Biomod/2012/UTokyo/KaseiRunners/MeetingSummary

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Study meeting

Folding DNA to create nanoscale shapes and patterns

//Paul W. K. Rothemund //Nature 2006

Arbitrary two-dimensional nanostructure can be made by raster-filling the shape with a 7-kilobase single stranded scaffold and by choosing over 200 short oligonucleotide staple strands. A desired shape can be folded by the intrinsic properties of self-organization, proceeded by simply mixing the scaffold DNA and staple strands. This provides us a new approachable method of DNA fabrication in the way the each oligonucleotide can serve as a 6-nm pixel so the structures can be programmed to bear complex patterns. This is now expanded from two dimensional to three dimensional shapes such as tubes and cubes.

Challenges and opportunities for structural DNA nanotechnology


//Andre V. Pinheiro, Dongran Han, William M. Shih and Hao Yan //Nat Nanotechnol. 2011

In this thesis, Authors examine the technical challenges in the field of structural DNA nanotechnology and outline some of the promising applications, giving many examples. The breakthrough in this field came with the concept of ‘DNA origami’, where a long scaffold strand (single-stranded DNA from the M13 phage genome) was folded with the help of hundreds of short ‘staple’ strands into defined two-dimensional(2D) shapes. Taking advantage of the sequence specificity and the resulting spatial addressability of DNA nanoarchitectures, these have been used for the organization of heteroelements such as proteins, peptides, virus capsids, nanoparticles and carbon nanotubes. And in turn, several of these DNA-directed assemblies have led to unique and improved functional properties, such as increased enzyme-cascade activities, and shifts of surface plasmon resonance controlled by custom arrangement of nanoparticles. However, authors say that there are many challenges that must be overcome to reach greater levels of control and functionality of DNA nanoarchitectures. Two of the most prominent obstacles are the high cost of DNA and the high error rate of self-assembly. If these hurdles can be overcome, DNA nanotechnology will be more developed. Authors highlight the potential use of DNA nanostructures in molecular and cellular biophysics, as biomimetic systems, in energy transfer and photonics, and in diagnostics and therapeutics for human health.

Nanomechanical DNA origami‘single-molecule beacons’directly imaged by atomic force microscopy


//Akinori Kuzuya, Yusuke Sakai, Takahiro Yamazaki, Yan Xu & Makoto Komiyama//Nature Communications 2011

In this study, authors made nano meter size DNA devices called DNA origami pliersÕ and ÔDNA origami forcepsÕ that can play a role of single-molecule beacons. These sub micro-size devices are composed of two DNA origami domains with immobile Holliday junctions. ÊThey change their shapes from Òcross formÓ into Òparallel closed formÓ in order to capture target single-molecules such as StreptAvidin, sodium ion, micro RNA and so on. Their conformational changes are visualized by atomic force microscopy, or fluorescence measurement. Therefore, researchers can indirectly detect the existence of the single target molecule by observing the DNA device that changes its form. In addition, there are three orthogonal mechanism; pinching for StreptAvidin, zipping for metal ion and unzipping for DNA strands. Any detection mechanisms can beused orthogonally with differently shaped origami devices in the same mixture using a single platform.

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

//Ebbe S. Andersen, Mingdong Dong, Morten M. Nielsen, Kasper Jahn, Ramesh Subramani, Wael Mamdouh, Monika M. Golas, Bjoern Sander, Holger Stark, Cristiano L. P. Oliveira,
Jan Skov Pedersen, Victoria Birkedal, Flemming Besenbacher, Kurt V. Gothelf & Jørgen Kjems //Nature 2009

The DNA origami technology enabled us to design molecular shapes made of DNA that you wanted, but they were only two-dimensional. This article reports that three-dimensional shapes can be designed by adding certain strands. This box is made of single-stranded DNA genome of the M13 bacteriophage and strands. The DNA is parted into six parts and creates six faces. Author confirmed the existence of DNA boxes by several methods like AFM, cryo-EM, SAXS. In addition, Author put a controllable lid into the box. This box is usually locked, but when certain substances exist, its lid opens. Thanks to a rectangular shaped DNA, it would be possible that the box contains substances inside it. These characteristics could realize the new drug delivery system. In other words, only when certain signal (for example, germs) exists, the DNA box’s lid is opened and release substances (drug).

A Logic-Gated Nanorobot for Targeted Transport of Molecular Payloads

//Shawn M. Douglas, Ido Bachelet, George M. Church//Science 2012

Authors designed an autonomous DNA nanorobot capable of transporting molecular payloads to cells, sensing cell surface inputs for conditional, triggered activation, and reconfiguring its structure for payload delivery. This DNA nanorobot consists of two domains that are covalently attached in the rear by single-stranded scaffold hinges. And, they incorporated the locks on the left and right sides of the front. The lock is staplesmodified with DNA aptamer–based locks,and,the key is antigen. When both aptamers recognize their keys, the lock duplexes dissociate and bind antigen keys. Payloads are premodified by covalent attachment to the 5′ end of a 15-base single stranded DNA oligonucleotide linker and are loaded inside the nanorobot. They designed that twelve payload attachment sites were arranged in an inward-facing ring in the middle of the robot. This nanorobot is active only when two locks is opened. This mechanism can be used as a logical AND gate, with possible inputs of cell surface antigens not binding or binding to aptamer locks(0 or 1), and possible outputs of nanorobot closed or opened(0 or 1,)

Autonomous multistep organic synthesis in a single isothermal solution mediated by a DNA walker

//Yu He and David R. Liu //Nat Nanotechnol. 2010

Authors report DNA walker automatically walks on DNA tile, causing multistep organic synthesis. It moves from a station to another station by the force of DNA hybridization. Once DNA walker associates with the initiation site, the reaction starts. Combining its D1 site to next station’s D1’ site (Fig. 1), the walker translocates from the initiation site to the first station (S1). It simultaneously triggers acylation of its amine group with N-hydroxysuccinimidyl (NHS) ester of S1. As a result, DNA walker gains first amino acid. DNAzyme in the walker induces the next step, cleaving the ribonucleotide linkage in S1. This leads to disassociation of DNA walker from S1, and in the same way as the first step, the walker moves from S1 to the next station (S2). Repeating this cycle, walker translocation, aminoacylation and DNAzyme cleavage, results in the walker with oligonucleotide reaching the final station. Each step requires no changes in temperature or pH. This multistep reaction sequence is absolutely spontaneous. Applying this strategy raises the possibility to perform highly efficient and selective multistep synthesis like in-vivo reactions.

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