title: Electronic coupling between base pair dimers of LNA:DNA oligomers.
abstract: We calculated ab initio electronic coupling elements between neighboring base-pair dimers in a set of LNA:DNA oligomers with different numbers of locked nucleotides and compared them by averaging the values over ensembles of snapshots from molecular dynamics trajectories. Averaging was based on coupling elements for various ensembles comprising of 33,000 structures. The known pronounced variations of coupling elements on the nanosecond timescale due to thermal fluctuations of the DNA structure were confirmed. We found significant differences in electronic coupling at the dimer level between a non-modified DNA:DNA duplex and the corresponding duplex containing one fully LNA-substituted strand. We rationalized these differences by very dissimilar overlap in the pi-stack as a consequence of the LNA-modified system approximating an A-DNA-type helix. The calculated coupling elements for the non-modified reference duplex were similar to those of standard B-DNA and those for the fully modified oligomer resembled the matrix elements estimated for standard A-DNA.
authors.affiliation: Department Chemie, Theoretische Chemie, Technische Universität München, 85747, Garching, Germany.
authors.forename: Anela
authors.initials: A
authors.lastname: Ivanova
authors.forename: Grzegorz
authors.initials: G
authors.lastname: Jezierski
authors.forename: Notker
authors.initials: N
authors.lastname: Rösch
mesh_terms: D020029:Base Pairing; D004247:DNA / Q000737:chemistry*; D019281:Dimerization; D009696:Nucleic Acids / Q000737:chemistry*
chemical_list: D009696:Nucleic Acids; D004247:DNA