Title: Exploring the Physics of 2D Polymers and Interdependent Dynamics of DNA and Protein
Speaker: Dr. Indresh Yadav, MIT, Boston, USA
Abstract: Biopolymers exhibit rich physics and play an important role in the machinery of life. To decipher their role in biological processes, it is crucial to understand biopolymer transport and molecular mechanics at the single-molecule level. The complexity, tunability, and accessibility of these systems can also be harnessed in the development of robust models for synthetic materials. For instance, two-dimensional (2D) polymers possess tremendous potential in diverse applications, including flexible electronics, coatings, and separation/filtration [1]. Due to their non-trivial topology, 2D polymers also pose many fundamental problems in statistical physics. In the first part of the talk, I will discuss our recent experimental findings, unveiling the static and dynamic properties of kinetoplast DNA (kDNA - catenated DNA rings) in solution [2,3]. Meticulous observations of conformational phase transition, topology-dependent dynamics, and universal scaling provide profound insights into 2D polymer physics and highlight kDNA as a promising model system. In the second part of the talk, I will discuss the influence of the internal dynamics of DNA on protein mobility [4,5]. The protein mobility shows a strong correlation to the internal motion of DNA. Under the paradigm of the Rouse dynamics, a model of released diffusion is proposed that very well captures the experimental features.
[1] A. D. Schlüter, P. Payamyar, and H. C. Öttinger, How the World Changes By Going from One- to Two-Dimensional Polymers in Solution, Macromol. Rapid Commun. 37, 1638 (2016).
[2] I. Yadav, D. Al Sulaiman, B. W. Soh, and P. S. Doyle, Phase Transition of Catenated DNA Networks in Poly(Ethylene Glycol) Solutions, ACS Macro Lett. 10, 1429 (2021).
[3] I. Yadav, D. Al Sulaiman, and P. S. Doyle, Tuning the Topology of a Two-Dimensional Catenated DNA Network, Phys. Rev. Res. 5, 013141 (2023).
[4] I. Yadav, W. Rosencrans, R. Basak, J. A. van Kan, and J. R. C. van der Maarel, Intramolecular Dynamics of DsDNA Confined to a Quasi-One-Dimensional Nanochannel, Phys. Rev. Res. 2, 013294 (2020).
[5] I. Yadav, R. Basak, P. Yan, J. A. Van Kan, V. Arluison, and J. R. C. Van Der Maarel, Role of Internal DNA Motion on the Mobility of a Nucleoid-Associated Protein, J. Phys. Chem. Lett. 11, 8424 (2020).