Header

UZH-Logo

Maintenance Infos

HgII binds to C–T mismatches with high affinity


Schmidt, Olivia P; Benz, Andrea S; Mata, Guillaume; Luedtke, Nathan W (2018). HgII binds to C–T mismatches with high affinity. Nucleic Acids Research, 46(13):6470-6479.

Abstract

Binding reactions of HgII and AgI to pyrimidine-pyrimidine mismatches in duplex DNA were characterized using fluorescent nucleobase analogs, thermal denaturation and 1H NMR. Unlike AgI, HgII exhibited stoichiometric, site-specific binding of C–T mismatches. The on- and off-rates of HgII binding were approximately 10-fold faster to C–T mismatches (kon ≈ 105 M−1 s−1, koff ≈ 10−3 s−1) as compared to T–T mismatches (kon ≈ 104 M−1 s−1, koff ≈ 10−4 s−1), resulting in very similar equilibrium binding affinities for both types of ‘all natural’ metallo base pairs (Kd ≈ 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 HgII (ΔTm = 6–19°C), as compared to those containing C–T mismatches (ΔTm = 1–4°C). In addition to revealing the high thermodynamic and kinetic stabilities of C–HgII–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.

Abstract

Binding reactions of HgII and AgI to pyrimidine-pyrimidine mismatches in duplex DNA were characterized using fluorescent nucleobase analogs, thermal denaturation and 1H NMR. Unlike AgI, HgII exhibited stoichiometric, site-specific binding of C–T mismatches. The on- and off-rates of HgII binding were approximately 10-fold faster to C–T mismatches (kon ≈ 105 M−1 s−1, koff ≈ 10−3 s−1) as compared to T–T mismatches (kon ≈ 104 M−1 s−1, koff ≈ 10−4 s−1), resulting in very similar equilibrium binding affinities for both types of ‘all natural’ metallo base pairs (Kd ≈ 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 HgII (ΔTm = 6–19°C), as compared to those containing C–T mismatches (ΔTm = 1–4°C). In addition to revealing the high thermodynamic and kinetic stabilities of C–HgII–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.

Statistics

Citations

Altmetrics

Downloads

5 downloads since deposited on 07 Mar 2019
5 downloads since 12 months
Detailed statistics

Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:07 Faculty of Science > Department of Chemistry
Dewey Decimal Classification:540 Chemistry
Uncontrolled Keywords:Genetics
Language:English
Date:27 July 2018
Deposited On:07 Mar 2019 07:57
Last Modified:07 Mar 2019 08:11
Publisher:Oxford University Press
ISSN:0305-1048
OA Status:Gold
Publisher DOI:https://doi.org/10.1093/nar/gky499
Project Information:
  • : FunderSNSF
  • : Grant ID205320_165949
  • : Project TitleLive-cell imaging of DNA conformation and metabolism

Download

Download PDF  'HgII binds to C–T mismatches with high affinity'.
Preview
Content: Published Version
Filetype: PDF
Size: 2MB
View at publisher
Licence: Creative Commons: Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)