Deformations of Nucleic Acids Induced by Stimuli: Physical Insights from Molecular Dynamics Simulations and Magnetic Tweezers Experiments

Abstract

Deformations of double-stranded (ds) DNA and dsRNA play crucial roles in many biological processes, including DNA packaging, nucleic acid-protein interactions, and gene expression. These cellular functions are dominated by the energy of distortional nucleic acids, which has been modelled as an elastic rod with measurable rigidities. For example, dsDNA overwinding can facilitate the formation of supercoil, which is used to realize DNA compaction by bacteria. Conversely, unwinding of DNA duplex will promote replication and transcription by lowering energy cost of separating two strands. While nucleic acid deformations are biologically important, the relevant understanding is limited due to the challenge in the precise measurement of DNA and RNA deformations with high-resolution and the complexity of interactions inside dsDNA or dsRNA.

The deformations of nucleic acids can be characterized by both the mechanical response and structural change. The mechanical properties of dsDNA and dsRNA have been studied for decades, such as the bending persistence length and stretch modulus. These elastic properties have a tremendous impact on protein-nucleic acid interactions. Structural transitions are based on analysing the three-dimensional nucleic acid structures, where canonical dsDNA and dsRNA adopt strikingly different helical forms (B-form for dsDNA and A-form for dsRNA). A standard reference frame is usually established to analyse spatial arrangements of constitutional base pairs, including intra-base pair parameters and step parameters, torsion angles, groove size, and etc. Accurate characterization of conformations for nucleic acid duplexes will provide detailed information in bending, twisting, and stretching parameters. Among these conformational parameters, special attention is paid to twist, which has been known to modulate helicity of double-helical structure of nucleic acids and regulate gene expression consequently.

In this thesis, we present quantitative and unified deformation mechanisms of dsDNA and dsRNA combining single-molecule magnetic tweezers (MT) experiments, all-atom molecular dynamics (MD) simulations, and physical interpretations. MT experiments provide an excellent opportunity to precisely measure dynamic structures and functions of dsDNA or dsRNA at single-molecule level. As an assist to MT experiments, MD simulations have become an efficient and powerful tool to capture structural deformations and dissect molecular mechanisms at atomic resolution. And our theoretical calculations dictate experimental and simulations results, unveil physical origins, and quantify the deformation pathways finally.

We reported systematic and comprehensive findings of dsDNA and dsRNA deformations by different environmental stimuli, covering different ion types, a wide range of salt concentrations, temperature, and force. We observed substantial and quantitatively consistent overwinding of dsDNA and dsRNA with the increase of monovalent salt concentrations comparing MT experiments and MD simulation results. The decrease in temperature induced overwinding for dsDNA and dsRNA similarly. These measurements motivate us to be aware of that some intrinsic relations exist in the double-stranded helices regarding applied driving forces. Even the nonintuitive opposite twist-stretch couplings between dsDNA and dsRNA under stretching force are rationalized to have the same conformational changes. As a result, we discovered universal deformation pathways underlying the response to strikingly different stimuli for dsDNA and dsRNA, respectively. For dsDNA, we found that the stimuli first modify diameter, which is transduced into twist change through twist-diameter coupling. For dsRNA, the stimuli were found to modify the major groove width at first, which is transduced into twist change through twist-groove coupling. The coupling strengths were resolved by obtaining potential of mean force from sampling approaches. The theoretical calculations based on parameters variation and coupling constants reproduced experimental and simulations results upon given stimuli, addressing the questions that are involved in our interpretation.

Our findings of twist-diameter coupling in dsDNA and twist-groove coupling in dsRNA were verified in nucleic acid-protein interactions, where twist and diameter change are along the direction of twist-diameter coupling for dsDNA-protein binding and twist and groove change are along the direction of twist-groove coupling for dsRNA-protein binding. These deformations along these intrinsic couplings of nucleic acids were suggested to save conformational energy cost and enhance nucleic acid-protein binding affinity. The results of this work are expected to contribute to understanding the physical mechanisms of nucleic acid deformations and utilizing the knowledge in life science research, drug design, and bionanotechnological and material applications of nucleic acid structures.

Date of Award	7 Sept 2023
Original language	English
Awarding Institution	City University of Hong Kong
Supervisor	Liang DAI (Supervisor)