FNANO 2020

Spontaneous assembly of DNA molecules into compact structures is ubiquitous in biological systems and has emerged as a new paradigm for practical nanotechnology. The properties of such assemblies are programmed at the molecular level by the handful of atoms that differentiate the letters of the genetic alphabet. This lecture describes our efforts to elucidate the microscopic rules that govern DNA self-assembly in biological systems using a computational microscope. The lecture illustrates how computer simulations are used to design synthetic molecular systems that reproduce and sometimes outperformed the functionality of biological machines.

 

Related publications and tutorials

MrDNA: a multi-resolution model for predicting the structure and dynamics of DNA systems

Christopher Maffeo, and Aleksei Aksimentiev
Nucleic Acids Research (2020)
DOI:10.1093/nar/gkaa200  BibTex

A synthetic enzyme built from DNA flips 10⁷ lipids per second in biological membranes

Alexander Ohmann, Chen-Yu Li, Christopher Maffeo, Kareem Al Nahas, Kevin N. Baumann, Kerstin Göpfrich, Jejoong Yoo, Ulrich F. Keyser, and Aleksei Aksimentiev
Nature Communications 9 2426 (2018)
DOI:10.1038/s41467-018-04821-5  BibTex

Sequence-Dependent DNA Condensation as a Driving Force of DNA Phase Separation

Hyunju Kang, Jejoong Yoo, Hong Soo Lee, Byeong-Kwon Sohn, Seung-Won Lee, Wenjie Ma, Jung-Min Kee, Aleksei Aksimentiev, and Hajin Kim
Nucleic Acids Research 46(18) 9401-9413 (2018)
DOI:10.1093/nar/gky639   BibTex

Multi-resolution simulations of self-assembled DNA nanostructures

Tutorial PDF (link): 
PDF
Tutorial Files (link): 
Required tutorial files

The DNA origami method has brought nanometer-precision fabrication to molecular biology labs, offering myriads of potential applications in the fields of synthetic biology, biomolecular medicine, molecular computation, etc. Advancing the method further requires controlling self-assembly down to the atomic scale. Hence, fast, accurate and detailed structure prediction can advance the development of complex, functional DNA origami constructs.

A Practical Guide to DNA Origami Simulations Using NAMD
Tutorial PDF: 
PDF icon origamiprotocols.pdf
Required tutorial files: 
Binary Data origamitutorial.tar.gz

In this tutorial, we walk through the protocol for all-atom simulations of DNA origami using the NAMD package starting from a caDNAno design. As an example, we use a caDNAno design of a six-helix cylinder structure, which is provided in the tutorial archive. We will convert the caDNAno file to an all-atom structure file in the PDB format, solvate the all-atom structure in a MgCl2 solution, and perform MD simulations. 

All-atom simulation membrane-spanning DNA nanopores
Tutorial PDF: 
PDF icon 2019.12.26_dnp_book_chapter.pdf
Required tutorial files: 
Package icon dnpinmembranetutorial.zip

Building on the recent technological advances, all atom molecular dynamics (MD) simulationshave become an indispensabletool to study the molecular behavior at nanoscale. Molecular simulations have been used to characterize the structure, dynamics, mechanical and electrical properties of DNA origami nanostructures. In this tutorial we describe a method to build all-atom model of lipid spanning DNA origami nanopores and perform molecular dynamics simulations in explicit electrolyte solutions.