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Refinement of DNA Structures through Near-Edge X-ray Absorption Fine Structure Analysis: Applications on Guanine and Cytosine Nucleobases, Nucleosides, and Nucleotides
KTH, School of Biotechnology (BIO), Theoretical Chemistry.ORCID iD: 0000-0002-6706-651X
KTH, School of Biotechnology (BIO), Theoretical Chemistry.ORCID iD: 0000-0002-1763-9383
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2010 (English)In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 114, no 41, 13214-13222 p.Article in journal (Refereed) Published
Abstract [en]

In this work we highlight the potential of NEXAFS-near-edge X-ray absorption fine structure-analysis to perform refinements of hydrogen-bond structure in DNA. For this purpose we have carried out first-principle calculations of the N1s NEXAFS spectra of the guanine and cytosine nucleobases and their tautomers, nucleosides, and nucleotides in the gas phase, as well as for five crystal structures of guanine, cytosine, or guanosine. The spectra all clearly show imine (pi*(1)) and amine (pi*(2)) nitrogen absorption bands with a characteristic energy difference (Delta). Among all of the intramolecule covalent connections, the tautomerism of hydrogens makes the largest influence, around +/- 0.4-0.5 eV change of Delta, to the spectra due to a switch of single-double bonds. Deoxyribose and ribose sugars can cause at most 0.2 eV narrowing of Delta, while the phosphate groups have nearly negligible effects on the spectra. Two kinds of intermolecule interactions are analyzed, the hydrogen bonds and the stacking effect, by comparing "compressed" and "expanded" models. or by comparing models including or excluding the nearest stacking molecules. The shortening of hydrogen-bond length by 0.2-0.3 angstrom can result in the reduction of Delta by 0.2-0.8 eV. This is because the hydrogen bonds make the electrons more delocalized, and the amine and imine nitrogens become less distinguishable. Moreover, the hydrogen bond has a different ability to influence the spectra of different crystals, with guanine crystals as the largest (change by 0.8 eV) and the guanosine crystal as the smallest (change by 0.2 eV). The stacking has negligible effects on the spectra in all studied systems. A comparison of guanosine to guanine crystals shows that the sugars in the crystal could create "blocks" in the pi-and hydrogen bonds network of bases and thus makes the imine and amine nitrogens More distinguishable with a larger Delta. Our theoretical calculations offer a good match with experimental findings and explain earlier discrepancies in the NEXAFS analysis.

Place, publisher, year, edition, pages
2010. Vol. 114, no 41, 13214-13222 p.
Keyword [sv]
National Category
Chemical Sciences
URN: urn:nbn:se:kth:diva-26300DOI: 10.1021/jp1034745ISI: 000282855100023ScopusID: 2-s2.0-77958039838OAI: diva2:381488
QC 20101227Available from: 2010-12-27 Created: 2010-11-21 Last updated: 2011-04-04Bibliographically approved
In thesis
1. Structure and spectroscopy of bio- and nano-materials from first-principles simulations
Open this publication in new window or tab >>Structure and spectroscopy of bio- and nano-materials from first-principles simulations
2011 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

This thesis is devoted to first-principles simulations of bio- and nano-materials,focusing on various soft x-ray spectra, ground-state energies and structures of isolated largemolecules, bulk materials, and small molecules in ambient solutions.

K-edge near-edge x-ray absorption fine structure (NEXAFS) spectra, x-ray emission spectra, andresonant inelastic x-ray scattering spectra of DNA duplexes have been studied by means oftheoretical calculations at the density functional theory level. By comparing a sequence of DNAduplexes with increasing length, we have found that the stacking effect of base pairs has verysmall influence on all kinds of spectra, and suggested that the spectra of a general DNA can bewell reproduced by linear combinations of composed base pairs weighted by their ratio.

The NEXAFS spectra study has been extended to other realistic systems. We have used cluster modelswith increasing sizes to represent the infinite crystals of nucleobases and nucleosides, infinitegraphene sheet, as well as a short peptide in water solution. And the equivalent core holeapproximation has been extensively adopted, which provides an efficient access to these largesystems. We have investigated the influence of external perturbations on the nitrogen NEXAFSspectra of guanine, cytosine, and guanosine crystals, and clarified early discrepancies betweenexperimental and calculated spectra. The effects of size, stacking, edge, and defects to theabsorption spectra of graphene have been systematically analyzed, and the debate on theinterpretation of the new feature has been resolved. We have illustrated the influence of watersolvent to a blocked alanine molecule by using the snapshots generated from molecular dynamics.

Multi-scale computational study on four short peptides in a self-assembled cage is presented. It isshown that the conformation of a peptide within the cage does not corresponds to its lowest-energyconformation in vacuum, due to the Zn-O bond formed between the peptide and the cage, and theconfinement effect of the cage.

Special emphasis has been paid on a linear-scaling method, the generalized energy basedfragmentation energy (GEBF) approach. We have derived the GEBF energy equation at the Hartree-Focklevel with the Born approximation of the electrostatic potential. Numerical calculations for amodel system have explained the accuracy of the GEBF equation and provides a starting point forfurther refinements. We have also presented an automatic and efficient implementation of the GEBFapproach which is applicable for general large molecules.

Place, publisher, year, edition, pages
Stockholm: KTH Royal Institute of Technology, 2011. xvi, 74 p.
Trita-BIO-Report, ISSN 1654-2312 ; 2011:05
soft x-ray spectroscopy, bio- and nano-materials, first-principles simulation, host-guest interaction, generalized energy-based fragmentation
National Category
Theoretical Chemistry Physical Chemistry
Research subject
SRA - Molecular Bioscience
urn:nbn:se:kth:diva-31944 (URN)978-91-7415-928-8 (ISBN)
Public defence
2011-04-28, FA31, AlbaNova University Center, Roslagstullsbacken 21, Stockholm, 14:00 (English)
QC 20110404Available from: 2011-04-04 Created: 2011-03-30 Last updated: 2011-04-13Bibliographically approved

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