Mechanical Constraints Promote Noncanonical Base‐Pairing Interactions
Abstract
Abstract Mechanical perturbations profoundly influence nucleobase interactions in cells, serving as key modulators of fundamental cellular processes such as transcriptional regulation. However, their precise roles remain elusive due to methodological limitations. Here, we have developed a DNA origami‐based nanobender system that probes base–base interactions under mechanical constraints. This system imposes tunable geometric and mechanical constraints on single‐stranded DNA/RNA by pulling its two ends together while adjusting its contour length, and enables the assessment of weak interactions between bases through the detection of DNA origami dimerization. Combining experiments and molecular dynamics simulations, we speculate that mechanical constraints promote stacking‐driven noncanonical base‐pairing via entropy compensation and favorable nucleobase orientation (hydrophobic exposure), advancing our understanding of base recognition diversity. Customizable nanobender parameters allow investigation of the effects of geometric and mechanical constraints on hybridization thermodynamics across DNA‐DNA, RNA‐RNA, DNA‐RNA, and epigenetically modified nucleotides. Notably, we suggest that entropy modulation mediated by mechanical constraints enables fine‐tuning of binding free energy, thereby expanding material assembly applications while conferring environmental sensitivity.
Article Details
Authors (11)
Na Wu
School of Chemistry and Chemical Engineering
Liqiong Niu
Institute of Analytical Chemistry and Instrument for Life Science The Key Laboratory of Biomedical Information Engineering of Ministry of Education School of Life Science and Technology Xi'an Jiaotong University Xi'an Shaanxi 710049 P.R. China
Jia Liu
Yuanyuan Luo
Institute for atmospheric and earth system research (INAR/physics)
Pengyan Hao
Institute of Analytical Chemistry and Instrument for Life Science The Key Laboratory of Biomedical Information Engineering of Ministry of Education School of Life Science and Technology Xi'an Jiaotong University Xi'an Shaanxi 710049 P.R. China
Xiaoya Sun
Chongqing University , , ,
Binju Wang
State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering
Biwu Liu
Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology
Feng Chen
Chunhai Fan
State Key Laboratory of Synergistic Chem-Bio Synthesis, School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhang Jiang Institute for Advanced Study and National Center for Translational Medicine
Yongxi Zhao
Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology