HgII binds to C–T mismatches with high affinity. Issue 13 (13th June 2018)

• Record Type: Journal Article
• Authors: Schmidt, Olivia P; Benz, Andrea S; Mata, Guillaume; Luedtke, Nathan W
• Is Part Of: Nucleic acids research. Volume 46:Issue 13(2018)
• Page Start: 6470
• Page End: 6479
• Publication Date: 2018-06-13
• Subjects: Nucleic acids -- Periodicals; Molecular biology -- Periodicals; 572.805
• DOI: 10.1093/nar/gky499
• Languages: English
• ISSNs: 0305-1048

Abstract

Abstract: Binding reactions of Hg II and Ag I to pyrimidine-pyrimidine mismatches in duplex DNA were characterized using fluorescent nucleobase analogs, thermal denaturation and 1 H NMR. Unlike Ag I, Hg II exhibited stoichiometric, site-specific binding of C–T mismatches. The on- and off-rates of Hg II binding were approximately 10-fold faster to C–T mismatches ( k on ≈ 10 5 M −1 s −1, k off ≈ 10 −3 s −1 ) as compared to T–T mismatches ( k on ≈ 10 4 M −1 s −1, k off ≈ 10 −4 s −1 ), resulting in very similar equilibrium binding affinities for both types of 'all natural' metallo base pairs ( K d ≈ 10–150 nM). These results are in contrast to thermal denaturation analyses, where duplexes containing T–T mismatches exhibited much larger increases in thermal stability upon addition of Hg II (Δ T m = 6–19°C), as compared to those containing C–T mismatches (Δ T m = 1–4°C). In addition to revealing the high thermodynamic and kinetic stabilities of C–Hg II –T base pairs, our results demonstrate that fluorescent nucleobase analogs enable highly sensitive detection and characterization of metal-mediated base pairs – even in situations where metal binding has little or no impact on the thermal stability of the duplex.