Self-assembly of mesogenic bent-core DNA nanoduplexes

Soft Matter
Khanh Thuy NguyenCristiano De Michele

Abstract

Short cylinder-like DNA duplexes, comprising 6 to 20 base pairs, self-assemble into semi-flexible chains, due to coaxial stacking interactions between their blunt ends. The mutual alignment of these chains gives rise to macroscopically orientationally ordered liquid crystal phases. Interestingly, experiments show that the isotropic-nematic phase boundary is sequence-dependent. We perform all-atom simulations of several sequences to gain insights into the structural properties of the duplex and correlate the resulting geometric properties with the observed location of the isotropic-nematic phase boundary. We identify in the duplex bending the key parameter for explaining the sequence dependence, suggesting that DNA duplexes can be assimilated to bent-core mesogens. We also develop a coarse-grained model for the different DNA duplexes to evaluate in detail how bending affects the persistence length and excluded volume of the aggregates. This information is fed into a recently developed formalism to predict the isotropic-nematic phase boundary for bent-core mesogens. The theoretical results agree with the experimental observations.

References

Nov 21, 1982·Journal of Theoretical Biology·N C Seeman
Mar 17, 1995·Journal of Molecular Biology·A A GorinW K Olson
Nov 25, 1994·Journal of Molecular Biology·T E HaranD M Crothers
Oct 9, 2002·Physical Review Letters·Alexei V Tkachenko
Jan 24, 2003·Nature·Nadrian C Seeman
Mar 15, 2003·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Yves LansacMatthew A Glaser
Jul 26, 2003·Science·Vinothan N ManoharanDavid J Pine
Nov 25, 2003·Advances in Protein Chemistry·Jay W Ponder, David A Case
Apr 20, 2004·Physical Review Letters·Bharat R AcharyaSatyendra Kumar
Jul 23, 2004·The Journal of Chemical Physics·Peter Virnau, Marcus Muller
Aug 25, 2004·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Alastair Dewar, Philip J Camp
Jan 25, 2005·Biophysical Journal·Eric J Sorin, Vijay S Pande
Aug 11, 2005·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·R L C Vink, T Schilling
Oct 4, 2005·Journal of Computational Chemistry·David A CaseRobert J Woods
Nov 10, 2005·Journal of the American Chemical Society·Young-Sang ChoSeung-Man Yang
Jan 6, 2006·The Journal of Chemical Physics·J L F Abascal, C Vega
Mar 17, 2006·Nature·Paul W K Rothemund
Apr 12, 2006·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Kevin Van Workum, Jack F Douglas
Sep 26, 2006·Nature Materials·Soong Ho UmDan Luo
May 10, 2007·Physical Chemistry Chemical Physics : PCCP·Jonathan P K DoyeRosie Lyus
Jan 1, 1993·Science·S I StuppL S Li
Feb 1, 2008·Nature·Dmytro NykypanchukOleg Gang
Feb 1, 2008·Nature·Sung Yong ParkChad A Mirkin
Sep 9, 2008·Journal of the American Chemical Society·Giuliano ZanchettaNoel A Clark
Sep 10, 2009·Langmuir : the ACS Journal of Surfaces and Colloids·Jin-Mi Jung, Raffaele Mezzenga
Mar 13, 2010·Nucleic Acids Research·Allison J DePaulEric J Sorin
Mar 26, 2010·Nature·S SacannaD J Pine
Jun 1, 2010·Langmuir : the ACS Journal of Surfaces and Colloids·Raffaele MezzengaJozef Adamcik
Sep 30, 2010·Proceedings of the National Academy of Sciences of the United States of America·Giuliano ZanchettaTommaso Bellini
Oct 5, 2010·Nature Materials·Matthew R JonesChad A Mirkin
Jul 5, 2006·Journal of Physics. Condensed Matter : an Institute of Physics Journal·Francis W Starr, Francesco Sciortino
Nov 19, 2008·Journal of Physics. Condensed Matter : an Institute of Physics Journal·Roberto BerardiClaudio Zannoni
Sep 11, 2013·Proceedings of the National Academy of Sciences of the United States of America·Silvia BiffiTommaso Bellini
Mar 22, 2014·ACS Nano·Lorenzo RovigattiFrancesco Sciortino
Apr 8, 2014·Langmuir : the ACS Journal of Surfaces and Colloids·Khanh Thuy NguyenCristiano De Michele

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Citations

Jul 21, 2015·The European Physical Journal. E, Soft Matter·Elena S PyanzinaCristiano De Michele
Apr 19, 2017·Physical Review. E·Suman SaurabhPrabal K Maiti
Jun 7, 2019·The European Physical Journal. E, Soft Matter·Alberto Giacomo Orellana, Cristiano De Michele
Dec 16, 2018·The European Physical Journal. E, Soft Matter·Khanh Thuy Nguyen, Cristiano De Michele
Nov 18, 2021·Soft Matter·R FoffiP I C Teixeira

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