Hole Wave Functions and Transport with Deazaadenines Replacing Adenines in DNA

• Published in: The journal of physical chemistry. B Vol. 117; no. 11; pp. 3086 - 3090
• Main Authors: Breindel, Alexander J, Stuart, Rachel E, Bock, William J, Stelter, David N, Kravec, Shane M, Conwell, Esther M
• Format: Journal Article
• Language: English
• Published: Washington, DC American Chemical Society 21.03.2013
• Subjects: Adenine - analogs & derivatives; Adenine - chemistry; Adenines; Analytical, structural and metabolic biochemistry; Biological and medical sciences; Deoxyribonucleic acid; DNA - chemistry; Dna, deoxyribonucleoproteins; Electronegativity; Fundamental and applied biological sciences. Psychology; Hydrogen bonds; Models, Molecular; Nanostructure; Nucleic acids; Quantum Theory; Simulation; Transport; Wave functions; Adenine derivatives; Speed; DNA; Wave function; Hole mobility; Activation energy; Hydrogen bond
• ISSN: 1520-6106; 1520-5207
• DOI: 10.1021/jp310636k

Transport of a hole along the base stack of DNA is relatively facile for a series of adenines (As) paired with thymines (Ts) or for a series of guanines (Gs) paired with cytosines (Cs). However, the speed at which a hole was found to travel was much too small to make useful semiconductor-type devices. Quite recently it was found that replacing one of the electronegative nitrogens (N3 or N7) with a carbon and a hydrogen, thus turning A into deazaadenine, increased the hole speed in what was A/T by a factor 30. To study the effect of the substitution we have carried out simulations for the wave function of a hole on an A/T oligomer with As modified by replacing N3 or N7, or both, with C–H’s. The simulations were carried out using QM/MM and the code CP2K. We find, for either N, or both, replaced, the wave function of the hole behaves similarly to that of a hole on A/T in being delocalized immediately after hole insertion for up to ∼20 fs, and then becoming localized on one of the modified As. The time for localization could be decreased by placing additional water within ∼1.8 Å of N3 or N7, encouraging the formation of hydrogen bonds with these nitrogens. Because of their positive charge the hydrogen bonds tend to repel holes. However, these bonds were found to decay on a femtosecond time scale, thus unlikely to affect the hole hopping, which occurs on approximately a nanosecond scale in A/T. Replacement with a C–H of one or both of the electronegative Ns, along with the structural changes that result, is expected to decrease the activation energy and thus account for the larger hole hopping rate in the deaza-modified DNA.