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Dependence of homo-lumo gap of DNA base pair steps on twist angle: A density fuctional approach
SMART, BioSyst & Micromech IRG BioSyM, 1 Create Way, Singapore 138602, Singapore.;MIT, Comp Sci & Artificial Intelligence Lab, 77 Massachusetts Ave, Cambridge, MA 02139 USA..
Prochem Solut Pte Ltd, 89C Sci Pk Dr,Rutherford 04-13,Singapore Sci Pk 1, Singapore 118261, Singapore..
Indian Inst Sci Educ & Res, Mohanpur 741246, W Bengal, India..
Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.ORCID iD: 0000-0002-3687-4223
2018 (English)In: Journal of biological systems, ISSN 0218-3390, Vol. 26, no 1, p. 23-40Article in journal (Refereed) Published
Abstract [en]

Electronic structure calculations of all 10 unique base pair (bp) steps have been calculated to study the interaction energies of the bp steps, density of states (DOS), projected density of states (pDOS) using the density functional theory (DFT). Plane wave basis with ultrasoft pseudo-potential method has been used within the local density approximation (LDA) for the exchange correlation functional. Electron densities of the bp steps corresponding to HOMO and LUMO level have been calculated to understand the difference in stacking energies of the bp steps. The variation of HOMO-LUMO gap (g) of all possible bp steps on twist angle has been studied. We have observed that out of the 10 bp steps, 4 purine-purine bp steps (d(AA), d(GG), d(AG) and d(GA)), show significant variation of g on twist angle. The observed variation on twist angle of d(AA) bp step has been explained by the calculated DOS and electron densities.

Place, publisher, year, edition, pages
WORLD SCIENTIFIC PUBL CO PTE LTD , 2018. Vol. 26, no 1, p. 23-40
Keyword [en]
DNA Base Pair Step, Stacking Energy, Density of States, HOMO-LUMO Gap, DFT Calculation
National Category
Theoretical Chemistry
Identifiers
URN: urn:nbn:se:uu:diva-351750DOI: 10.1142/S021833901850002XISI: 000429222700002OAI: oai:DiVA.org:uu-351750DiVA, id: diva2:1212876
Available from: 2018-06-04 Created: 2018-06-04 Last updated: 2018-06-04Bibliographically approved

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