Influence of Base-Pair Interaction on Vibrational Spectrum of a Poly-dG Molecule Bonded to Si Substrates

A theoretical investigation is presented that characterizes the interaction dynamics of a double deoxyguanonsine molecular system, where two guanine bases are coupled via a sugar-phosphate backbone that is bound to the surface of silicon. Molecular dynamical simulations show that the influence of the coupling between the guanine bases (i.e., as compared with individual deoxyguanonsine molecules) leads to a significant increase of the absorption intensity from microwave to infrared (IR) frequencies. Furthermore, these results show that the strong coupling between the guanine bases leads to a much larger number of distinguishable vibrational modes at frequency below the IR at ~ 1350 cm^-1. These effects also produce double-peak features in the Far-IR absorption intensity, which represent a splitting of the individual peaks associated with a single deoxyguanonsine molecule. Guanine base coupling also leads to a general shifting of all the absorption peaks towards the terahertz frequency regime (i.e., ~10 THz and below), which is also accompanied by a reduction of the absorption intensity as one progresses to longer wavelengths. Most importantly, this interaction phenomenon creates additional spectral features, which may be useful in a long-wavelength optics-based technique for DNA sequencing.