# Theoretical Modeling of the Vibrational Spectroscopy of Nucleic Acids

> **NIH NIH R01** · RUTGERS, THE STATE UNIV OF N.J. · 2020 · $151,365

## Abstract

PROJECT SUMMARY/ABSTRACT
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.
.

## Key facts

- **NIH application ID:** 9858368
- **Project number:** 5R01GM130697-02
- **Recipient organization:** RUTGERS, THE STATE UNIV OF N.J.
- **Principal Investigator:** Lu Wang
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $151,365
- **Award type:** 5
- **Project period:** 2019-02-01 → 2023-01-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9858368

## Citation

> US National Institutes of Health, RePORTER application 9858368, Theoretical Modeling of the Vibrational Spectroscopy of Nucleic Acids (5R01GM130697-02). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/9858368. Licensed CC0.

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