Interactions between nucleotides and their environment are essential in determining the recognition and pairing of nucleic acids, which are intimately connected to their ability to transmit and maintain the integrity of genetic information. Linear and ultrafast vibrational spectroscopy is a powerful tool to probe these interactions and reveal the molecular mechanism of nucleic acids hybridization with bond-specific structural resolution over a wide range of time scales. Despite their importance, experimental spectra are usually highly congested and a general rule that accurately assigns the complex spectral features to the underlying structure and dynamics of nucleic acids is currently not available. The objectives of the proposed research are to develop a theoretical framework that accurately and efficiently calculates the vibrational spectra of nucleic acids in the base carbonyl stretch region, and thereby to establish a structure-spectrum relation and elucidate the mechanism and key interactions in the hybridization of DNA oligonucleotides.
Aim 1 supports the objectives by developing a frequency map that generates instantaneous site frequencies directly from molecular dynamics (MD) simulations.
Aim 2 is to establish coupling schemes that model the interactions between chromophores. Upon building the theoretical framework, Aim 3 is to combine MD simulations and theoretical spectroscopy modeling and perform a systemic study of DNA and RNA oligonucleotides to build a structure-spectrum relation and to investigate the hybridization of DNA oligonucleotides in aqueous solution and on membrane surfaces. The proposed research will provide a novel theoretical framework that can be readily applied to model a variety of linear and non-linear vibrational spectroscopy, in particular two-dimensional infrared and sum-frequency generation spectroscopy. This approach provides a practical way to bridge MD simulations and spectroscopy experiments, which enables the interpretation of the complex experimental spectra at the molecular level. Combining atomistic MD simulations and theoretical spectroscopy modeling, the proposed research will elucidate the mechanism and key interactions in the molecular recognition and pairing of complementary DNA and RNA strands, which will guide the design of new vibrational spectroscopy experiments to temporally and spatially control these processes for applications in DNA-based technology. .
Linear and ultrafast vibrational spectroscopy provides a powerful tool to unravel the fundamental principles that govern the hybridization of nucleic acids, which is essential to a molecular-level understanding of how DNA and RNA transmit and faithfully maintain the integrity of genetic information. The proposed research will provide a novel theoretical framework for the calculation of linear and non-linear vibrational spectra of nucleic acids directly from MD simulations. Combining atomistic MD simulations and theoretical spectroscopy modeling, the proposed research will establish a structure-spectrum relation and elucidate the mechanism and key interactions in the hybridization of nucleic acids.