DPGA

This repository contains source codes in the DPGA paper. including:

DNA sequence generation

using Python3

DNA compiler

using Python3

MD simulation

using oxDNA

Visual DSD codes for SDR kinetics simulation

Please run the codes in: https://ph1ll1ps.github.io/visualdsd/index.html

CRN mode

ref: Matthew R. Lakin, Simon Youssef, Filippo Polo, Stephen Emmott, Andrew Phillips, Visual DSD: a design and analysis tool for DNA strand displacement systems, Bioinformatics, Volume 27, Issue 22, November 2011, Pages 3211–3213, https://doi.org/10.1093/bioinformatics/btr543

Matlab SimBiology models for DPGA circuits simulation