Force-Induced Unravelling of DNA Origami

ACS Nano
Megan C EngelJonathan P K Doye

Abstract

The mechanical properties of DNA nanostructures are of widespread interest as applications that exploit their stability under constant or intermittent external forces become increasingly common. We explore the force response of DNA origami in comprehensive detail by combining AFM single molecule force spectroscopy experiments with simulations using oxDNA, a coarse-grained model of DNA at the nucleotide level, to study the unravelling of an iconic origami system: the Rothemund tile. We contrast the force-induced melting of the tile with simulations of an origami 10-helix bundle. Finally, we simulate a recently proposed origami biosensor, whose function takes advantage of origami behavior under tension. We observe characteristic stick-slip unfolding dynamics in our force-extension curves for both the Rothemund tile and the helix bundle and reasonable agreement with experimentally observed rupture forces for these systems. Our results highlight the effect of design on force response: we observe regular, modular unfolding for the Rothemund tile that contrasts with strain-softening of the 10-helix bundle which leads to catastropic failure under monotonically increasing force. Further, unravelling occurs straightforwardly from the sc...Continue Reading

References

Apr 6, 1993·Biochemistry·T J Fu, N C Seeman
Apr 1, 1997·Biophysical Journal·E Evans, K Ritchie
Oct 29, 1997·Proceedings of the National Academy of Sciences of the United States of America·B Essevaz-RouletF Heslot
Apr 14, 1999·Nature Structural Biology·M RiefH E Gaub
Sep 29, 1999·Proceedings of the National Academy of Sciences of the United States of America·T StrunzH J Güntherodt
Jul 12, 2001·Proceedings of the National Academy of Sciences of the United States of America·S CoccoJ F Marko
May 23, 2002·Biophysical Journal·Jay R WennerVictor A Bloomfield
Jan 24, 2003·Nature·Carlos BustamanteSteven B Smith
May 29, 2003·Biophysical Journal·Phiset Sa-ArdyenNadrian C Seeman
Jun 28, 2003·Biophysical Journal·Gerhard Hummer, Attila Szabo
Feb 26, 2004·Journal of the American Chemical Society·Dage LiuChengde Mao
Apr 14, 2005·Nano Letters·Frederick MathieuNadrian C Seeman
Oct 4, 2005·Biophysical Journal·Richard A Neher, Ulrich Gerland
Jan 4, 2006·FEBS Letters·G NeuertH E Gaub
Mar 17, 2006·Nature·Paul W K Rothemund
Apr 12, 2006·Physical Review Letters·Olga K DudkoAttila Szabo
Oct 10, 2006·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·J T Padding, A A Louis
Jan 16, 2007·Biophysical Journal·Ferdinand KühnerHermann E Gaub
Jun 4, 2008·Physical Review Letters·Scott ForthMichelle D Wang
Aug 9, 2008·Science·Peng YinJohn H Reif
Apr 28, 2009·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·S Fugmann, I M Sokolov
May 2, 2009·The European Physical Journal. E, Soft Matter·H FuC T Lim
May 9, 2009·Nature·Ebbe S AndersenJørgen Kjems
Jun 18, 2009·Nucleic Acids Research·Shawn M DouglasWilliam M Shih
Jul 10, 2009·The Journal of Chemical Physics·John RussoFrancesco Sciortino
Oct 21, 2009·Proceedings of the National Academy of Sciences of the United States of America·Joost van MamerenErwin J G Peterman
Nov 13, 2009·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·D B McIntoshO A Saleh
Mar 9, 2010·Journal of the American Chemical Society·Hongzhou GuNadrian C Seeman
Mar 13, 2010·Annual Review of Biochemistry·Nadrian C Seeman
Jun 22, 2010·Nature Nanotechnology·Tim LiedlWilliam M Shih
Aug 19, 2010·Proceedings of the National Academy of Sciences of the United States of America·Josep M HuguetFelix Ritort
Jan 12, 2011·The Journal of Chemical Physics·Praveen DepaJanna K Maranas
Mar 2, 2011·Nature Methods·Carlos Ernesto CastroHendrik Dietz
Mar 3, 2011·The Journal of Chemical Physics·Thomas E OuldridgeJonathan P K Doye
Nov 8, 2011·Nature Nanotechnology·Andre V PinheiroHao Yan
Dec 27, 2011·Nano Letters·Nicholas A W BellUlrich F Keyser
Jan 14, 2012·Journal of the American Chemical Society·Tong WangNadrian C Seeman
Mar 13, 2012·Biophysical Journal·Sebastian Getfert, Peter Reimann
Apr 4, 2012·Nano Letters·Mathias StrackharnHermann E Gaub

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Citations

Jul 14, 2019·Journal of Computational Chemistry·Antonio SumaLorenzo Rovigatti
Feb 12, 2020·Nucleic Acids Research·Antonio SumaVincenzo Carnevale
Jul 19, 2019·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Charlotte KielarAdrian Keller
Jan 4, 2019·Nucleic Acids Research·Benedict E K SnodinJonathan P K Doye
Jul 28, 2020·Advanced Science·Yaqin HuYanfei Liu
Oct 4, 2018·Biophysics Reviews·Jasleen Kaur Daljit SinghShelley F J Wickham
Oct 13, 2020·Nucleic Acids Research·Fan HongPetr Šulc
Jan 6, 2021·Soft Matter·Jonah ProcykPetr Šulc
Nov 24, 2019·Current Opinion in Chemical Biology·Charlie GosseDorota Kostrz
May 1, 2021·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Martin GlaserDavid M Smith
May 20, 2021·Physical Review. E·Enrico SkoruppaEnrico Carlon
May 20, 2021·Nucleic Acids Research·Erik PoppletonPetr Šulc
Nov 5, 2020·Journal of Chemical Theory and Computation·Megan C EngelJonathan P K Doye
Nov 10, 2020·Journal of Chemical Theory and Computation·Hemani ChhabraJonathan P K Doye
Apr 21, 2020·Journal of the American Chemical Society·Weina FangLihua Wang
Sep 27, 2018·Langmuir : the ACS Journal of Surfaces and Colloids·Sophie ThammWolfgang Fritzsche
Nov 25, 2020·ACS Nano·Jonathan F BerengutLawrence K Lee
Sep 10, 2021·Chemical Society Reviews·Jiahao JiHanbin Mao
Nov 12, 2021·Journal of the American Chemical Society·Hanquan SuKhalid Salaita
Oct 31, 2021·Advanced Healthcare Materials·Chung Yi TsengLeo Y T Chou

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