Introduction to ENSnano and DNA nanostructures

I am very happy to announce the first release of ENSnano, the software that I am developing as part of my PhD project.

ENSnano

ENSnano is a software for designing 3D DNA nanostructures. It offers a 3D visualization and edition interface as well as a 2D interface similar to those of cadnano and scadnano from which it is inspired.

ENSnano is written in Rust a programing language that puts emphasis on safety and performance. Among the many crates (Rust modules) that ENSnano depends on, one can cite

wgpu for 2D and 3D graphics
iced for the GUI components
ultraviolet for linear algebra

The aim of this post is to present ENSnano to an audience that is not necessarily familiar with DNA nanostructures.

The reader is also invited to check our paper introducing ENSnano that will be presented at the DNA 27 conference in September 2021.

Building nanoscopic objects with DNA

DNA and its molecular structure

DNA is the chemical support of genetic information. In its most common form, it has the shape of a double-stranded helix. Each strand of the helix is made of a backbone that is made of alternating sugar and phosphate residues.

dna_schem dna_drawing ) DNA_orientation

Molecular structure of DNA. (left): Schematic representation of the chemical organisation of one strand of DNA. (middle) Schematic representation of a DNA double helix. (right): Two reverse complementary strands of DNA. Left and middle panel commes from the original article from Watson and Crick. Right panel commes from Wikipedia

On each sugar of the backbone, there is a basic residue which can be either Adenine (A), Guanine (G), Thymine (T) or Cytosine (C). Adenine and Thymine are said to be complementary because they have a tendency to bind to each other. The same is true for Guanine and Cytosine. The affinity of the complementary bases is what holds the two DNA strands together.

Articificial DNA nanostructures

In 1982, Nadrian Seeman introduced the idea of using DNA as a programmable material to build nanostructures. The idea was to used the capacity of DNA molecule to bind to their reverse complementary strand to form branched junction that would create 3D geometric crystals.

seeman_cube

Nadrian Seeman introduced the idea of building nanoscopic shapes with DNA. This cube is made of several DNA strands that each bind to several other strands. By binding together strands adopt a 3-dimensional shape. Image taken from a review by Bath & Rothemund (2017).

In 2006, Paul Rothemund introduced the idea of DNA origami and used it to produce a variety of shapes. In a DNA origami, a long (often about 7000 bases long) DNA strands called the scaffold is put in solution with several short (often between 10 and 60 bases long) strands called the staples. Each staple is designed to be the reverse complementary of several region of the scaffold. By attaching to these region, the staples will bend the scaffold and give it its desired shape.

origami_principle smiley_origami

(left): Principle of DNA origami. The scaffold (in black) is put in a solution with several staples (in color). Each staple binds with several distant domains of the scaffold and brind them together, giving the desired shape to the scaffold. (right) DNA origami that were realised by Rothemund in the article that introduced DNA origami. Both images were extracted from the said article (Rothemund 2006)

Making a DNA origami with ENSnano

To make a DNA origami with ENSnano, one can start by drawing the shape of the scaffold using the 2D and 3D interfaces.

In this rocket design, the scaffold goes through all the helices of both the rocket and the stand. Drawing the part where the scaffold is contained only in the rocket or only in the stand is arguably easier in the 2D interface. However, to make the connection between the two layers, being able to see the junction in 3D is really useful.

Once the scaffold is done, one must draw the staples. The DNA sequence of the scaffold is then given as an input to the program. The DNA sequence of the staples is then determined by the region of the scaffold on which they should bind.

The above example shows an unfinished design where the scaffold and some staples have been drawn. The full sequence of the scaffold (that is a natural DNA molecule) has been given has input to ENSnano.

This allows the sequences of the staples to be deduced using the complementarity rule (G in front of C, A in front of T etc..). For example, the sequence of the red staple going through helices 5 and 6 is AGGGGGTAA...GCCAG. Once the design is finished, ENSnano can produce an excel file containing the sequence of the staples.

This file can then be used to place an order on a specialized platform that will create artificial DNA molecules with these sequences.

A nanostructure designed with ENSnano

Here is an example of a DNA nanostructure that was designed in ENSnano. It is a DNA origami representing a rocket lying on a stand. This design was chosen to illustrate the capacity of ENSnano because the helices of the rocket are not parallel to those of the stand. We believe that such a design is a good example where ENSnano’s concept of mixing a 2D and a 3D interface shines.

Once the design is finished in ENSnano, one can use the software functionalities to export a list of DNA sequences that can be ordered on specialized platforms. The strands can then be mixed together to obtain the desired structure. The assembled object is at the nanometer scale and is smaller that the wavelength of visible light. Therefore it must be imaged using specific tool such as an atomic force microscope.

Here is an image of the rocket obtained by atomic force microscopy.