Features

doi:10.1038/nindia.2011.86 Published online 22 June 2011

Shape-me-up DNA

Pawan Kumar Dhar

Ever imagined folding a long strand of DNA into smileys, stars or hexagons? Our genetic building blocks, the DNA, have always been a cause of awe and thrill for researchers. Small wonder then that the emerging field of DNA origami is catching the attention of every genetic scientist.

DNA origami helps fold DNA strands into various shapes.

DNA origami, as evident, is the self-assembly and artificial folding of DNA into non-natural two and three dimensional shapes. The concept is very simple. That is probably why it is so powerful!

The trick is to artificially induce controlled complementary base pairing through small DNA fragments that act as 'staples', folding a long strand of DNA into pre-designed shapes.

How

The overall strategy goes like this. The image of the DNA design that one wants to deliver is hand drawn and fed into a computer programme for pixelating. A continuous line (resembling a folded wire) is drawn to identify the points along which a long DNA sequence must fold to produce the desired shape. The computer design is stapled to generate specific bends and then the staple strands are chemically synthesized and mixed with the long scaffold DNA.

The DNA solution is heated to melt the scaffold and strands stapled. It is then cooled down. As the DNA cools, the Watson-Crick base pairing between staple DNA and the target DNA self assembles the long DNA scaffold into pre-designed super structures. The artificial DNA nanostructures can be visualized through fluorescence microscopy or atomic force microscopy.

Origin

In the original 2006 experiment, Paul Rothemund described a simple method for folding long, single-stranded DNA molecules into two-dimensional shapes, using a 7-kilobase single-stranded scaffold and over 200 short oligonucleotide 'staple strands' to hold the scaffold in place. The DNA super structures resembling squares, discs and stars were roughly 100 nm in diameter with a spatial resolution of 6 nm.

The stable patterns on the 100-nm-sized DNA shapes showed a tenfold higher complexity than that of any previously self-assembled arbitrary pattern. The idea was so interesting that Nature ran a cover story on this work1.

The simplicity of the method has been used to construct complex DNA shapes. Given that the height of a basic two dimensional shape is equal to 2 nanometer thickness of DNA, additional DNA layers over the basic scaffold add 2 nm at each level. A five pointed star has been designed with 1.5 turn spacing, 32 mer stables over folding a linear scaffold.

Applications

Currently the methods of DNA orgami are somewhat error prone, subject to variations leading to synthesis of alternative forms of folded DNA. For example, 70% of experimentally fabricated designs showed smiley configurations, 11% showed star shape configurations, and so on.

It is important to note that the artificially parallelized DNA scaffold did not run very close, presumably due to electrostatic repulsion. According to Rothemund, strand invasion, an excess number of staples, cooperative effects (each correctly stapled DNA builds template for subsequent binding of new staples), self stapling and non-binding among staples are the key factors to ensure success of the experiment.

As staples are not designed to bind to each other, their relative concentrations do not seem to matter.

The idea of stapling long DNA strand has been used to develop three dimensional cubes, map of countries and so on. Moving on from toy origami structures, the idea of custom-making DNA nanostructures is now being explored to create next generation electronic circuits.

The future might see functional DNA nanostructures that are custom built to drive a specific cellular role. Also, programmable folding of DNA into stable non-native configurations will also see application at the level of nanoscale engineering.

Given that DNA is both a tough and flexible material, the targeted modification of DNA combined with programmable self-assembly and DNA fine tuning in terms of number, arrangement and length of helices should generate interesting inventions.


References

  1. Rothemund, P. W. K. Folding DNA to create nanoscale structure and patterns. Nature 440, 297-302 (2006) | Article | PubMed | ISI | ADS |