Rational design of DNA-actuated enzyme nanoreactors guided by single molecule analysis

Nanoscale
Soma DhakalNils G Walter

Abstract

The control of enzymatic reactions using nanoscale DNA devices offers a powerful application of DNA nanotechnology uniquely derived from actuation. However, previous characterization of enzymatic reaction rates using bulk biochemical assays reported suboptimal function of DNA devices such as tweezers. To gain mechanistic insight into this deficiency and to identify design rules to improve their function, here we exploit the synergy of single molecule imaging and computational modeling to characterize the three-dimensional structures and catalytic functions of DNA tweezer-actuated nanoreactors. Our analysis revealed two important deficiencies--incomplete closure upon actuation and conformational heterogeneity. Upon rational redesign of the Holliday junctions located at their hinge and arms, we found that the DNA tweezers could be more completely and uniformly closed. A novel single molecule enzyme assay was developed to demonstrate that our design improvements yield significant, independent enhancements in the fraction of active enzyme nanoreactors and their individual substrate turnover frequencies. The sequence-level design strategies explored here may aid more broadly in improving the performance of DNA-based nanodevices incl...Continue Reading

References

Nov 1, 1991·Journal of Neuroscience Methods·S H Chung, R A Kennedy
Nov 8, 1996·Journal of Molecular Biology·C Altona
Aug 19, 1997·Proceedings of the National Academy of Sciences of the United States of America·S M MiickW J Chazin
Apr 13, 2000·Proceedings of the National Academy of Sciences of the United States of America·B F EichmanP S Ho
Aug 19, 2000·Nature·B YurkeJ L Neumann
Jun 3, 2004·Nucleic Acids Research·Jeffrey WatsonP Shing Ho
Mar 9, 2005·Trends in Biochemical Sciences·Nadrian C Seeman
Oct 14, 2005·Journal of Computational Chemistry·James C PhillipsKlaus Schulten
Jan 18, 2006·Nature Chemical Biology·Brian P EnglishX Sunney Xie
Jan 25, 2006·Journal of Nanoscience and Nanotechnology·David Rueda, Nils G Walter
Mar 17, 2006·Nature·Paul W K Rothemund
May 11, 2006·Nano Letters·Rahul ChhabraHao Yan
Oct 31, 2006·Journal of Neuroscience Methods·Boris Gourévitch, Jos J Eggermont
Jul 26, 2008·Nature Nanotechnology·Jonathan Bath, Andrew J Turberfield
Jul 29, 2008·Journal of Molecular Biology·Miguel J B PereiraNils G Walter
May 8, 2009·Nature Nanotechnology·Souvik ModiYamuna Krishnan
Jun 18, 2009·Nucleic Acids Research·Shawn M DouglasWilliam M Shih
Jul 25, 2009·Nucleic Acids Research·R LaveryK Zakrzewska
Oct 8, 2009·Journal of the American Chemical Society·Yonggang KeHao Yan
Mar 23, 2010·Nature Structural & Molecular Biology·John AbelsonNils G Walter
Jan 25, 2011·Nature Chemistry·David Yu Zhang, Georg Seelig
Mar 2, 2011·Nature Methods·Carlos Ernesto CastroHendrik Dietz
Apr 8, 2011·Bioinformatics·Ahmet BakanIvet Bahar
Oct 28, 2011·Biochemistry·Gordon G HammesSharon Hammes-Schiffer
Nov 8, 2011·Nature Nanotechnology·Andre V PinheiroHao Yan
Dec 2, 2011·Wiley Interdisciplinary Reviews. Nanomedicine and Nanobiotechnology·Nicole MichelottiNils G Walter
Jan 11, 2012·Journal of the American Chemical Society·Chao ZhouDongsheng Liu
Mar 22, 2012·Journal of Molecular Recognition : JMR·Nam NguyenNadrian C Seeman
May 31, 2012·Accounts of Chemical Research·Jinglin FuHao Yan
Oct 24, 2012·Nature Chemistry·Changbong HyeonD Thirumalai
Nov 13, 2012·Trends in Cell Biology·Yamuna Krishnan, Mark Bathe
Jul 4, 2013·Nature Communications·Minghui LiuHao Yan
Nov 19, 2013·Nature Structural & Molecular Biology·Ramya KrishnanNils G Walter
Nov 22, 2013·Journal of the American Chemical Society·Bryan WeiPeng Yin
Aug 20, 2015·Nature·Katherine E DunnJonathan Bath
Apr 10, 2012·Journal of Chemical Theory and Computation·Olof AllnérAlessandra Villa
Dec 5, 2015·Journal of Chemical Theory and Computation·Reza Sharifi SedehMark Bathe

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Citations

Sep 23, 2016·Journal of Chemical Information and Modeling·Stavros ChatzieleftheriouNikos D Lagaros
Jun 3, 2017·Langmuir : the ACS Journal of Surfaces and Colloids·Daniel MieritzDong-Kyun Seo
Oct 21, 2016·Nature Protocols·Jinglin FuHao Yan
Jun 6, 2019·Methods and Protocols·Dalton R GibbsSoma Dhakal
Jan 1, 2016·Nanomaterials·Veikko LinkoMauri A Kostiainen
Aug 18, 2020·Current Opinion in Biotechnology·Rebecca P ChenWilfred Chen
Mar 10, 2020·Analytical Chemistry·Jinjie LiHeyou Han
Sep 1, 2018·ACS Nano·Alexander E MarrasCarlos E Castro

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