Understanding Universal DNA and RNA Deformation Mechanisms

DNA and RNA deformations play crucial roles in biological processes, such as DNA packaging and nucleic acid recognition by proteins. The research team led by Professor Liang Dai, Associate Professor from CityU’s Department of Physics, revealed universal deformation mechanisms governing eight phenomena: DNA and RNA deformations induced by salt, temperature change, stretching force, and protein binding. Based on the unified physical mechanism revealed, their theory can quantitatively explain experimental results of DNA and RNA deformations induced by salt, temperature change, stretching force, and protein binding.

While DNA and RNA deformations are of great biological importance, the current relevant understanding is limited due to the challenge of making precise measurements of nucleic acid deformations and the complexity of nucleic acid interactions. Professor Dai’s team has overcome these hurdles using experiments, simulations, and theory. Their magnetic tweezers experiments provided an excellent opportunity to precisely measure DNA and RNA twist changes induced by salt, temperature change, and stretching.

Surprisingly, their simulations and theory discovered that common deformation pathways drive DNA and RNA deformations induced by different stimuli. Furthermore, the common deformation pathways appeared to be utilised by protein binding to reduce the energy cost of DNA and RNA deformations.

Professor Dai’s team found that DNA deformations are usually driven by twist-diameter coupling, i.e., the strong coupling between DNA twist and diameter, and RNA deformations are usually driven by twist-groove coupling, i.e., the strong coupling between RNA twist and major groove width. The team quantified both the twist-diameter coupling constant and RNA twist-groove coupling constant, and applied the coupling constants to explain DNA and RNA deformations.

The above research’s results can facilitate a better understanding of DNA packaging in cells and the relevant deformation energy cost. The results also provided insights into how proteins recognise DNA and RNA and induce deformations, which are key steps in gene expression and regulation.

Their research findings were published in PNAS (Proceedings of the National Academy of Sciences USA) entitled “Universality in RNA and DNA Deformations Induced by Salt, Temperature Change, Stretching Force, and Protein Binding” in May 2023. Apart from Professor Liang Dai, other co-authors are Fujia Tian, Chen Zhang, Erchi Zhou, Hai-Long Dong, Zhi-Jie Tan, Xing-Hua Zhang.

 

Common deformation pathways in RNA and DNA

 

Find out more about the Department of Physics at the City University of Hong Kong.