Structural and Magnetic Properties of a Variety of Transition Metal Incorporated DNA Double Helices

Abstract

By using density functional theory calculations, the structural, energetic, magnetic, and optical properties for a variety of transition metal (M = Mn, Fe, Co, Ni and Cu) ions incorporated modified-DNA (M-DNA) double helices has been investigated. The DNA is modified with either hydroxypyridone (H) or bis(salicylaldehyde)ethylenediamine (S-en) metalated bases. We find the formation of extended M-O network leading to the ferromagnetic interactions for the case of H-DNA for all the metal ions. More ordered stacking arrangement was found for S-en-DNA. We calculate the exchange coupling constant (J) considering Heisenberg Hamiltonian for quantitative description of magnetic interactions. The ferromagnetic and antiferromagnetic interactions are obtained by varying different transition metal ions. The extent of the magnetic interaction depends on the number of transition metal ions. Optical profiles show peaks below 2 eV, a clear signature of spin-spin coupling.

Sequence-specific recognition of DNA minor groove by an NIR-fluorescence switch-on probe and its potential applications

“…Two possible modes (intercalation and groove binding) were considered for the binding of the bent QCy–DT to duplex DNA. The DNA phosphate backbone was neutralized by adding hydrogen to one of the oxygen atoms of the phosphate groups that would not alter any property of the duplex DNA structure ( 52 , 53 ). To calculate the binding energies of QCy–DT with DNA, we chose AT- and GC-rich duplexes (A/T and G/C) for each of these modes (supplementary Table S5).…”

A Thiazole Coumarin (TC) Turn-On Fluorescence Probe for AT-Base Pair Detection and Multipurpose Applications in Different Biological Systems

“…We used 6-31g(d) basis set for all the atoms (see supplementary information). The DNA phosphate backbone was neutralized by protonating one of the oxygen atoms of the phosphate groups, which does not alter any property of the DNA duplex structure434445. The DFT and TD-DFT calculations were performed with surrounding water, using a Polarized Continuum Model (PCM) to include the solvent (water) effect.…”

Structures, physicochemical properties, and applications of T–HgII–T, C–AgI–C, and other metallo-base-pairs

“…81 The rational design and optimisation of metallo-DNAs for their use in technological applications could be achieved through knowledge of their 3D structures and properties, as deduced from thermodynamic and spectroscopic parameters (see Sections 1.1 and 1.2 for currently available 3D structures of metallo-DNAs). 49,[82][83][84][85] The knowledge of the 3D structure of metallo-DNA containing Im-Ag I -Im base-pairs allowed for reliable TD-DFT calculations of electronic and optical properties. 85 The thorough structural characterisation of the T-Hg II -T basepair, employing spectroscopic data in conjunction with the 3D structure of metallo-DNA(T-Hg II -T), allowed us to calculate the thermodynamic parameters for the T-Hg II -T base-pairing by using the ONIOM (B3LYP:BP86) method (Table 4).…”