Smectic phase in suspensions of gapped DNA duplexes
Abstract
Smectic ordering in aqueous solutions of monodisperse stiff double-stranded DNA fragments is known not to occur, in spite of the fact that these systems exhibit both chiral nematic and columnar mesophases. Here, we show, unambiguously, that a smectic-A type of phase is formed by increasing the DNA's flexibility through the introduction of an unpaired single-stranded DNA spacer in the middle of each duplex. This is unusual for a lyotropic system, where flexibility typically destabilizes the smectic phase. We also report on simulations suggesting that the gapped duplexes (resembling chain-sticks) attain a folded conformation in the smectic layers, and argue that this layer structure, which we designate as smectic-fA phase, is thermodynamically stabilized by both entropic and energetic contributions to the system's free energy. These results demonstrate that DNA as a building block offers an exquisitely tunable means to engineer a potentially rich assortment of lyotropic liquid crystals.
- Authors:
-
- Kent State Univ., Kent, OH (United States)
- Forschungszentrum Julich (Germany); Chinese Academy of Sciences (CAS), Beijing (China)
- University of Groningen, Groningen, (Netherlands)
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Advanced Light Source (ALS)
- Forschungszentrum Julich (Germany)
- Sapienza Univ. of Rome (Italy)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Basic Energy Sciences (BES)
- OSTI Identifier:
- 1377590
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Nature Communications
- Additional Journal Information:
- Journal Volume: 7; Journal ID: ISSN 2041-1723
- Publisher:
- Nature Publishing Group
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
Salamonczyk, Miroslaw, Zhang, Jing, Portale, Giuseppe, Zhu, Chenhui, Kentzinger, Emmanuel, Gleeson, James T., Jakli, Antal, De Michele, Cristiano, Dhont, Jan K. G., Sprunt, Samuel, and Stiakakis, Emmanuel. Smectic phase in suspensions of gapped DNA duplexes. United States: N. p., 2016.
Web. doi:10.1038/ncomms13358.
Salamonczyk, Miroslaw, Zhang, Jing, Portale, Giuseppe, Zhu, Chenhui, Kentzinger, Emmanuel, Gleeson, James T., Jakli, Antal, De Michele, Cristiano, Dhont, Jan K. G., Sprunt, Samuel, & Stiakakis, Emmanuel. Smectic phase in suspensions of gapped DNA duplexes. United States. https://doi.org/10.1038/ncomms13358
Salamonczyk, Miroslaw, Zhang, Jing, Portale, Giuseppe, Zhu, Chenhui, Kentzinger, Emmanuel, Gleeson, James T., Jakli, Antal, De Michele, Cristiano, Dhont, Jan K. G., Sprunt, Samuel, and Stiakakis, Emmanuel. Tue .
"Smectic phase in suspensions of gapped DNA duplexes". United States. https://doi.org/10.1038/ncomms13358. https://www.osti.gov/servlets/purl/1377590.
@article{osti_1377590,
title = {Smectic phase in suspensions of gapped DNA duplexes},
author = {Salamonczyk, Miroslaw and Zhang, Jing and Portale, Giuseppe and Zhu, Chenhui and Kentzinger, Emmanuel and Gleeson, James T. and Jakli, Antal and De Michele, Cristiano and Dhont, Jan K. G. and Sprunt, Samuel and Stiakakis, Emmanuel},
abstractNote = {Smectic ordering in aqueous solutions of monodisperse stiff double-stranded DNA fragments is known not to occur, in spite of the fact that these systems exhibit both chiral nematic and columnar mesophases. Here, we show, unambiguously, that a smectic-A type of phase is formed by increasing the DNA's flexibility through the introduction of an unpaired single-stranded DNA spacer in the middle of each duplex. This is unusual for a lyotropic system, where flexibility typically destabilizes the smectic phase. We also report on simulations suggesting that the gapped duplexes (resembling chain-sticks) attain a folded conformation in the smectic layers, and argue that this layer structure, which we designate as smectic-fA phase, is thermodynamically stabilized by both entropic and energetic contributions to the system's free energy. These results demonstrate that DNA as a building block offers an exquisitely tunable means to engineer a potentially rich assortment of lyotropic liquid crystals.},
doi = {10.1038/ncomms13358},
journal = {Nature Communications},
number = ,
volume = 7,
place = {United States},
year = {Tue Nov 15 00:00:00 EST 2016},
month = {Tue Nov 15 00:00:00 EST 2016}
}
Web of Science
Works referenced in this record:
Solid-state phosphorus-31 NMR studies of DNA liquid crystalline phases. Isotropic to cholesteric transition
journal, July 1987
- Strzelecka, Teresa E.; Rill, Randolph L.
- Journal of the American Chemical Society, Vol. 109, Issue 15
End-to-End Stacking and Liquid Crystal Condensation of 6- to 20-Base Pair DNA Duplexes
journal, November 2007
- Nakata, M.; Zanchetta, G.; Chapman, B. D.
- Science, Vol. 318, Issue 5854
Entropy-induced smectic phases in rod coil copolymers
journal, November 2002
- D. chs, Dominik; Sullivan, D. E.
- Journal of Physics: Condensed Matter, Vol. 14, Issue 46
Flexibility of DNA
journal, June 1988
- Hagerman, Paul J.
- Annual Review of Biophysics and Biophysical Chemistry, Vol. 17, Issue 1
Isotropic-nematic phase transition in suspensions of filamentous virus and the neutral polymer Dextran
journal, May 2004
- Dogic, Zvonimir; Purdy, Kirstin R.; Grelet, Eric
- Physical Review E, Vol. 69, Issue 5
Polydispersity and Ordered Phases in Solutions of Rodlike Macromolecules
journal, February 1996
- Bohle, Anne M.; Hołyst, Robert; Vilgis, Thomas
- Physical Review Letters, Vol. 76, Issue 8
Self-Assembly of Bifunctional Patchy Particles with Anisotropic Shape into Polymers Chains: Theory, Simulations, and Experiments
journal, December 2011
- De Michele, Cristiano; Bellini, Tommaso; Sciortino, Francesco
- Macromolecules, Vol. 45, Issue 2
Phase separation and liquid crystallization of complementary sequences in mixtures of nanoDNA oligomers
journal, January 2008
- Zanchetta, G.; Nakata, M.; Buscaglia, M.
- Proceedings of the National Academy of Sciences, Vol. 105, Issue 4
Crowding-induced organization of cytoskeletal elements. III. Spontaneous bundling and sorting of self-assembled filaments with different flexibilities
journal, December 1995
- Kulp, Daniel T.; Herzfeld, Judith
- Biophysical Chemistry, Vol. 57, Issue 1
Liquid crystalline phases in concentrated aqueous solutions of Na+ DNA.
journal, January 1986
- Rill, R. L.
- Proceedings of the National Academy of Sciences, Vol. 83, Issue 2
Smectic Phase in a Colloidal Suspension of Semiflexible Virus Particles
journal, March 1997
- Dogic, Zvonimir; Fraden, Seth
- Physical Review Letters, Vol. 78, Issue 12
On the spontaneous symmetry breaking in the mesophases of achiral banana-shaped molecules
journal, October 2001
- Dozov, I.
- Europhysics Letters (EPL), Vol. 56, Issue 2
Monte Carlo simulations of smectic phase transitions in flexible–rigid–flexible molecules
journal, June 1999
- Casey, Alison; Harrowell, Peter
- The Journal of Chemical Physics, Vol. 110, Issue 24
DNA packaging by the double-stranded DNA bacteriophages
journal, September 1980
- Earnshaw, William C.; Casjens, Sherwood R.
- Cell, Vol. 21, Issue 2
Smectic phases in rod–coil diblock copolymers
journal, August 2007
- Hidalgo, Raul Cruz; Sullivan, D. E.; Chen, Jeff Z. Y.
- Journal of Physics: Condensed Matter, Vol. 19, Issue 37
Spontaneous self-assembly of nucleic acids: liquid crystal condensation of complementary sequences in mixtures of DNA and RNA oligomers
journal, September 2009
- Zanchetta, Giuliano
- Liquid Crystals Today, Vol. 18, Issue 2
Liquid crystal phases of achiral banana-shaped molecules: a computer simulation study
journal, April 2002
- Memmer, R.
- Liquid Crystals, Vol. 29, Issue 4
The highly concentrated liquid-crystalline phase of DNA is columnar hexagonal
journal, June 1989
- Livolant, F.; Levelut, A. M.; Doucet, J.
- Nature, Vol. 339, Issue 6227
Refusing to Twist: Demonstration of a Line Hexatic Phase in DNA Liquid Crystals
journal, April 2000
- Strey, H. H.; Wang, J.; Podgornik, R.
- Physical Review Letters, Vol. 84, Issue 14
Liquid crystalline phases given by helical biological polymers (DNA, PBLG and xanthan). Columnar textures
journal, January 1986
- Livolant, F.; Bouligand, Y.
- Journal de Physique, Vol. 47, Issue 10
Probing Single-Stranded DNA Conformational Flexibility Using Fluorescence Spectroscopy
journal, April 2004
- Murphy, M. C.; Rasnik, Ivan; Cheng, Wei
- Biophysical Journal, Vol. 86, Issue 4, p. 2530-2537
DNA length and concentration dependencies of anisotropic phase transitions of DNA solutions
journal, December 1997
- Merchant, K.; Rill, R. L.
- Biophysical Journal, Vol. 73, Issue 6
DNA-DNA interactions
journal, June 1998
- Strey, Helmut H.; Podgornik, Rudi; Rau, Donald C.
- Current Opinion in Structural Biology, Vol. 8, Issue 3
Tracing the phase boundaries of hard spherocylinders
journal, January 1997
- Bolhuis, Peter; Frenkel, Daan
- The Journal of Chemical Physics, Vol. 106, Issue 2
A re‐examination of the phase diagram of hard spherocylinders
journal, May 1996
- McGrother, Simon C.; Williamson, Dave C.; Jackson, George
- The Journal of Chemical Physics, Vol. 104, Issue 17
Nematic ordering in semiflexible polymer chains
journal, June 1993
- Chen, Zheng Yu
- Macromolecules, Vol. 26, Issue 13
Statistical Thermodynamics of Mixtures of Rodlike Particles. 5. Mixtures with Random Coils
journal, November 1978
- Flory, Paul J.
- Macromolecules, Vol. 11, Issue 6
Accurate phase diagram of tetravalent DNA nanostars
journal, April 2014
- Rovigatti, Lorenzo; Bomboi, Francesca; Sciortino, Francesco
- The Journal of Chemical Physics, Vol. 140, Issue 15
Magnetic ordering of DNA liquid crystals
journal, October 1986
- Brandes, Rolf; Kearns, David R.
- Biochemistry, Vol. 25, Issue 20
Hierarchical Propagation of Chirality through Reversible Polymerization: The Cholesteric Phase of DNA Oligomers
journal, January 2016
- De Michele, Cristiano; Zanchetta, Giuliano; Bellini, Tommaso
- ACS Macro Letters, Vol. 5, Issue 2
Nematic Phase Transitions in Mixtures of Thin and Thick Colloidal Rods
journal, February 2005
- Purdy, Kirstin R.; Varga, Szabolcs; Galindo, Amparo
- Physical Review Letters, Vol. 94, Issue 5
Colloidal DNA
journal, October 1998
- Podgornik, Rudi; Strey, Helmut H.; Parsegian, V. Adrian
- Current Opinion in Colloid & Interface Science, Vol. 3, Issue 5
Structure of Short DNA Fragment Solutions
journal, August 1998
- van der Maarel, J. R. C.; Kassapidou, K.
- Macromolecules, Vol. 31, Issue 17
DNA mesophases induced by spermidine: structural properties and biological implications
journal, July 1996
- Pelta, J.; Durand, D.; Doucet, J.
- Biophysical Journal, Vol. 71, Issue 1
Cholesteric helical pitch of near persistence length DNA
journal, September 1990
- Van Winkle, David H.; Davidson, Michael W.; Chen, Wan Xu
- Macromolecules, Vol. 23, Issue 18
A Monte Carlo study of the influence of molecular flexibility on the phase diagram of a fused hard sphere model
journal, December 2002
- McBride, Carl; Vega, Carlos
- The Journal of Chemical Physics, Vol. 117, Issue 22
Probability of DNA knotting and the effective diameter of the DNA double helix.
journal, June 1993
- Rybenkov, V. V.; Cozzarelli, N. R.; Vologodskii, A. V.
- Proceedings of the National Academy of Sciences, Vol. 90, Issue 11
Elongation and Fluctuations of Semiflexible Polymers in a Nematic Solvent
journal, March 2004
- Dogic, Z.; Zhang, J.; Lau, A. W. C.
- Physical Review Letters, Vol. 92, Issue 12
Structure of hard-core models for liquid crystals
journal, June 1988
- Frenkel, Daan
- The Journal of Physical Chemistry, Vol. 92, Issue 11
Chiral heliconical ground state of nanoscale pitch in a nematic liquid crystal of achiral molecular dimers
journal, September 2013
- Chen, D.; Porada, J. H.; Hooper, J. B.
- Proceedings of the National Academy of Sciences, Vol. 110, Issue 40, p. 15931-15936
Orientation of Nucleic Acids in High Magnetic Fields
journal, August 1975
- Maret, G.; Schickfus, M. v.; Mayer, A.
- Physical Review Letters, Vol. 35, Issue 6
The Effects of Shape on the Interaction of Colloidal Particles
journal, May 1949
- Onsager, Lars
- Annals of the New York Academy of Sciences, Vol. 51, Issue 4
Structure and interactions of biological helices
journal, August 2007
- Kornyshev, Alexei A.; Lee, Dominic J.; Leikin, Sergey
- Reviews of Modern Physics, Vol. 79, Issue 3
Magnetic ordering in synthetic oligonucleotides. A deuterium nuclear magnetic resonance investigation
journal, June 1990
- Alam, Todd M.; Drobny, Gary
- The Journal of Chemical Physics, Vol. 92, Issue 11
Simulation study of the phase behavior of a primitive model for thermotropic liquid crystals: Rodlike molecules with terminal dipoles and flexible tails
journal, May 2000
- van Duijneveldt, Jeroen S.; Gil-Villegas, Alejandro; Jackson, George
- The Journal of Chemical Physics, Vol. 112, Issue 20
Recent experiments on a small-angle/wide-angle X-ray scattering beam line at the ESRF
journal, April 2003
- Bras, W.; Dolbnya, I. P.; Detollenaere, D.
- Journal of Applied Crystallography, Vol. 36, Issue 3
Multiple liquid crystal phases of DNA at high concentrations
journal, February 1988
- Strzelecka, Teresa E.; Davidson, Michael W.; Rill, Randolph L.
- Nature, Vol. 331, Issue 6155
A cluster algorithm for Monte Carlo simulation at constant pressure
journal, January 2009
- Almarza, N. G.
- The Journal of Chemical Physics, Vol. 130, Issue 18
Condensed phases of DNA: Structures and phase transitions
journal, January 1996
- Livolant, Françoise; Leforestier, Amélie
- Progress in Polymer Science, Vol. 21, Issue 6
Morphology and Kinetics of the Isotropic−Nematic Phase Transition in Dispersions of Hard Rods
journal, April 1999
- van Bruggen, M. P. B.; Dhont, J. K. G.; Lekkerkerker, H. N. W.
- Macromolecules, Vol. 32, Issue 7
Ordered phases of DNA in vivo and in vitro
journal, August 1991
- Livolant, Françoise
- Physica A: Statistical Mechanics and its Applications, Vol. 176, Issue 1
The parabolic focal conic : a new smectic a defect
journal, January 1977
- Rosenblatt, Ch. S.; Pindak, R.; Clark, N. A.
- Journal de Physique, Vol. 38, Issue 9
Phase behavior of colloidal silica rods
journal, January 2012
- Kuijk, Anke; Byelov, Dmytro V.; Petukhov, Andrei V.
- Faraday Discussions, Vol. 159
Self-assembly of short DNA duplexes: from a coarse-grained model to experiments through a theoretical link
journal, January 2012
- De Michele, Cristiano; Rovigatti, Lorenzo; Bellini, Tommaso
- Soft Matter, Vol. 8, Issue 32
Electron microscopy of liquid crystalline DNA: direct evidence for cholesteric-like organization of DNA in dinoflagellate chromosomes
journal, October 1989
- Rill, Randolph L.; Livolant, Fran�oise; Aldrich, Henry C.
- Chromosoma, Vol. 98, Issue 4
Hexagonal and nematic phases of chains. II. Phase transitions
journal, March 1991
- Selinger, Jonathan V.; Bruinsma, Robijn F.
- Physical Review A, Vol. 43, Issue 6
Works referencing / citing this record:
Structure and stimuli-responsiveness of all-DNA dendrimers: theory and experiment
journal, January 2019
- Jochum, Clemens; Adžić, Nataša; Stiakakis, Emmanuel
- Nanoscale, Vol. 11, Issue 4
Lyotropic liquid crystals and linear supramolecular polymers of end-functionalized oligosaccharides
journal, January 2019
- Myllymäki, Teemu T. T.; Guliyeva, Aynur; Korpi, Antti
- Chemical Communications, Vol. 55, Issue 78
Liquid crystals and precious metal: from nanoparticle dispersions to functional plasmonic nanostructures
journal, August 2017
- Atorf, Bernhard; Funck, Timon; Hegmann, Torsten
- Liquid Crystals
Speeding up Monte Carlo simulation of patchy hard cylinders
journal, April 2018
- Orellana, Alberto Giacomo; Romani, Emanuele; De Michele, Cristiano
- The European Physical Journal E, Vol. 41, Issue 4
Thermotropic Liquid Crystal-Assisted Chemical and Biological Sensors
journal, December 2017
- Popov, Nicolai; Honaker, Lawrence W.; Popova, Maia
- Materials, Vol. 11, Issue 1
Liquid-crystalline nanoarchitectures for tissue engineering
journal, January 2018
- Sung, Baeckkyoung; Kim, Min-Ho
- Beilstein Journal of Nanotechnology, Vol. 9
Structure and stimuli-responsiveness of all-DNA dendrimers: theory and experiment
preprint, January 2018
- Jochum, Clemens; Adžić, Nataša; Stiakakis, Emmanuel
- arXiv