Structure and Electronic Spectra of DNA Mini-hairpins with Gn:CnStems
- 25 October 2007
- journal article
- research article
- Published by American Chemical Society (ACS) in The Journal of Physical Chemistry B
- Vol. 111 (45), 13101-13106
- https://doi.org/10.1021/jp072303m
Abstract
The solution structure of a synthetic DNA mini-hairpin possessing a stilbenediether linker and three G:C base pairs has been obtained using 1H NMR spectral data and constrained torsion angle molecular dynamics. Notable features of this structure include a compact hairpin loop having a short stilbene-guanine plane-to-plane distance and approximate B-DNA geometry for the three base pairs. Comparison of the electronic spectra of mini-hairpins having one-to-four G:C base pairs and stilbenediether or hexamethyleneglycol linkers reveals the presence of features in the UV and CD spectra of the stilbene-linked hairpins that are not observed for the ethyleneglycol-linked hairpins. Investigation of the electronic structure of a stilbene-linked hairpin having a single G:C base pair by means of time-dependent density functional theory shows that the highest occupied molecular orbital, but not the lowest unoccupied molecular orbital, is delocalized over the stilbene and adjacent guanine. The calculated UV and CD spectra are highly dependent upon hairpin conformation, but reproduce the major features of the experimental spectra. These results illustrate the utility of an integrated experimental and theoretical approach to understanding the complex electronic spectra of π-stacked chromophores.Keywords
This publication has 15 references indexed in Scilit:
- Pathways for Photoinduced Charge Separation in DNA HairpinsJournal of the American Chemical Society, 2003
- Face-to-Face and Edge-to-Face π−π Interactions in a Synthetic DNA Hairpin with a Stilbenediether LinkerJournal of the American Chemical Society, 2003
- Chemistry with ADFJournal of Computational Chemistry, 2001
- The VMD-XPLOR Visualization Package for NMR Structure RefinementJournal of Magnetic Resonance, 2001
- Ensuring proper short-range and asymptotic behavior of the exchange-correlation Kohn-Sham potential by modeling with a statistical average of different orbital model potentialsInternational Journal of Quantum Chemistry, 2000
- GNA Trinucleotide Loop Sequences Producing Extraordinarily Stable DNA MinihairpinsBiochemistry, 1997
- A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules J. Am. Chem. Soc. 1995, 117, 5179−5197Journal of the American Chemical Society, 1996
- Use of a Stilbenedicarboxamide Bridge in Stabilizing, Monitoring, and Photochemically Altering Folded Conformations of OligonucleotidesJournal of the American Chemical Society, 1995
- Most compact hairpin-turn structure exerted by a short DNA fragment, d(GCGAAGC) in solution: an extraordinarily stable structure resistant to nucleases and heatNucleic Acids Research, 1994
- Principles of Nucleic Acid StructureSpringer Advanced Texts in Chemistry, 1984