Theoretical Modeling of the Vibrational Spectroscopy of Nucleic Acids

核酸振动光谱的理论模型

• 批准号: 10330456
• 负责人: Lu Wang
• 金额: $ 15.37万
• 依托单位: RUTGERS, THE STATE UNIV OF N.J.
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-02-01 至 2025-01-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10330456
• 关键词: Base Pairing; Biotechnology; Characteristics; Complementary DNA; Complementary RNA; Complex; Coupling; DNA; Development; Dissociation; Engineering; Environment; Event; Frequencies; Generations; Goals; Hydrogen Bonding; Linear Models; Maps; Measurement; Membrane; Methods; Modeling; Molecular; Molecular Conformation; Nucleic Acid Hybridization; Nucleic Acids; Nucleotides; Oligonucleotides; Process; RNA; Research; Resolution; Scheme; Series; Site; Solvents; Spectrum Analysis; Stretching; Structure; Sum; Surface; Technology; Theoretical model; Time; aqueous; base; chromophore; design; electric field; experimental study; genetic information; insight; molecular dynamics; molecular recognition; nanomaterials; novel; nucleic acid detection; nucleic acid structure; nucleobase; quantum; three dimensional structure; tool; two-dimensional; vibration

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. .

项目总结/文摘

项目成果

Modeling the vibrational couplings of nucleobases.

模拟核碱基的振动耦合。

• DOI: 10.1063/1.5141858
• 发表时间: 2020
• 期刊: The Journal of chemical physics
• 作者: Jiang,Yaoyukun;Wang,Lu
• 通讯作者: Wang,Lu

Modeling the Infrared Spectroscopy of Oligonucleotides with 13C Isotope Labels.

• DOI: 10.1021/acs.jpcb.2c08915
• 发表时间: 2023-03
• 期刊: The journal of physical chemistry. B
• 作者: Wenting Meng;Hao-Che Peng;Yuanhao Liu;A. Stelling;Lu Wang

Development of Vibrational Frequency Maps for Nucleobases.

• DOI: 10.1021/acs.jpcb.9b04633
• 发表时间: 2019-06
• 期刊: The journal of physical chemistry. B
• 作者: Yaoyukun Jiang;Lu Wang