I came across a publication by Senthilkumar et al. [1] in order to compute charge transfer through the DNA. Table 3, for instance, gives the coupling between bases along the leading (or retarded) strand of DNA:
Table 3. Charge-Transfer Integrals, $J$ (in eV), Overlap Matrix Elements, S, and Generalized Charge-Transfer Integrals, $J′$ (in eV), for Nucleobases Stacked at a Distance of 3.38 Å with a Twist Angle of 36°
For concreteness I will talk about only on columns 3 and 6 of the aforementioned table. I have two questions:
For instance, is it 5'-A-C-3' physically different from 5'-C-A-3'? If I 'erase' the direction 5' to 3', then A-C or C-A should be coupled by the same number (for instance, 0.042). However, I think that 5'-A-C-3' is different from 5'-C-A-3', because in the first example, a phosphate is "attached" to A from the left and a sugar is attached to C to the right; in the second case, C is attached to the phosphate to the left and A is attached to the sugar to the right. Is this interpretation correct?
5'-A-C-3' the coupling says it is 0.042, for 5'-C-A-3' it is −0.002. If I regard the previous argument as true, then both DNA systems are different, but not too different since they contain the same basis A and C. Does it make sense that by just changing the position of phosphates and sugars, one is approx. 40 times bigger than the other?
Reference
- Senthilkumar, K.; Grozema, F. C.; Guerra, C. F.; Bickelhaupt, F. M.; Lewis, F. D.; Berlin, Y. A.; Ratner, M. A.; Siebbeles, L. D. A. Absolute Rates of Hole Transfer in DNA. J. Am. Chem. Soc. 2005, 127 (42), 14894–14903. DOI: 10.1021/ja054257e.
