More Like this

1. Conformational Control of DNA Origami by DNA Oligomers, Intercalators and UV Light

   https://doi.org/10.3390/mps4020038  

   Li, Ruixin; Chen, Haorong; Lee, Hyeongwoon; Choi, Jong Hyun (June 2021, Methods and Protocols)

   null (Ed.)

   DNA origami has garnered great attention due to its excellent programmability and precision. It offers a powerful means to create complex nanostructures which may not be possible by other methods. The macromolecular structures may be used as static templates for arranging proteins and other molecules. They are also capable of undergoing structural transformation in response to external signals, which may be exploited for sensing and actuation at the nanoscale. Such on-demand reconfigurations are executed mostly by DNA oligomers through base-pairing and/or strand displacement, demonstrating drastic shape changes between two different states, for example, open and close. Recent studies have developed new mechanisms to modulate the origami conformation in a controllable, progressive manner. Here we present several methods for conformational control of DNA origami nanostructures including chemical adducts and UV light as well as widely applied DNA oligomers. The detailed methods should be useful for beginners in the field of DNA nanotechnology. 

   more » « less
2. DNA Looping Mediated by Site-Specific SfiI–DNA Interactions

   https://doi.org/10.1021/acs.jpcb.1c00763  

   Vemulapalli, Sridhar; Hashemi, Mohtadin; Kolomeisky, Anatoly B.; Lyubchenko, Yuri L. (May 2021, The Journal of Physical Chemistry B)

   null (Ed.)
3. Facilitation of DNA loop formation by protein–DNA non-specific interactions

   https://doi.org/10.1039/c9sm00671k  

   Shin, Jaeoh; Kolomeisky, Anatoly B. (July 2019, Soft Matter)

   Complex DNA topological structures, including polymer loops, are frequently observed in biological processes when protein molecules simultaneously bind to several distant sites on DNA. However, the molecular mechanisms of formation of these systems remain not well understood. Existing theoretical studies focus only on specific interactions between protein and DNA molecules at target sequences. However, the electrostatic origin of primary protein–DNA interactions suggests that interactions of proteins with all DNA segments should be considered. Here we theoretically investigate the role of non-specific interactions between protein and DNA molecules on the dynamics of loop formation. Our approach is based on analyzing a discrete-state stochastic model via a method of first-passage probabilities supplemented by Monte Carlo computer simulations. It is found that depending on a protein sliding length during the non-specific binding event three different dynamic regimes of the DNA loop formation might be observed. In addition, the loop formation time might be optimized by varying the protein sliding length, the size of the DNA molecule, and the position of the specific target sequences on DNA. Our results demonstrate the importance of non-specific protein–DNA interactions in the dynamics of DNA loop formations. 

   more » « less
4. Programming DNA Self-Assembly by Geometry

   https://doi.org/10.1021/jacs.2c02456  

   Zhang, Cuizheng; Zheng, Mengxi; Ohayon, Yoel P.; Vecchioni, Simon; Sha, Ruojie; Seeman, Nadrian C.; Jonoska, Natasha; Mao, Chengde (May 2022, Journal of the American Chemical Society)
5. Algebraic Systems Motivated by DNA Origami

   Garrett, J.; Jonoska, N.; Saito, M (January 2019, Algebraic Informatics)

   Ćirić, M.; Droste, M.; Pin, JÉ. (Ed.)

   We initiate an algebraic approach to study DNA origami structures. We identify two types of basic building blocks and describe a DNA origami structure by their composition. These building blocks are taken as generators of a monoid, called the origami monoid, and motivated by the well studied Temperley-Lieb algebras, we identify a set of relations that characterize the origami monoid. We present several observations about Green’s relations for the origami monoid and study the relations to a direct product of Jones monoids, which is a morphic image of an origami monoid. 

   more » « less