[PO-H1] Poster Session 1

[P1-54] Quantification and validation of the mechanical properties of DNA nicks

^○Jae Young Lee, Jae Gyung Lee, Do-Nyun Kim (Dept. of Mechanical and Aerospace Engineering, Seoul National Univ., Korea)

Understanding the mechanical properties at a nick site of double-stranded DNA is important to precisely design self-assembling DNA nanostructures because they inevitably contain many nicks that are structural discontinuities of DNA backbones. It is, however, difficult to characterize the mechanical properties of DNA nicks experimentally due to its resolution limit while those for normal DNA double helix without nicks have been relatively well measured. Here, we quantitatively studied the sequence-dependent characteristics of DNA nicks at the base-pair scale using the molecular dynamics (MD) simulation. We found that a primary structural role of DNA nicks is the relaxation of torsional constraint by sugar-phosphate backbones and that neighboring base-pair sequences affect the degree of mechanical rigidity changes by a nick. To validate these findings, we designed DNA nanostructures sensitive to torsion where the torsional rigidity at nick sites was regulated by using various sequences of DNA nicks and measured their overall twist angle using the atomic force microscope (AFM). We expect our study for nicks offers a versatile way of fine tuning the shape and properties of DNA nanostructures.

This work was supported by the National Research Foundation of Korea (NRF) grants funded by the Korea government (Ministry of Science and ICT) (NRF-2016R1C1B2011098, NRF-2017M3D1A1039422, and NRF-2014M3A6B3063711).