Issue 28, 2023

Exhaustive classification and systematic free-energy profile study of single-stranded DNA inter-overhang migration

Abstract

Migration of a short single-stranded DNA (ssDNA) between DNA overhangs is a basic molecular process that is widely used in dynamic DNA nanotechnology. The migration rate is sensitive to migration gaits, and limits the speed of dynamic DNA systems like DNA nanowalkers and other functional devices. Here, we identify and exhaustively classify all possible inter-overhang migration gaits of a ssDNA into only four categories based on their intrinsic symmetry. Using the oxDNA package, we conduct a systematic computational study for a typical migrator-overhang system to identify the lowest-energy pathway for all four migration categories. The one-dimensional free-energy profile along this pathway allows a parameter-free estimation of migration rates for all the four categories by the first passage time theory plus benchmarking from experimental rates available for one migration category. The obtained rates indicate a big room to improve DNA nanowalkers’ speed above 1 μm per minute. The free-energy profile for each migration category possesses distinct and robust symmetric patterns, which largely decide local barriers, trapping states, and thereby a migration's rate-limiting processes and capacity for directional bias. This study thus provides a unified symmetry-based framework to analyze and optimize ssDNA migrations in kinetics, bias capacity, and structural design for better dynamic DNA nanotechnology.

Graphical abstract: Exhaustive classification and systematic free-energy profile study of single-stranded DNA inter-overhang migration

Supplementary files

Article information

Article type
Paper
Submitted
07 Mar 2023
Accepted
16 Jun 2023
First published
11 Jul 2023

Nanoscale, 2023,15, 11915-11926

Exhaustive classification and systematic free-energy profile study of single-stranded DNA inter-overhang migration

H. L. Too and Z. Wang, Nanoscale, 2023, 15, 11915 DOI: 10.1039/D3NR01058A

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