Molecule Break Junctions. Angew. Chem. Int. Ed. 2011, 50, 8886–8890.
   PubMed Web of Science ®Google Scholar
  (d) Kondo, J.; Tada, Y.; Dairaku, T.; Hattori, Y.; Saneyoshi, H.; Ono, A.; Tanaka, Y. A Metallo-DNA Nanowire with Uninterrupted One-Dimensional Silver Array. Nat. Chem. 2017, 9, 956–960.
   PubMed Web of Science ®Google Scholar
  (e) Vecchion, S.; Capece, M. C.; Toomey, E.; Ngyuyen, L.; Ray, A.; Greenberg, A.; Fujishima, K.; Urbina, J.; Paulino-Lima, I. G.; Pinheiro, V.; et al. Construction and Characterization of Metal Ion-Containing DNA Nanowires for Synthetic Biology and Nanotechnology. Sci. Rep. 2019, 9:6942.
   PubMed Web of Science ®Google Scholar
• Clever, G. H.; Reitmeier, S. J.; Carell, T.; Schiemann, O. Antiferromagnetic Coupling of Stacked CuII–Salen Complexes in DNA. Angew. Chem. Int. Ed. Engl. 2010, 49, 4927–4929. DOI: 10.1002/anie.200906359.
   PubMed Web of Science ®Google Scholar
• Kuzuya, A.; Sakai, Y.; Yamazaki, T.; Xu, Y.; Komiyama, M. Nanomechanical DNA Origami ‘Single-Molecule Beacons’ Directly Imaged by Atomic Force Microscopy. Nat. Commun. 2011, 2, 449. DOI: 10.1038/ncomms1452.
   PubMed Web of Science ®Google Scholar
• (a) Ono, A.; Togashi, H. Highly Selective Oligonucleotide-Based Sensor for Mercury(II) in Aqueous Solutions. Angew. Chem. Int. Ed. 2004, 43, 4300–4302.
   PubMed Web of Science ®Google Scholar
  (b) Lee, J.-S.; Han, M. S.; Mirkin, C. A. Colorimetric Detection of Mercuric Ion (Hg2+) in Aqueous Media using DNA-Functionalized Gold Nanoparticles. Angew. Chem. Int. Ed. 2007, 46, 4093–4096.
   PubMed Web of Science ®Google Scholar
  (c) Liu, J.; Liu, Y. Rational Design of “Turn-On” Allosteric DNAzyme Catalytic Beacons for Aqueous Mercury Ions with Ultrahigh Sensitivity and Selectivity. Angew. Chem. Int. Ed. 2007, 46, 7587–7590.
   PubMed Web of Science ®Google Scholar
  (d) Zhu, G.; Li, Y.; Zhang, C.-y. Simultaneous Detection of Mercury(II) and Silver(I) Ions with Picomolar Sensitivity. Chem. Commun. 2014, 50, 572–574.
   PubMed Web of Science ®Google Scholar
  (e) Qi, L.; Xiao, M.; Wang, F.; Wang, L.; Ji, W.; Man, T.; Aldalbahi, A.; Naziruddin, K. M.; Periyasami, G.; Rahaman, M.; et al. Polycytosine-Mediated Nanotags for SERS Detection of Hg2+. Nanoscale 2017, 9, 14184–14191.
   PubMed Web of Science ®Google Scholar
• (a) Kaul, C.; Müller, M.; Wagner, M.; Schneider, S.; Carell, T. Reversible Bond Formation Enables the Replication and Amplification of a Crosslinking Salen Complex as an Orthogonal Base Pair. Nat. Chem. 2011, 3, 794–800.
   PubMed Web of Science ®Google Scholar
  (b) Kim, E. K.; Switzer, C. Polymerase Recognition of a Watson–Crick-Like Metal-Mediated Base Pair: Purine-2,6-Dicarboxylate • Copper(II) • Pyridine. ChemBioChem 2013, 14, 2403–2407.
   PubMed Web of Science ®Google Scholar
• (a) Miyake, Y.; Togashi, H.; Tashiro, M.; Yamaguchi, H.; Oda, S.; Kudo, M.; Tanaka, Y.; Kondo, Y.; Sawa, R.; Fujimoto, T.; et al., MercuryII-Mediated Formation of Thymine-HgII-Thymine Base Pairs in DNA Duplexes. J. Am. Chem. Soc. 2006, 128, 2172–2173.
   PubMed Web of Science ®Google Scholar
  (b) Tanaka, Y.; Oda, S.; Yamaguchi, H.; Kondo, Y.; Kojima, C.; Ono, A. 15N–15N J-Coupling Across HgII: Direct Observation of HgII-Mediated T–T Base Pairs in a DNA Duplex. J. Am. Chem. Soc. 2007, 129, 244–245.
   PubMed Web of Science ®Google Scholar
  (c) Yamaguchi, H.; Šebera, J.; Kondo, J.; Oda, S.; Komuro, S.T.; Kawamura, T.; Dairaku, T.; Kondo, Y.; Okamoto, I.; Ono, A.; et al. The Structure of Metallo-DNA with Consecutive Thymine–HgII-Thymine Base Pairs Explains Positive Entropy for the Metallo Base Pair Formation. Nucleic Acid Res. 2014, 42, 4094–4099.
   PubMed Web of Science ®Google Scholar
  (d) Kondo, J.; Yamada, T.; Hirose, C.; Okamoto, I.; Tanaka, Y.; Ono, A. Crystal Structure of Metallo DNA Duplex Containing Consecutive Watson–Crick-like T–HgII–T Base Pairs. Angew. Chem. Int. Ed. 2014, 9, 2385–2388.
   Google Scholar
• (a) Ono, A.; Cao, S.; Togashi, H.; Tashiro, M.; Fujimoto, T.; Machinami, T.; Oda, S.; Miyake, Y.; Okamoto, I.; Tanaka, Y. Specific Interactions Between Silver(I) Ions and Cytosine–Cytosine Pairs in DNA Duplexes. Chem. Commun. 2008, 4825–4827.
   PubMed Web of Science ®Google Scholar
  (b) Torigoe, H.; Okamoto, I.; Dairaku, T.; Tanaka, Y.; Ono, A.; Kozasa, T. Thermodynamic and Structural Properties of the Specific Binding Between Ag+ Ion and C:C Mismatched Base Pair in Duplex DNA to form C–Ag–C Metal-Mediated Base Pair. Biochimie 2012, 94, 2431–2440.
   PubMed Web of Science ®Google Scholar
  (c) Kondo, J.; Tada, Y.; Dairaku, T.; Saneyoshi, H.; Okamoto, I.; Tanaka, Y.; Ono, A. High-Resolution Crystal Structure of a Silver(I)–RNA Hybrid Duplex Containing Watson–Crick-like C–Silver(I)–C Metallo-Base Pairs. Angew. Chem. Int. Ed. 2015, 45, 13323–13326.
   Google Scholar
  (d) Dairaku, T.; Furuita, K.; Sato, H.; Severa, J.; Nakashima, K.; Kondo, J.; Ymanaka, D.; Kondo, Y.; Okamoto, I.; Ono, A.; et al. Structure Determination of an AgI-Mediated Cytosine–Cytosine Base Pair within DNA Duplex in Solution with 1H/15N/109Ag NMR Spectroscopy. Chem. Eur. J. 2016, 22, 13208–13031.
   Web of Science ®Google Scholar
• Tanaka, Y.; Kondo, J.; Sychrovsky, V.; Šebera, J.; Dairaku, T.; Saneyoshi, H.; Urata, H.; Torigoe, H.; Ono, A. Structures, Physicochemical Properties, and Applications of T–HgII–T, C–AgI–C, and other Metallo-Base-Pairs. Chem. Commun. 2015, 51, 17343–17360. DOI: 10.1039/c5cc02693h.
   PubMed Web of Science ®Google Scholar
• (a) Funai, T.; Miyazaki, Y.; Aotani, M.; Yamaguchi, E.; Nakagawa, O.; Wada, S.; Torigoe, H.; Ono, A.; Urata, H. AgI Ion Mediated Formation of a C–A Mispair by DNA Polymerases. Angew. Chem. Int. Ed. 2012, 51, 6464–6466.
   PubMed Web of Science ®Google Scholar
  (b) Yang, H.; Seela, F. Silver Ions in Non-canonical DNA Base Pairs: Metal-Mediated Mismatch Stabilization of 2′-Deoxyadenosine and 7-Deazapurine Derivatives with 2′-Deoxycytidine and 2′-Deoxyguanosine. Chem. Eur. J. 2016, 22, 13336–13346.
   PubMed Web of Science ®Google Scholar
• (a) Urata, H.; Yamaguchi, E.; Nakamura, Y.; Wada, S.; Pyrimidine–Pyrimidine Base Pairs Stabilized by Silver(I) Ions. Chem. Commun. 2011, 47, 941–943.
   PubMed Web of Science ®Google Scholar
  (b) Ono, A.; Torigoe, H.; Tanaka, Y.; Okamoto, I. Binding of Metal Ions by Pyrimidine Base Pairs in DNA Duplexes. Chem. Soc. Rev. 2011, 40, 5855–5866.
   PubMed Web of Science ®Google Scholar
• (a) Urata, H.; Shinohara, K.; Ogura, E.; Ueda, Y.; Akagi, M. Mirror-image DNA. J. Am. Chem. Soc. 1991, 113, 8174–8175.
   Web of Science ®Google Scholar
  (b) Urata, H.; Ogura, E.; Shinohara, K.; Ueda, Y.; Akagi, M. Synthesis and Properties of Mirror-Image DNA. Nucleic Acids Res. 1992, 20, 3325–3332. DOI: 10.1093/nar/20.13.3325.
   PubMed Web of Science ®Google Scholar
• Urata, H.; Kumashiro, T.; Kawahata, T.; Otake, T.; Akagi, M. Anti-HIV-1 Activity and Mode of Action of Mirror Image Oligodeoxynucleotide Analogue of Zintevir. Anti-HIV-1 Activity and Mode of Action of Mirror Image Oligodeoxynucleotide Analogue of Zintevir. Biochem. Biophys. Res. Commun. 2004, 313, 55–61. DOI: 10.1016/j.bbrc.2003.11.094.
   PubMed Web of Science ®Google Scholar
• (a) Williams, K. P.; Liu, X.-H.; Schumacher, T. N. M.; Lin, H. Y.; Ausiello, D. A.; Kim, P. S.; Bartel, D. P. Bioactive and Nuclease-Resistant l-DNA Ligand of Vasopressin. Proc. Natl. Acid. Sci. USA. 1997, 94, 11285–11290.
   PubMed Web of Science ®Google Scholar
  (b) Purschke, W. G.; Radtke, F.; Kleinjung, F.; Klussmann, S. A DNA Spiegelmer to Staphylococcal Enterotoxin B. Nucleic Acids Res. 2003, 31, 3027–3032.
   PubMed Web of Science ®Google Scholar
  (c) Sczepanski, J. T.; Joyce, G. F. Binding of a Structured d-RNA Molecule by an l-RNA Aptamer. J. Am. Chem. Soc. 2013, 135, 13290–13293.
   PubMed Web of Science ®Google Scholar
  (d) Yatime, L.; Maasch, C.; Hoehilg, K.; Klussmann, S.; Andersen, G. R.; Vater, A. Structural Basis for the Targeting of Complement Anaphylatoxin C5a Using a Mixed L-RNA/L-DNA Aptamer. Nat. Commun. 2015, 6:6481.
   PubMed Web of Science ®Google Scholar
  (e) Oberthür, D.; Achenbach, J.; Gadbulkhakov, A.; Buchner, K.; Maasch, C.; Falke, S.; Rehders, D.; Klussmann, S.; Betzel, C. Crystal Structure of a Mirror-Image L-RNA Aptamer (Spiegelmer) in Complex with the Natural L-Protein Target CCL2. Nat. Commun. 2015, 6:6923. DOI: 10.1038/ncomms7923.
   PubMed Web of Science ®Google Scholar
• (a) Cui, L.; Peng, R.; Fu, T.; Zhang, X.; Wu, C.; Chen, H.; Liang, H.; Yang, C. J.; Tan, W. Biostable L-DNAzyme for Sensing of Metal Ions in Biological Systems. Anal. Chem. 2016, 88, 1850–1855.
   PubMed Web of Science ®Google Scholar
  (b) Liang, H.; Xie, S.; Cui, L.; Wu, C.; Zhang, X. Designing a Biostable L-DNAzyme for Lead(II) Ion Detection in Practical Samples. Anal. Methods 2016, 8, 7260–7264. DOI: 10.1039/C6AY01791F.
   PubMed Web of Science ®Google Scholar
• Kim, K.-R.; Lee, T.; Su. Kim, B.; Ahn, D.-R. Utilizing the Bioorthogonal Basepairing System of L-DNA to Design Ideal DNA Nanocarriers for Enhanced Delivery of Nucleic Acid Cargos. Chem. Sci. 2014, 5, 1533–1537. DOI: 10.1039/C3SC52601A.
   Web of Science ®Google Scholar
• Lin, C.; Ke, Y.; Li, Z.; Wang, H.; Liu, Y.; Yan, H. Mirror Image DNA Nanostructures for Chiral Supramolecular Assemblies. Nano Lett. 2009, 9, 433–436. DOI: 10.1021/nl803328v.
   PubMed Web of Science ®Google Scholar
• Ke, G.; Wang, C.; Ge, Y.; Zheng, N.; Zhu, Z.; Yang, C. J. l-DNA Molecular Beacon: A Safe, Stable, and Accurate Intracellular Nano-thermometer for Temperature Sensing in Living Cells. J. Am. Chem. Soc. 2012, 134, 18908–18911. DOI: 10.1021/ja3082439.
   PubMed Web of Science ®Google Scholar
• Garbesi, A.; Capobianco, M. L.; Colonna, F. P.; Tondelli, L.; Arcamone, F.; Manzini, G.; Hilbers, C. W.; Aelen, J. M.; Blommers, M. J. L-DNAs as Potenital Antimessenger Oligonucleotides: A Reassessment. Nucleic Acids Res. 1993, 21, 4159–4165. DOI: 10.1093/nar/21.18.4159.
   PubMed Web of Science ®Google Scholar
• (a) Urata, H.; Ueda, Y.; Suhara, H.; Nishioka, E.; Akagi, M. NMR Study of a Heterochiral DNA: Stable Watson-Crick-type Base-Pairing Between the Enantiomeric Residues. J. Am. Chem. Soc. 1993, 115, 9852–9853.
   Web of Science ®Google Scholar
  (b) Damha, M. J.; Giannaris, P. A.; Marfey, P. Antisense L/D-Oligodeoxynucleotide Chimeras: Nuclease Stability, Base-Pairing Properties, and Activity at Directing Ribonuclease H. Biochemistry 1994, 33, 7877–7885.
   PubMed Web of Science ®Google Scholar
  (c) Urata, H.; Shimizu, H.; Hiroaki, H.; Kohada, D.; Akagi, M. Thermodynamic Study of Hybridization Properties of Heterochiral Nucleic Acids. Biochem. Biophys. Res. Commum. 2003, 309, 79–83.
   PubMed Web of Science ®Google Scholar
  (d) Kawakami, J.; Tsujita, K.; Sugimoto, N. Thermodynamic Analysis of Duplex Formation of the Heterochiral DNA with L-Deoxyadenosine. Anal. Sci. 2005, 21, 77–82.
   PubMed Web of Science ®Google Scholar
• Ogawa, S.; Wada, S.; Urata, H. Base Recognition by L-nucleotides in Heterochiral DNA. RSC Adv. 2012, 2, 2274–2275.
   Web of Science ®Google Scholar
  (Ogawa, S.; Wada, S.; Urata, H. RSC Adv. 2019, 9, 9692–9693.)
   Web of Science ®Google Scholar
• Urata, H.; Ogawa, S.; Wada, S. Thermal Stability of Oligodeoxynucleotide Duplexes Containing l-deoxynucleotide at Termini. Bioorg. Med. Chem. Lett. 2013, 23, 2909–2911. DOI: 10.1016/j.bmcl.2013.03.058.
   PubMed Web of Science ®Google Scholar
• Schmidt, O. P.; Benz, A. S.; Mata, G.; Luedtke, N. W. HgII Binds to C–T Mismatches with High Affinity. Nucleic Acids Res. 2018, 46, 6470–6479. DOI: 10.1093/nar/gky499.
   PubMed Web of Science ®Google Scholar
• (a) Patel, D. J.; Hilbers, C. W. Proton Nuclear Magnetic Resonance Investigations of Fraying in Double-Stranded d-ApTpGpCpApT in Aqueous Solution. Biochemistry 1975, 12, 2651–2656.
   Google Scholar
  (b) Nonin, S.; Leroy, J.-L.; Guéron, M. Terminal Base Pairs of Oligodeoxynucleotides: Imino Proton Exchange and Fraying. Biochemistry 1995, 34, 10652–10659.
   PubMed Web of Science ®Google Scholar
  (c) Ferreira, I.; Amarante, T. D.; Weber, G. DNA Terminal Base Pairs have Weaker Hydrogen Bonds Especially for AT under Low Salt Concentration. J. Chem. Phys. 2015, 143, 175101–175104.
   PubMed Web of Science ®Google Scholar
  (d) Zgabova, M.; Otyepka, M.; Šponer, J.; Lankaš, F.; Jurečka, P. Base Pair Fraying in Molecular Dynamics Simulations of DNA and RNA. J. Chem. Theory Comput. 2014, 10, 3177–3189.
   PubMedGoogle Scholar
• Colizzi, F.; Bussi, G. RNA Unwinding from Reweighted Pulling Simulations. J. Am. Chem. Soc. 2012, 134, 5173–5179. DOI: 10.1021/ja210531q.
   PubMed Web of Science ®Google Scholar
• Taherpour, S.; Lönnberg, H.; Lönnberg, T. 2,6-Bis(Functionalized) Purines as Metal-Ion-Binding Surrogate Nucleobases that Enhance Hybridization with Unmodified 2′-O-Methyl Oligoribonucleotides. Org. Biomol. Chem. 2013, 11, 991–1000. DOI: 10.1039/c2ob26885j.
   PubMed Web of Science ®Google Scholar
• (a) Bleczinski, C. F.; Richert, C. Steroid–DNA Interactions Increasing Stability, Sequence-Selectivity, DNA/RNA Discrimination, and Hypochromicity of Oligonucleotide Duplexes. J. Am. Chem. Soc. 1999, 121, 10889–10894.
   Web of Science ®Google Scholar
  (b) Patra, A.; Richert, C. High Fidelity Base Pairing at the 3′-Terminus. J. Am. Chem. Soc. 2009, 131, 12671–12681.
   PubMed Web of Science ®Google Scholar
  (c) Egetenmeyr, S.; Richert, C. A 5′-Cap for DNA Probes Binding RNA Target Strands. Chem. Eur. J. 2011, 17, 11813–11827. DOI: 10.1002/chem.201101828.
   PubMed Web of Science ®Google Scholar