Biomod/2011/DAIICT/DANanoTrons:Project

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Abstract

The research on the constructions of 3D origami is attracting many researchers to explore the possibility for making useful tools as well as novel structures. In particular, in April 2011 Hao Yan group has demonstrated curved surfaces using 3D DNA origami. Motivated by this in this project we aim to develop highly complex non-trivial 3D structure of Taj Mahal. This will involve new algorithms and software development. We have identified the basic building blocks of Taj Mahal namely Decagonal Dome (29nm radius, 10 crossovers, 8 rings), Cylindrical Tubes (10nm radius tubular), Pyramidal Tops (13nm radius, 5 crossovers, 5 rings), Cubical Body (85nm width) and square base. Combining these basic shapes is still a challenge and experimental validation for the same is needed. Prior to this work, we have also created the 2D structures of the map of India and Gujarat state. Currently, we utilize tools like caDNAno, Nanorex and Autodesk Maya.

DNA Origami - An introduction

Origami is the traditional Japanese folk art of paper folding. The goal of this art is to transform a flat sheet of material into a finished sculpture through folding and sculpting techniques. The technique of DNA origami (as well as many other techniques of DNA nanotechnology) will be used in future to build smaller, faster computers and many other devices. Developed by Paul Rothemund at the California Institute of Technology, the process involves the folding of a long single strand of viral DNA aided by multiple smaller "staple" strands. These shorter strands bind the longer in various places, resulting in various shapes including a smiley face and a coarse map of the Americas, along with many three dimensional molecules such as cubes DNA origami is the nanoscale folding of DNA to create arbitrary two and three dimensional shapes at the nanoscale. The specificity of the interactions between complementary base pairs makes DNA a useful construction material through design of its base sequences.

We will be using the software caDNAno initially for demonstration of the origami.

Basic Concept

To produce a desired shape, images are drawn with a raster fill of a single long DNA molecule. This design is then fed into a computer program which calculates the placement of individual staple strands. Each staple binds to a specific region of the DNA template, and thus due to Watson-Crick base pairing the necessary sequences of all staple strands are known and displayed. The DNA is mixed and then heated and cooled. As the DNA cools the various staples pull the long strand into the desired shape. Designs are directly observable via several methods including atomic force microscopy, or fluorescence microscopy when DNA is coupled to fluorescent materials. The DNA created would be able to devour certain pollutants in the air, or be able to determine which cells in a person's body are cancerous and destroy them before the cancer spreads.

caDNAno

caDNAno is open-source software for design of 3D DNA origami nanostructures. This free open source software is based on Adobe AIR platform. It was written with the goal of providing a fast and intuitive means to create and modify DNA origami designs. This free software makes heavy use of several fantastic open-source libraries and resources, especially Papervision3D for 3D rendering.

Features

• Very easy – No programming required
• Effectively Integrated 2D and 3D interfaces
• Visual cues to aid design process
• Export formats: SVG, X3D, JSON
• Platform independent
• Open source License

Our Goal for the first task

“Our goal is to choose a continuous route through the scaffold path and then generate a list of staples that would force the scaffold to adopt that configuration in the test-tube.”