Theory of tunneling across hydrogen-bonded base pairs for DNA recognition and sequencing

• Published in: Physical review. E, Statistical, nonlinear, and soft matter physics Vol. 79; no. 5 Pt 1; p. 051911
• Main Authors: Lee, Myeong H, Sankey, Otto F
• Format: Journal Article
• Language: English
• Published: United States 01.05.2009
• Subjects: Base Pairing; Base Sequence; Computer Simulation; DNA - chemistry; DNA - ultrastructure; Hydrogen Bonding; Models, Chemical; Models, Molecular; Molecular Sequence Data
• ISSN: 1539-3755
• DOI: 10.1103/PhysRevE.79.051911

We present the results of first-principles calculations for the electron tunnel current through hydrogen-bonded DNA base pairs and for (deoxy)nucleoside-nucleobase pairs. Electron current signals either through a base pair or through a deoxynucleoside-nucleobase pair are a potential mechanism for recognition or identification of the DNA base on a single-stranded DNA polymer. Four hydrogen-bonded complexes are considered: guanine-cytosine, diaminoadenine-thymine, adenine-thymine, and guanine-thymine. First, the electron tunneling properties are examined through their complex band structure (CBS) and the metal contact's Fermi-level alignment. For gold contacts, the metal Fermi level lies near the highest occupied molecular orbital for all DNA base pairs. The decay constant determined by the complex band structure at the gold Fermi level shows that tunnel current decays more slowly for base pairs with three hydrogen bonds (guanine-cytosine and diaminoadenine-thymine) than for base pairs with two hydrogen bonds (adenine-thymine and guanine-thymine). The decay length and its dependence on hydrogen-bond length are examined. Second, the conductance is computed using density functional theory Green's-function scattering methods and these results agree with estimates made from the tunneling decay constant obtained from the CBS. Changing from a base pair to a deoxynucleoside-nucleobase complex shows a significant decrease in conductance. It also becomes difficult to distinguish the current signal by only the number of hydrogen bonds.