DNA nanotechnology | The Aksimentiev Group

DNA nanotechnology is a rapidly expanding field that enables high-throughput construction of DNA-based sub-micron-size nanomachines with nanoscale accuracy. Similar to the computer-aided design (CAD) of the real-world machines (e.g., airplanes), our group is pioneering CAD for nanoscale machines made using DNA nanotechnology. Below you can explore our achievements, publicly available services, and instructuional materials.

Horizontal Tabs

Publications

Christopher Maffeo, and Aleksei Aksimentiev. "MrDNA: a multi-resolution model for predicting the structure and dynamics of DNA systems." Nucleic Acids Research (2020).

supplement.pdf (3.94 MB)

Mette D. E. Jepsen, Rasmus Schøler Sørensen, Christopher Maffeo, Aleksei Aksimentiev, Jørgen Kjems, and Victoria Birkedal. "Single molecule analysis of structural fluctuations in DNA nanostructures." Nanoscale 11:18475-18482 (2019).

Patrick M. Arnott, Himanshu Joshi, Aleksei Aksimentiev, and Stefan Howorka. "Dynamic Interactions between Lipid-Tethered DNA and Phospholipid Membranes." Langmuir 34:15084-15092 (2018).

supplementary_information.pdf (2.54 MB)

Alexander Ohmann, Kerstin Göpfrich, Himanshu Joshi, Rebecca F. Thompson, Diana Sobota, Neil A. Ranson, Aleksei Aksimentiev, and Ulrich F. Keyser. "Controlling aggregation of cholesterol-modified DNA nanostructures." Nucleic Acid Research 47:11441-11451 (2019).

si.pdf (1.74 MB)

Elisa Alina Hemmig, Clare Fitzgerald, Christopher Maffeo, Lisa Hecker, Sarah Elisabeth Ochmann, Aleksei Aksimentiev, Philip Tinnefeld, and Ulrich F. Keyser. "Optical voltage sensing using DNA origami." Nano Letters 18:1962-1971 (2018).

nl7b05354_si_001.pdf (2.72 MB)

Kerstin Göpfrich*, Chen-Yu Li*, Maria Ricci, Satya Prathyusha Bhamidimarri, Jejoong Yoo, Bertalan Gyenes, Alexander Ohmann, Mathias Winterhalter, Aleksei Aksimentiev, and Ulrich F. Keyser. "Large-Conductance Transmembrane Porin Made from DNA Origami." ACS Nano 10:8207-8214 (2016).

supporting_information.pdf (3.19 MB)

Kerstin Göpfrich, Chen-Yu Li, Iwona Mames, Satya Prathyusha Bhamidimarri, Maria Ricci, Jejoong Yoo, Adam Mames, Alexander Ohmann, Mathias Winterhalter, Eugen Stulz, Aleksei Aksimentiev, and Ulrich F. Keyser. "Ion Channels Made from a Single Membrane-Spanning DNA Duplex." Nano Letters 16:4665-4669 (2016).

supporting_information.pdf (1.32 MB)

Scott Michael Slone, Chen-Yu Li, Jejoong Yoo, and Aleksei Aksimentiev. "Molecular mechanics of DNA bricks: in situ structure, mechanical properties and ionic conductivity." New Journal of Physics 18:055012 (2016).

supporting_information.pdf (7.84 MB)

Christopher Maffeo, Jejoong Yoo, and Aleksei Aksimentiev. "De Novo Reconstruction of DNA Origami Structures through Atomistic Molecular Dynamics Simulation." Nucleic Acids Research 44:3013-3019 (2016).

Jejoong Yoo, and Aleksei Aksimentiev. "Molecular Dynamics of Membrane-Spanning DNA Channels: Conductance Mechanism, Electro-Osmotic Transport, and Mechanical Gating." The Journal of Physical Chemistry Letters 6:4680-4687 (2015).

Supporting Information (8.97 MB)

Chen-Yu Li, Elisa A. Hemmig, Jinglin Kong, Jejoong Yoo, Silvia Hernández-Ainsa, Ulrich F. Keyser, and Aleksei Aksimentiev. "Ionic Conductivity, Structural Deformation, and Programmable Anisotropy of DNA Origami in Electric Field." ACS Nano 9:1420-1433 (2015).

Supporting Information (8.81 MB)

Jejoong Yoo, and Aleksei Aksimentiev. "In situ structure and dynamics of DNA origami determined through molecular dynamics simulations." Proc Natl Acad Sci U S A 110:20099-104 (2013).

Supporting Information (4.15 MB)

Services

DNA Origami Structure Prediction

This service performs a series of brief coarse-grained simulations of a DNA origami object, first at low resolution to produce rapid relaxation of a structure, then at high-resolution to enable mapping to an atomistic structure.

LegoGen for DNA Brick Structures

Access LegoGen at Nanohub here. You will need a Nanohub account in order to use LegoGen.

Legogen is a tool for converting arbitrary CAD models into DNA nanostructures through the DNA brick method. It provides files suitable for all-atom molecular dynamics simulations in NAMD, as well as a list of nucleotide sequences for use in experiments. Legogen allows you to design complex structures with ease, especially when the overall shape of the structure is the design focus. The internal connectivity is automated by LegoGen, as well as the nucleotide sequences, allowing designs to be created in a fraction of the usual time. By taking advantage of DNA brick structures having no central scaffold strand traversing through the entire structure, vastly different structures can be built from a dedicated strand library, rather than custom strands for each structure. This also allows structures to be designed iteratively, with modifications to existing designs requiring fewer new strands than brand new designs.

Converting caDNAno design JSON file to all-atom PDB file

CaDNAno is a software with graphical interface for designing DNA origami. This service converts caDNAno designs in JSON format to atomic models suitable for 3D visualization.

Converting NanoEngineer-1 DNA structure design (MMP file) to all-atom PDB file

NanoEngineer-1 is a popular software package for designing arbitrary DNA nanostructures in a 3D workspace. Here we provide a service that converts a DNA nanostructure in NanoEngineer-1 (MMP format) to an all-atom structure in PDB format. It also generates files suitable for all-atom simulation.

ENRG MD for Origami Structure Prediction

DNA origami is a cost-effective method of assembling nanoscale objects by folding a long DNA strand using a custom set of complementary strands. Experimental characterization of DNA origami structure is essential for accurate design, but has been limited to rather low-resolution techniques. We developed a protocol that predicts DNA origami structure at atomic resolution with high accuracy using modest computational resources. Here we provide a service that prepares configuration files for a DNA origami structure prediction simulation from a caDNAno design file.

Tutorials

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:

origamiprotocols.pdf

Required tutorial files:

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.

Using LegoGen to build DNA Brick structures

Tutorial PDF:

legogentutorial.pdf

Required tutorial files:

templates_and_simulation_tools.zip

DNA brick structures are largely similar to DNA origami structures, but differ in the average number of helical connections and in strand length. DNA brick structures use a standardized 32-nucleotide-long "brick" strand that is repeated throughout the structure, unlike DNA origami which uses a single long scaffold strand and numerous custom staple strands. In this tutorial, we will build several DNA brick structures of varying complexity.

Molecular Dynamics Simulation of Custom DNA Nanostructures Created by NanoEngineer-1

In this tutorial, we will briefly introduce the protocols for all-atom molecular dynamics (MD) simulation of customized DNA nanostructure using NanoEngineer-1. We will start with introducing the basic usage of NanoEngineer-1 by a video tutorial. Then, we will guide you to convert the design of NanoEngineer-1 (mmp file) to all-atom coordinates in PDB format using our service. Finally, we will direct you to follow the steps in the origami tutorial and perform all-atom MD simulation.