Understanding atomic bonding and electronic distributions of a DNA molecule using DFT calculation and BOLS-BC model

Deng, Anlin; Li, Hanze; Bo, Maolin; Huang, Zhongkai; Li, Lei; Yao, Chuang; Li, Fengqin

doi:10.1016/j.bbrep.2020.100804

Cited by 5 publications

(4 citation statements)

References 23 publications

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“…Spin‐polarized electronic calculations were performed using Density Functional Theory 34,35 within the generalized gradient approximation (GGA) using the PBE functional 36 as implemented in the SIESTA code 37 . Such functional was employed considering that it has been extensively used in previous similar studies 38,39 . The wave functions for the valence electrons were represented by a linear combination of pseudo‐atomic numerical orbitals using a double‐ζ polarized basis (DZP) 40 .…”

Section: Computational Detailsmentioning

confidence: 99%

“…37 Such functional was employed considering that it has been extensively used in previous similar studies. 38,39 The wave functions for the valence electrons were represented by a linear combination of pseudo-atomic numerical orbitals using a double-ζ polarized basis (DZP). 40 Norm-conserving Troullier-Martins pseudopotentials represented the core electrons in the Kleinman-Bylander non-local form.…”

Section: Introductionmentioning

confidence: 99%

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Electronic and magnetic properties of TATA‐DNA sequence driven by chemical functionalization

2023

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The TATA box is a promoter sequence able to interact directly with the components of the basal transcription initiation machinery. We investigate the changes in the electronic and magnetic properties of a TATA-DNA sequence when functionalized with different chemical groups; using the first-principles density functional theory specifically, the TATA-DNA sequences were functionalized with methyl groups (CH 3 , methylation), amino groups (NH 2 , amination), imine groups (NH, imination), chloroamine groups (NCl 2 , chloramination), H-adatom (hydrogenation), and Cl-adatom (chlorination). The functional groups were anchored at nitrogen atoms from adenine and oxygen atoms from thymine at sites pointed as reactive regions. We demonstrated that chemical functionalization induces significant changes in charge transfer, hydrogen bond distance, and hydrogen bond energy. The hydrogenation and imination increased the hydrogen bond energy. Results also revealed that the chemical functionalization of DNA molecules exhibit a ferromagnetic ground state, reaching magnetization up to 4.665 μ B and complex magnetic ordering. We further demonstrated that the functionalization could induce tautomerism (proton migration in the base pair systems). The present study provides a theoretical basis for understanding the functionalization further into DNA molecules and visualizing possible future applications.

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Section: Computational Detailsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Electronic and magnetic properties of TATA‐DNA sequence driven by chemical functionalization

2023

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“…Quantum chemistry provides chemists with critical insight into the electronic structure behavior of DNA or protein molecules, but its extensive computational requirements limit the scope and variety of systems that can be effectively analyzed. (64)(65)(66)(67)(68) The tight-binding (TB) method offers a more practical alternative for describing the electronic Hamiltonian using smaller and more sparse matrices. (69)(70)(71)(72)(73)(74) In early work, the TB model was applied to materials science or (75)(76)(77)(78)(79)(80)(81) Traditionally, the TB Hamiltonians have relied on empirical or semi-empirical parameters, which raises concerns about their accuracy and general applicability.…”

Section: Introductionmentioning

confidence: 99%

Elucidating Electronic Structure Variations in Nucleic Acid-Protein Complexes Involved in Transcription Regulation Using a Tight-Binding Approach

Du,

Liu

2024

Preprint

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Transcription factor (TF) are proteins that regulates the transcription of genetic information from DNA to messenger RNA by binding to a specific DNA sequence. Nucleic acid-protein interactions are crucial in regulating transcription in biological systems. This work presents a quick and convenient method for constructing tight-binding models and offers physical insights into the electronic structure properties of transcription factor complexes and DNA motifs. The tight binding Hamiltonian parameters are generated using the random forest regression algorithm, which reproduces the given ab-initio level calculations with reasonable accuracy. We present a library of residue-level parameters derived from extensive electronic structure calculations over various possible combinations of nucleobases and amino acid side chains from high-quality DNA-protein complex structures. As an example, our approach can reasonably generate the subtle electronic structure details for the orthologous transcription factors human AP-1 and Epstein-Barr virus Zta within a few seconds on a laptop. This method potentially enhances our understanding of the electronic structure variations of gene-protein interaction complexes, even those involving dozens of proteins and genes. We hope this study offers a powerful tool for analyzing transcription regulation mechanisms at an electronic structural level.

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“…On the theoretical side, numerous computational studies, including tight-binding models, , quantum chemistry calculations, − and quantum mechanics/molecular mechanics (QM/MM) studies − have been carried out on DNA and polynucleotide structures to predict their charge-transport properties. However, the vast majority of these computational studies focused on nucleobase oligomers and did not address band structure properties in a fully periodic geometry.…”

Section: Introductionmentioning

confidence: 99%

Electron/Hole Mobilities of Periodic DNA and Nucleobase Structures from Large-Scale DFT Calculations

et al. 2023

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Electron/hole transfer mechanisms in DNA and polynucleotide structures continue to garner considerable interest as emerging charge-transport systems and molecular electronics. To shed mechanistic insight into these electronic properties, we carried out large-scale density functional theory (DFT) calculations (up to 650 atoms) to systematically analyze the structural and electron/hole transport properties of fully periodic single- and double-stranded DNA. We examined the performance of various exchange–correlation functionals (LDA, BLYP, B3LYP, and B3LYP-D) and found that single-stranded thymine (T) and cytosine (C) are predominantly hole conductors, whereas single-stranded adenine (A) and guanine (G) are better electron conductors. For double-stranded DNA structures, the periodic A-T and G-C electronic band structures undergo a significant renormalization, which causes hole transport to only occur on the A and G nucleobases. Our calculations (1) provide new benchmarks for periodic nucleobase structures using dispersion-corrected hybrid functionals with large basis sets and (2) highlight the importance of dispersion effects for obtaining accurate geometries and electron/hole mobilities in these extended systems.

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Understanding atomic bonding and electronic distributions of a DNA molecule using DFT calculation and BOLS-BC model

Cited by 5 publications

References 23 publications

Electronic and magnetic properties of TATA‐DNA sequence driven by chemical functionalization

Electronic and magnetic properties of TATA‐DNA sequence driven by chemical functionalization

Elucidating Electronic Structure Variations in Nucleic Acid-Protein Complexes Involved in Transcription Regulation Using a Tight-Binding Approach

Electron/Hole Mobilities of Periodic DNA and Nucleobase Structures from Large-Scale DFT Calculations

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