Real-Time Study of Interactions between Cytosine–Cytosine Pairs in DNA Oligonucleotides and Silver Ions Using Dual Polarization Interferometry

Abstract

The real-time conformational changes of cytosine (C)-rich ssDNA oligonucleotides upon binding with silver ions (Ag(+)) were studied using dual polarization interferometry (DPI). Upon the addition of Ag(+), Ag(+) selectively bound to cytosine-cytosine mismatches and formed C-Ag(+)-C complexes, inducing change of the structure of the C-rich ssDNA from random coil conformation to duplex conformation, whereas the control ssDNA without cytosine-cytosine mismatches had no such signal, which was consistent with circular dichroism (CD) characterization. The conformational change of DNA was reflected on the changes of the mass, thickness, and density values resolved by DPI. The calibration curves showed that as the concentration of Ag(+) increased from 10 nM to 8 μM, the thickness and mass values increased linearly while the density values decreased linearly. Other metal ions such as K(+), Ca(2+), Na(+), Mg(2+), Zn(2+), Mn(2+), Ni(2+), and Pb(2+) did not interfere with the interaction between Ag(+) and C-rich ssDNA, indicating that this method had a good selectivity. The practical application of this biosensor was also investigated in real samples such as drinking water. Besides, cysteine could specifically capture Ag(+) from C-Ag(+)-C complexes and transformed the structure of the C-rich DNA back from rigid double-stranded conformation to random coil conformation, which allowed cysteine to be detected selectively as well. It is expected that this biosensing strategy may be utilized to study the interaction of DNA with other molecules.

Thioflavin T binds dimeric parallel-stranded GA-containing non-G-quadruplex DNAs: a general approach to lighting up double-stranded scaffolds

“…metal ions) to modulate the formation of parallel duplexes ( 36 ). As we know, Ag + can specifically interact with the C-C mismatches in a DNA duplex and improve the structural stability via the formation of C–Ag + –C base pairs ( 21 , 37 , 38 ). Accordingly, a novel fluorescent Ag + sensor is here constructed by introducing four C–C mismatches into the parallel duplex (GA) 3 -ps, whose fluorescence enhancement is highest after being assembled into parallel duplexes (see Supplementary Figure S9 in Supporting Information).…”

Bio-Recognition in Spectroscopy-Based Biosensors for *Heavy Metals-Water and Waterborne Contamination Analysis

“…DNAzymes have also been exploited for Ag + detection [56]. As known, the most studied interaction between DNA and Ag + is the specific binding with C residues [33,57,58]. This interaction was used to develop Ag + biosensors [56,59,60] and for the assembling of fluorescent Ag nanoclusters [61,62].…”

Dual polarization interferometry (DPI): a new tool in studying the biomolecular interaction

“…Hg 2+ 传感器的检测限达到27 nM. 利用DPI技术实时研 究了多胞嘧啶单链DNA与Ag + 的相互作用 [50] . [57,58] 图 5 DPI技术用于研究DNA与金属离子Hg 2+ [49] (a), Ag + [50] (b)和Pb 2+ [51] (c)的相互作用(网络版彩图)…”