The electronic properties of double strands composed of trimeric LNA, PNA, DNA and RNA single strands were investigated by density-functional molecular orbital calculations. The computed hybridization energies for the double strands involving PNA or LNA are larger than those for DNA-DNA and RNA-RNA. The larger stability is attributed to the presence of a larger positive charge of the hydrogen atoms contributing to the hydrogen bonds in the PNA-DNA and LNA-DNA doublestrands. These results are comparable to the experimental finding that PNA and LNA single strands display high affinity toward a complementary DNA or RNA single strand.

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A novel approach to estimate DNA conductance based upon Kubo formula is presented and discussed. Using this approach, the effects of base pair mismatches, different conformational changes and base pair sequence on DNA electrical properties were investigated. The results were compared with the data from other methods. The new approach makes possible very fast estimation of conductance spectra for oligonucleotides with hundreds of base pairs and can easily be extended to treat arbitrary chemical modifications of DNA.

A combined molecular dynamics/density-functional theoretical study was carried out to address the propensity of ambient water to form cross-strand bridging water (CSBW) and their effects on the electronic properties of a fully hydrated DNA duplex 5'-d(CCATTAATGG)(2)-3'. The simulation shows ubiquitous presence of up to five CSBWs along the minor groove, each with residence time ranging from 400 ps to 750 ps. The molecular orbitals localized on these CSBWs are nearly degenerate in energy with the highest occupied molecular orbital of DNA localized on guanine bases, strongly indicating that the hole transport along the guanines is mediated by the ubiquitous CSBWs.

ABSTRACT:The electronic properties of DNA-DNA and PNA-DNA double strands having 3-6 base pairs (bp) were investigated by density functional theory (DFT) calculations. The binding energies and the highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO) energy gaps for the PNA-DNA hybrids in the vapor phase are found to be greater than those for the DNA-DNA hybrids, regardless of the number of base pairs involved. The study supports the experimental finding that PNA displays high affinity toward a complementary DNA and that PNA-DNA strands are much more thermodynamically stable than their DNA-DNA counterparts. The results suggest much higher sensitivity in DNA sequencing with the arrays of PNA than with those of DNA.