Defined Bilayer Interactions of DNA Nanopores Revealed with a Nuclease-Based Nanoprobe Strategy

ACS Nano
Jonathan R Burns, Stefan Howorka

Abstract

DNA nanopores are a recent class of bilayer-puncturing nanodevices that can help advance biosensing, synthetic biology, and nanofluidics. Here, we create archetypal lipid-anchored DNA nanopores and characterize them with a nanoprobe-based approach to gain essential information about their interactions with bilayers. The strategy determines the molecular accessibility of DNA pores with a nuclease and can thus distinguish between the nanopores' membrane-adhering and membrane-spanning states. The analysis reveals, for example, that pores interact with bilayers in two steps whereby fast initial membrane tethering is followed by slower reorientation to the puncturing state. Tethering occurs for pores with one anchor, while puncturing requires multiple anchors. Both low and high-curvature membranes are good substrates for tethering, but efficient insertion proceeds only for high-curvature bilayers of the examined lipid composition. This is likely due to the localized lipid misalignments and the associated lower energetic barrier for pore permeation. Our study advances the fields of DNA nanotechnology and nanopores by overcoming the considerable experimental hurdle of efficient membrane insertion. It also provides mechanistic insights...Continue Reading

References

Dec 3, 2003·Science·Brian J PeterHarvey T McMahon
Nov 24, 2004·Nature Neuroscience·Matthew BanghartRichard H Kramer
Jan 13, 2006·Nature Chemical Biology·Matthew VolgrafDirk Trauner
Mar 17, 2006·Nature·Paul W K Rothemund
Oct 20, 2007·Current Opinion in Cell Biology·Mark Yeager, Andrew L Harris
Nov 11, 2008·Nature Reviews. Microbiology·Jean-Marie PagèsMathias Winterhalter
Jun 18, 2009·Nucleic Acids Research·Shawn M DouglasWilliam M Shih
Jul 23, 2009·Chemical Society Reviews·Stefan Howorka, Zuzanna Siwy
Mar 13, 2010·Annual Review of Biochemistry·Nadrian C Seeman
Sep 6, 2011·Nature Nanotechnology·Yong WangLi-Qun Gu
Sep 20, 2011·Nature Nanotechnology·Bala Murali Venkatesan, Rashid Bashir
Nov 8, 2011·Nature Nanotechnology·Andre V PinheiroHao Yan
Dec 27, 2011·Nano Letters·Nicholas A W BellUlrich F Keyser
Mar 13, 2012·Nature Nanotechnology·Ruoshan WeiUlrich Rant
Sep 20, 2012·Chemical Society Reviews·Benjamin N MilesJoshua B Edel
Oct 6, 2012·Chemical Reviews·Christopher MaffeoAleksei Aksimentiev
Nov 20, 2012·Chemical Reviews·Joseph E ReinerJohn J Kasianowicz
Nov 20, 2012·Science·Martin LangeckerFriedrich C Simmel
Dec 26, 2012·Current Opinion in Biotechnology·Daniel H Stoloff, Meni Wanunu
Apr 25, 2013·Nano Letters·Jonathan R BurnsStefan Howorka
Apr 26, 2013·Accounts of Chemical Research·Guihua WangXiyun Guan
Sep 10, 2013·Angewandte Chemie·Jonathan R BurnsStefan Howorka
Feb 24, 2015·Science·Matthew R JonesChad A Mirkin
Mar 17, 2015·Journal of Cell Science·Harvey T McMahon, Emmanuel Boucrot
Mar 31, 2015·Nano Letters·Kerstin GöpfrichUlrich F Keyser
Sep 4, 2015·Nature Nanotechnology·Yuan-Jyue ChenGeorg Seelig
Sep 22, 2015·Nature Nanotechnology·Jiandong FengAleksandra Radenovic
Dec 8, 2015·Nature Reviews. Microbiology·Matteo Dal Peraro, F Gisou van der Goot
Feb 4, 2016·Nature Nanotechnology·Stephanie J Heerema, Cees Dekker
Feb 4, 2016·Nature·Joshua QuickMiles W Carroll
Apr 16, 2016·Science·Daniel H LinAndré Hoelz
May 21, 2016·Science·Stefan Howorka
Jun 22, 2016·Nano Letters·Kerstin GöpfrichUlrich F Keyser
Aug 10, 2016·ACS Nano·Kerstin GöpfrichUlrich F Keyser
Aug 17, 2016·The Journal of Cell Biology·Iris K JarschJennifer L Gallop
Aug 26, 2016·Angewandte Chemie·Lea MessagerStefan Howorka
Sep 24, 2016·Nature Communications·Swati KrishnanFriedrich C Simmel
Dec 20, 2016·Nature Nanotechnology·Erik C YuskoMichael Mayer
Feb 16, 2017·Scientific Reports·Roland HagerStefan Howorka
Mar 21, 2017·Nature Communications·Vishal MaingiMark S P Sansom
Jul 7, 2017·Nature Nanotechnology·Stefan Howorka

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Citations

Oct 6, 2018·Angewandte Chemie·Xiaoguo LiuChunhai Fan
Jun 23, 2018·Nature Communications·Alexander OhmannAleksei Aksimentiev
Apr 3, 2019·Nanomaterials·Jonathan R Burns, Stefan Howorka
Jan 15, 2020·Advanced Biosystems·Qi ShenChenxiang Lin
Nov 7, 2019·Nature Communications·Tim DiederichsStefan Howorka
Dec 23, 2020·Nature Protocols·Conor LanphereStefan Howorka
Jan 26, 2021·ACS Nano·Nishkantha ArulkumaranStefan Howorka
May 21, 2021·Journal of the American Chemical Society·Sioned F JonesStefan Howorka
Mar 2, 2019·Bioconjugate Chemistry·William L WhitehouseStefan Howorka
Dec 10, 2019·ACS Applied Materials & Interfaces·Liang ChenYuanqing Zhang
Dec 18, 2018·Journal of the American Chemical Society·Pongphak ChidchobHanadi F Sleiman
Sep 9, 2021·Biomaterials Science·Qunye HeZhenbao Liu
Sep 28, 2021·ACS Applied Materials & Interfaces·Barbora SmolkováOleg Lunov

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