Biomod/2011/MIT/Origami



=Team MIT Origami= Ladies and gentlemen, welcome to the MIT Origami Wiki! This is where we shall be chronicling the activities and adventures of the inaugural MIT BIOMOD Team, as they work towards the development of novel ideas in the realm of biological nanotechnology.

Faculty Mentor

 * Professor Mark Bathe
 * mark.bathe@mit.edu

Graduate Student Mentor

 * Matthew Adendorff
 * mraden@mit.edu

Team Members

 * Ishan Gupta
 * Aliya Dincer
 * Michael Hernandez
 * Maria-Elena Martinez

Literature
Under this section you can find links to some useful papers, programs, websites, etc. If you come across anything that you think might be useful to the group, please upload it to the page.

Papers

The supramolecular architecture, function, and regulation of thylakoid membranes in red algae: an overview -
 * Photosynthesis:

The native architecture of a photosynthetic membrane -

Virus-templated self-assembled single-walled carbon nanotubes for highly efficient electron collection in photovoltaic devices -

Energy conversion in photosynthesis: A paradigm for solar fuel production -


 * Origami:

Self-assembly of a nanoscale DNA box with a controllable lid -

DNA origami as a nanoscale template for protein assembly -

Folding and cutting DNA into reconfigurable topological nanostructures -

Folding DNA to create nanoscale shapes and patterns -

Gold nanoparticle self-similar chain structure organized by DNA origami -

Self-assembled water-soluble nucleic acid probe tiles for label-free RNA hybridization assays -

A DNA nanomachine that maps spatial and temporal pH changes inside living cells -

Molecular robots guided by prescriptive landscapes -

A primer to scaffolded DNA origami -

Programmable periodicity of quantum dot arrays with DNA origami nanotubes -

DNA origami with complex curvatures in three-dimensional space -

Recovery of intact DNA nanostructures after agarose gel–based separation -

Self assembly of DNA into nanoscale three-dimensional shapes -

Folding DNA into twisted and curved nanoscale shapes -

Multilayer DNA origami packed on a square lattice -

Rapid prototyping of 3D DNA origami shapes with caDNAno -

DNA curvature and flexibility in vitro and in vivo -

Focus Issue on DNA Origami -

Aptamer Switch Probe Based on Intramolecular Displacement -


 * DNA / RNA:

Programming biomolecular self-assembly pathways -

Thermodynamic analysis of interacting nucleic acid strands -

Nucleic acid sequence design via efficient ensemble defect optimization -

The thermodynamics of DNA structural motifs -

A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics -

A partition function algorithm for nucleic acid secondary structure including pseudoknots -

The stability of Seeman JX DNA topoisomers of paranemic crossover (PX) molecules as a function of crossover number -


 * Artificial Immune System:

Comparison of strategies for the construction of libraries of artificial antibodies -

Programs

CanDo is a code, developed by LCBB at MIT, that applies a finite-element-based modeling framework for DNA with single base-pair resolution. The output from the code is a computational prediction of single- and multi-layer DNA origami structures, including their mean deformed 3D conformation and conformational flexibility.
 * CanDo -

NUPACK is a software suite, developed by the Pierce Lab at CalTech, that focuses on the design and energetics of nucleic acid systems.
 * NUPACK -

caDNAno is software for design of three-dimensional DNA origami nanostructures. It was written with the goal of providing a simple and user-friendly interface to facilitate a process that can be complex and error-prone.
 * caDNAno -

UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. This program is utilized for the visualization of CanDo output files.
 * CHIMERA -

VirtualBox is an operating system emulator that allows you to run guest operating systems, e.g. Linux and Windows, within your host system. As most of the scripts being developed in our group utilize opensource codes/software and are themselves coded with a Unix environment in mind, setting up a Linux system would be useful.
 * VirtualBox -

Maya is a very powerful suite of design software from Computer Aided Design (CAD) giant AutoDesk. Normally this software costs a small fortune, however as MIT students all you need to do is follow the links to register and you can get a licence for 13 months. Do it...any self respecting engineer should get up to speed with these kinds of design tools and this is a terrific opportunity to do so!
 * Maya -


 * General Interest


 * News story on the MIT webpage about work currently being done in the LCBB on DNA Origami -


 * Websites


 * Laboratory for Cell Biology and Biophysics, MIT-
 * Laboratory for Biomolecular Nanotechnology, TUM -
 * International Bio-Molecular Design Competition -