Quantum chemical modeling of longitudinal hydrogen bonds in DNA
Alexander Samchenko1, Ivan Savelev1, Anton Klimov1, Lev Shishkin1, Oksana Polesskaya2, Alexander Vetcher1,3,4, Eugenia Kananykhina1, Elena Zhigmitova1, Richard Alan Miller5, Max Myakishev-Rempel1
1DNA Resonance Research Foundation, San Diego, CA, USA
2University of California, San Diego, USA
3 Nanotechnology Scientific and Educational Center, Institute of Biochemical Technology and Nanotechnology, Peoples Friendship University of Russia, Moscow, Russian Federation
4 Shishonin Complementary and Integrative Health Clinic, Moscow, Russian Federation
5 OAK, Inc., Grants Pass, OR, USA
Abstract
This work is inspired by the potential existence of electromagnetic signal paths in biological regulation at the tissue and subcellular scales. Previously, we suggested that mechanisms of such signaling could directly implicate genomic DNA. While searching for possible sequence-dependent oscillators in DNA, we stumbled upon the likely existence and functional importance of longitudinal hydrogen bonds, i.e the hydrogen bonds formed between all successive basepairs except in the dinucleotide AT. With the use of molecular modeling, we developed an algorithm that predicted continuous stretches of these bonds in DNA and proposed that they form delocalized proton wires. We analyzed genome sequences of various species and demonstrated that certain patterns of proton wires are enriched and conserved in evolution and are colocalized with gene transcription starts. Here, we utilized quantum chemical modeling to verify our previously proposed models of longitudinal hydrogen bonds in DNA and to improve the prediction algorithm of sequence-dependent delocalized proton wires in the genome. This strengthened the proposed models of proton wires and offered additional support for the proposed mechanisms of electromagnetic signaling. Also discussed are approaches to experimental verification of sequence-dependent resonances in proton wires in DNA.
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Max Myakishev-Rempel
DNA Resonance Research Foundation, San Diego, CA,
USA
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