Periodic Stiffness Encoded in DNA Sequence Governs the Looping Behavior of DNA

Hajin Kim^1*

¹Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan, Korea

* Presenter:Hajin Kim, email:hajin.kim.kr@gmail.com

Sequence-dependent mechanical properties of DNA has long been studied to understand the mechanical code of the genome and the principles behind 3D chromatin organization. Here, we designed DNA sequences of several hundred base-pairs (bp) with controlled stiffness patterns, based on the theoretical stiffness values of dinucleotide stacks predicted from a computational study, which oscillate with the helical period of DNA, in order to bias the bending of the DNA and hence its looping behavior. AFM imaging revealed that the DNA’s with periodic stiffness pattern makes larger rotation compared to those with random pattern. Consistent with the AFM data, single molecule FRET measurements revealed that the DNA’s with periodic stiffness pattern looped with higher frequency by up to an order of magnitude, regardless of the salt conditions used. The discrepancy between periodic and random DNA’s persisted for varying lengths, nucleotide composition, or average stiffness of the DNA. Taking advantage of the increase in looping propensity, DNA minicircles that could not be produced due to the drop of yield for short length could be produced by incorporating periodic stiffness pattern in the minicircle sequence. AFM imaging of DNA minicircles showed that those with periodic stiffness pattern formed more supercoiled conformations, hinting the role of sequence pattern in compacting DNA or improving DNA uptake for gene therapy. The analysis of the stiffness periodicity around transcription start sites (TSS) across different eukaryotic organisms revealed that TSS regions show pronounced 10.4 bp periodicity of stiffness, suggesting that genomic evolution may have exploited the mechanical code of DNA to enhance its bending or looping properties. We further show the correlation between nucleosome occupancy and 10.4 bp periodicity of stiffness, suggesting that the spontaneous bending of DNA might be crucial in defining nucleosome position.

Keywords: DNA looping, DNA stiffness, Sequence periodicity