Workshop on Design of DNA Origami to be held 26 April, 2010
This proposal will support a day long workshop on design of DNA origami immediately prior to the 7th conference on the Foundations of Nanoscience (FNANO 2010). Intellectual Merit The workshop is designed to outfit each participant with information and tools that will enable them to design DNA nanostructures using the templated DNA origami method. Participants will return to their home institutions equipped with software, DNA sequence information, experimental hints and tips, and experience with AFM imaging that will allow them to design, fabricate and image a test origami structure. Workshop participants will also have the opportunity to attend the 2010 FNANO meeting, which this year features a double track on self-assembled DNA nanostructures. Most of the main researchers in DNA origami (Nadrian Seeman, Paul Rothemund, William Shih, Ebbe Andersen, Eric Winfree, Satoshi Murata, Masayuki Endo, Akinori Kuzuya, Hao Yan, Chengde Mao, Thom LaBean) attend this meeting. Coupling the workshop with the conference will enable younger scientists (postdocs, grad students, and junior faculty) to interact professionally with many of the top researchers in DNA origami. Broader Impact The workshop will be open to up to 15 NSF-supported participants, including 5 graduate students, 5 postdocs, and 5 junior faculty members. The workshop will be publicized to attract a wide range of applicants, who will be selected by the conference and program chairs of FNANO. The chairs will choose participants who are relatively new to FNANO, who will increase the diversity of the conference attendees, and who are likely to actually put the workshop content to use in their research.
Background on DNA origami The templated ?DNA origami? method offers a stunning assembly method for 100-nm sized nanostructures.? DNA origami offer a combination of high yield, non-repetitive structures, and potential for synthetic modification on a sub-10 nm length scale.? Each origami consists of a template DNA strand that interacts with many short oligonucleotides (?oligos?) whose sequences are designed to fold the template strand into a well-defined shape. Recent work has extended the design strategies for DNA origami from 2 dimensional (flat) structures, to 3 dimensional objects such as boxes (with void spaces large enough to fit a virus particle), to abstract construction elements.? These elements can self assemble into structures that are comparable in size and complexity with cellular organelles and virus capsids. ? Workshop content & leaders:? This 6+ hour workshop was aimed at faculty, grad students, and postdoctoral students who are interested in using DNA origami in their research.? We were aiming for 15-18 participants (1/3 each grad students, PD, and faculty). ?Instead, we got 46 participants.? Half were grad students/postdocs, half were faculty.? ??? The workshop addressed three critical aspects of DNA origami:? how to design origami in 2- and 3-D, how to image origami via AFM in air and liquid, and how to attach non-DNA materials to DNA origami.? ?Session 1 was led by Prof. William Shih (Harvard) who is an international leader in the area of design of large 2D and 3D origami.? Dr. Shih shared software (S. M. Douglas, A. H. Marblestone, S. Teerapittayanon,? A. Vasquez, G. M. Church, and W. H. Shih, ?Rapid Prototyping of DNA origami with caDNAno,? Nucl. Acids Res.;? 37, 5001-5006, (2009)) that his lab developed to automate origami design. It allows users to get from the desired shape of the origami, to a list of the required DNA sequences ready to send to a DNA synthesis company. In the next section of the workshop, Kyoung Nan Kim and Dr Koshala Sarveswaran from Prof. Marya Lieberman?s group at Notre Dame explained in detail how to deposit origami on mica and silicon and how to get good AFM images. Dr. Baoquan Ding (representing Prof. Hao Yan?s group at ASU) gave a tutorial on how to attach nanoparticles, proteins, and other non-DNA components to DNA origami. William Shih ?designing origami in caDNAno??? 32.7 MB http://dl.dropbox.com/u/2852226/100426_FNANO.pdf Kyoung-Nan Kim and Koshala Sarveswaran ?deposition and air imaging of DNA origami? and procedures for EBL on silicon:? 10.2 MB www.nd.edu/~mlieberm/fnano2010/workshop/imagingorigamiandebl.pptx Baoquan Ding ?review of methods for decorating DNA origami with non-DNA components?? 19.2 MB www.nd.edu/~mlieberm/fnano2010/workshop/decoratingorigami.pptx Cost-sharing and industrial participation: The NDnano Center at the University of Notre Dame supplied each participant with 10 AFM tips for use in the imaging section of the workshop. We bought the tips in bulk (2 wafers) and split them up into gel-packs for the participants.? ($4,000 value) Veeco set up an AFM for use by the workshop participants at the conference site at no charge.?? The FNANO conference organization paid the registration fee for a Veeco representative ($550 value)? All participants had the opportunity to sign up for a 2-3 hour session of hands-on time on the AFM;? at least 30 people took advantage of this opportunity, and two groups brought samples to image.? ?