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

Abstract

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 Index Terms-Biomolecular sensing, deoxyribonucleic acid (DNA), THz or infrared (IR) wave, vibrational spectral.

First Principle Study of the Terahertz and Far-Infrared Spectral Signatures in DNA Bonded to Silicon Nanodots

“…Hence, this issue motivates the search for alternative methods for extracting long-wavelength spectral information from single (or few) numbers of biomolecules. One potential alternative for the detection of ultra-low concentrations of biomaterial was recently suggested [2]. In this sensor concept, a known single strand of DNA is to be bonded to silicon nanoprobes and active THz illumination will be applied to induce phonon vibrations that are sensed by direct electron current measurements.…”

“…Currently, the bonding of DNA to semiconductor substrates is less understood than the dynamics and spectral characteristics of DNA in solution. Previously, one and two deoxyguanosine (dG) residues were simulated where harmonic motions were analyzed without accounting for the effects of a realistic silicon substrate [2]. This paper reports on a first principle study of dG residues chemically bonded via (CH) linkers to the surface of hydrogen-terminated silicon (111) nanosized clusters.…”

Vibrational Characteristics of Genetic Codons: 5$'$-GGX-3$'$ and 5$'$-XGG-3$'$ (${\rm X} = {\rm A}, {\rm C}$, and T)

“…In real practice, electrospray mass spectrometry (ESI-MS) can be used to transfer large biomolecular complexes from the solution to the gas phase [18]- [20]. These simulation results are of paramount importance to the understanding of the vibrational characteristics of a DNA molecule bound on the surface of electrodes and the radiation modulated transport of electrons through the target DNA molecule, which is crucial to the development of the DNA sequencing technique suggested earlier [21], [22]. Section II of this paper discusses the models of the codons and the calculation methods used in this paper.…”