Differentiating a Least-Stable Single Nucleotide Mismatch
in DNA Via Metal Ion-Mediated Base Pairing and Using Thioflavin T
as an Extrinsic Fluorophore
posted on 2021-03-08, 21:06authored bySrikrishna Pramanik, Laxmikanta Khamari, Saptarshi Mukherjee
Monitoring
the DNA dynamics in solution has great potential to
develop new nucleic acid-based sensors and devices. With spectroscopic
approaches, both at the ensemble average and single-molecule resolution,
this study is directed to differentiate a single nucleotide mismatch
(SNM) via a metal ion-stabilized mismatched base-pairing (C–Ag+–C/C–Cu2+–T) (C = cytosine,
T = thymine) and site-selective extrinsic fluorophore, specifically,
Thioflavin T (ThT). This is the first approach of its kind where dynamic
quantities like molecular diffusion coefficients and diffusion times
have been utilized to distinguish the least-stable SNM (CC & CT)
formed by the most discriminating nucleobase, specifically, cytosine
in a 20-mer duplex DNA. Additionally, this work also quantifies metal
ions (Ag+ and Cu2+) at lower concentrations
using fluorescence correlation spectroscopy. Our results can provide
greater molecular-level insights into the mismatch-dependent metal–DNA
interactions and also illuminate ThT as a new fluorophore to monitor
the dynamics involved in DNA–metal composites.