Role of Adenine and Guanine Sites in Hole Hopping in DNA Nanowire

Transfer integrals for oligos with different bases have been calculated using INDO/Koopman's approximation to unveil the charge transport mechanism in DNA. The sequences, G(A)nG, n = 1, 2, …, 10; G(A)xG(A)yG, x + y = 9; and G(A)xG(A)y G(A)zG, x + y + z = 8, were employed to interpret the Guanine (G) and Adenine(A) hopping. Adenine hopping is found to be faster in G(A)nG sequences with longer Adenine bridges (n ≥ 3). Inserting G-bases in between G(A)10G led to a decrease in the value of transfer integrals. Close analysis has revealed that bridge closer to 3′-end forms a hopping bottleneck; however, the presence of bridge at 5′-end enhances the charge transfer through A-hopping. Further insertion of single G sites in G(A)xG(A)yG (where x + y = 9) reduces the transfer integrals, thus explaining the hampering of A-hopping. Hence, sequences of the type G(A)nG, n > 3, are better suited for their application as molecular wire. Finally, studies on the effect of flipping of bases, i.e. flipping G:C to C:G on transfer integrals, have revealed that helical distortions and conformational changes due to sequence variations lead to changes in coupling, which is highly unpredictable