Steric crowding and the kinetics of DNA hybridization within a DNA nanostructure system

ACS Nano
Andre V PinheiroYan Liu

Abstract

The ability to generate precisely designed molecular networks and modulate the surrounding environment is vital for fundamental studies of chemical reactions. DNA nanotechnology simultaneously affords versatility and modularity for the construction of tailored molecular environments. We systematically studied the effects of steric crowding on the hybridization of a 20 nucleotide (nt) single-stranded DNA (ssDNA) target to a complementary probe strand extended from a rectangular six-helix tile, where the number and character of the surrounding strands influence the molecular environment of the hybridization site. The hybridization events were monitored through an increase in the quantum yield of a single reporter fluorophore (5-carboxyfluorescein) upon hybridization of the 20-nt ssDNA, an effect previously undocumented in similar systems. We observed that as the hybridization site moved from outer to inner positions along the DNA tile, the hybridization rate constant decreased. A similar rate decrease was observed when noncomplementary single- and double-stranded DNA flanked the hybridization site. However, base-pairing interactions between the hybridization site of the probe and the surrounding DNA resulted in a reduction in the...Continue Reading

References

Jan 1, 1976·Annual Review of Biophysics and Bioengineering·J G Wetmur
Dec 14, 1971·Journal of Molecular Biology·M E CraigP Doty
Apr 21, 1998·Bioconjugate Chemistry·C M NiemeyerR M Hoedemakers
May 8, 2002·Analytical Sciences : the International Journal of the Japan Society for Analytical Chemistry·M TorimuraR Kurane
May 14, 2004·Annual Review of Biophysics and Biomolecular Structure·John SantaLucia, Donald Hicks
Oct 20, 2004·Proceedings of the National Academy of Sciences of the United States of America·Robert M Dirks, Niles A Pierce
Mar 30, 2006·Journal of the American Chemical Society·Yonggang KeHao Yan
Apr 14, 2007·Nucleic Acids Research·Chunlai ChenXin Sheng Zhao
Jan 19, 2008·Nature·Peng YinNiles A Pierce
Mar 12, 2008·Biochimie·Daisuke Miyoshi, Naoki Sugimoto
Jul 26, 2008·Nature Nanotechnology·Russell P GoodmanAndrew J Turberfield
Sep 27, 2008·Science·Faisal A AldayeHanadi F Sleiman
Nov 11, 2008·Chemical Communications : Chem Comm·Yonggang KeYan Liu
Dec 6, 2008·Chemical Communications : Chem Comm·Bi-feng YuanZheng Tan
May 29, 2009·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Sören DooseMarkus Sauer
Jul 22, 2009·Biophysical Journal·Jeanette NangreaveYan Liu
Nov 10, 2009·Journal of the American Chemical Society·David Yu Zhang, Erik Winfree
Dec 17, 2009·Photochemistry and Photobiology·Roberto F Delgadillo, Lawrence J Parkhurst
May 12, 2010·Current Opinion in Structural Biology·William M Shih, Chenxiang Lin
May 14, 2010·Nature·Hongzhou GuNadrian C Seeman
May 14, 2010·Nature·Kyle LundHao Yan
Jun 12, 2010·Current Opinion in Biotechnology·Xi Chen, Andrew D Ellington
Jul 21, 2010·Nanoscale·Akinori Kuzuya, Makoto Komiyama
Oct 5, 2010·Nature Nanotechnology·Dongran HanHao Yan
Nov 3, 2010·Nature Biotechnology·Harry M T ChoiNiles A Pierce
Dec 3, 2010·Nature Chemistry·Pik Kwan LoHanadi F Sleiman
Jan 25, 2011·Nature Chemistry·David Yu Zhang, Georg Seelig
Feb 8, 2011·Nature Nanotechnology·Shelley F J WickhamAndrew J Turberfield
Mar 9, 2011·Journal of the American Chemical Society·Jeanette NangreaveYan Liu
May 20, 2011·Chemical Society Reviews·Thomas TørringKurt V Gothelf
Jun 28, 2011·Science·Camille J DelebecqueFaisal A Aldaye
Jul 2, 2011·Accounts of Chemical Research·Yandong Yin, Xin Sheng Zhao
Nov 8, 2011·Nature Nanotechnology·Andre V PinheiroHao Yan

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Citations

May 6, 2014·ACS Nano·Shuoxing JiangYan Liu
Aug 31, 2013·Scientific Reports·Shiv K RedhuAllen W Nicholson
Jul 5, 2012·Small·Barbara SaccàChristof M Niemeyer
Mar 8, 2014·Methods : a Companion to Methods in Enzymology·Alexander Johnson-Buck, Nils G Walter
Aug 2, 2013·The Journal of Physical Chemistry. B·Jacqueline R SikoraAlice Deckert
May 24, 2014·Accounts of Chemical Research·Xixi WeiYan Liu
Mar 30, 2013·Journal of the American Chemical Society·Xixi WeiYan Liu
Mar 5, 2014·Accounts of Chemical Research·Nan ChenChunhai Fan
Jun 13, 2018·Proceedings of the National Academy of Sciences of the United States of America·Martin SajfutdinowDavid M Smith
Mar 12, 2021·ACS Nano·Shuoxing JiangYan Liu
Aug 17, 2017·ACS Nano·Shuoxing JiangYan Liu

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