Liquid Crystal Ordering of Four-Base-Long DNA Oligomers with Both G–C and A–T Pairing

Fraccia, Tommaso P.; Smith, Gregory P.; Clark, Noel A.; Bellini, Tommaso

doi:10.3390/cryst8010005

Cited by 13 publications

(13 citation statements)

References 28 publications

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“…22 Moreover, the existence of a LC-coacervate phase is predicted only at sufficient polyanion rigidity. 28 The observation of bulk s-dsDNA LC phases at high temperatures and experimental verification of DNA hybridization under such conditions has been reported in previous works 24,25,51 through monitoring the fluorescence emission of intercalating ethidium bromide molecules. LC phase and duplex DNA existence at high temperatures is a direct consequence of the fact that the high DNA concentration achieved in the LC phase, which in this case is enhanced within the dense coacervate phase (Figures 2D−F), leads to an increase in duplex melting temperature, T m (as DNA melting depends on strand concentration).…”

Section: Resultsmentioning

confidence: 83%

Liquid Crystal Coacervates Composed of Short Double-Stranded DNA and Cationic Peptides

Fraccia

Jia

2020

ACS Nano

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Phase separation of nucleic acids and proteins is a ubiquitous phenomenon regulating sub-cellular compartment structure and function. While complex coacervation of flexible single stranded nucleic acids is broadly investigated, coacervation of double stranded DNA (dsDNA) is less studied because of its propensity to generate solid precipitates. Here, we reverse this perspective by showing that short dsDNA and poly-L-lysine coacervates can escape precipitation while displaying a surprisingly complex phase diagram, including the full set of liquid crystal (LC) mesophases observed to date in bulk dsDNA. LC-coacervate structure was characterized upon variations in temperature and monovalent salt, DNA and peptide concentrations, which allow continuous transitions between all accessible phases. A deeper understanding of LC-coacervates can gain insights to decipher structures and phase transition mechanisms within biomolecular condensates, to design stimuli-responsive multi-phase synthetic compartments with different degrees of order and to exploit self-assembly driven cooperative prebiotic evolution of nucleic acids and peptides. File list (6) download file view on ChemRxiv LC-Coacervates-chemRxive_final.pdf (4.63 MiB) download file view on ChemRxiv Figure 1.png (4.47 MiB) download file view on ChemRxiv SI_chemRxive_final_2.pdf (4.97 MiB) download file view on ChemRxiv Movie_S1.avi (212.88 KiB) download file view on ChemRxiv Movie_S2.avi (1.66 MiB) download file view on ChemRxiv Movie_S3_.avi (6.90 MiB)

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Section: Resultsmentioning

confidence: 83%

Liquid Crystal Coacervates Composed of Short Double-Stranded DNA and Cationic Peptides

Fraccia

Jia

2020

ACS Nano

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“…Concentrated aqueous solutions of DNA oligomers paired in duplexes have been reported to order into Liquid Crystal (LC) phases [1][2][3][4]. This tendency toward LC ordering is quite robust, being found in a variety of systems, ranging from well-paired ("blunt ended") duplexes [1], to duplexes with mutually interacting ("sticky") overhangs [2], to duplexes including various degrees of defects, to structures alternating double and single strands [5], to fully random sequences [6].…”

Section: Introductionmentioning

confidence: 99%

“…This tendency toward LC ordering is quite robust, being found in a variety of systems, ranging from well-paired ("blunt ended") duplexes [1], to duplexes with mutually interacting ("sticky") overhangs [2], to duplexes including various degrees of defects, to structures alternating double and single strands [5], to fully random sequences [6]. LC have been found in longer (up to 20 bases) and shorter (down to 4 bases) DNA sequences [3,4]. Recently, LC have been observed even in solutions of single nucleobases [7], a finding that demonstrates that stacking attractive forces [8] are the main driving force of LC ordering.…”

Section: Introductionmentioning

confidence: 99%

“…Thus, the measure of the pressure of the phase transition, which in the experimental systems would be the osmotic pressure () of the DNA solution, enables estimating the strength of the intercylinder attractive interactions. Evaluations of DNA inter-duplex interactions were elaborated before by a quantitative analysis of the ISO-LC phase boundary [3,4,7]. The measure of the pressure would enable a different, and possibly more direct route to this quantity.…”

Section: Introductionmentioning

confidence: 99%

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Phase separations, liquid crystal ordering and molecular partitioning in mixtures of PEG and DNA oligomers

et al. 2018

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Liquid crystals ordering of DNA and RNA oligomers relies on the presence of inter-duplex end-to-end attraction, driving the formation of linear aggregates. Such interactions are gauged, at a macroscopic level, by the osmotic pressure at the isotropic-nematic and nematic-columnar phase transitions. We studied aqueous solutions of PEG and DNA duplex-forming oligomers, finding that there is a wide range of concentrations in which these mixtures phase separate into coexisting PEG-rich and DNA-rich phases, the latter being either in the isotropic state or ordered as a nematic or columnar liquid crystal. We determined the phase diagram in mixtures of PEG and DNA duplexes with different terminal motifsblunt ends, sticky overhangs, aggregation-preventing overhangsand measured the partitioning of the species in the coexisting phases. On this basis, we determined the osmotic pressure as a function of the DNA concentration across the phase diagram. We compared the equation of state obtained in this way with both the Carnahan-Starling equation of state for hard spheres and with the pressure predicted by computer simulations of a system of aggregating cylinders. We obtain a good agreement between experiments and simulations, and end-to-end attraction energies of the order of 6 kcal/mol, a bit larger than expected, but still in agreement with the current models for DNA-DNA interactions.

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“…Noel Clark's research into the connection between biology and liquid crystals (LCs) represents some of his most important recent scientific work. Over a period of a little more than a decade, Noel and his co-workers have discovered the liquid crystal properties and suggested the biological significance of short duplexes of DNA [1][2][3][4][5][6][7][8][9][10][11][12][13]. It all started in 2007 with the discovery that (1) short DNA duplexes spontaneously stack in solution, forming longer assemblies that form liquid crystal phases, and (2) mixtures with uneven concentrations of complementary oligomers phase separate into a liquid crystal phase formed by paired strands and an isotropic phase formed by unpaired strands [1].…”

Section: Introductionmentioning

confidence: 99%

The Genetic Algorithm: Using Biology to Compute Liquid Crystal Director Configurations

Yang

Collings

2020

Crystals

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The genetic algorithm is an optimization routine for finding the solution to a problem that requires a function to be minimized. It accomplishes this by creating a population of solutions and then producing “offspring” solutions from this population by combining two “parental” solutions in much the way that the DNA of biological parents is combined in the DNA of offspring. Strengths of the algorithm include that it is simple to implement, no trial solution is required, and the results are fairly accurate. Weaknesses include its slow computational speed and its tendency to find a local minimum that does not represent the global minimum of the function. By minimizing the elastic, surface, and electric free energies, the genetic algorithm is used to compute the liquid crystal director configuration for a wide range of situations, including one- and two-dimensional problems with various forms of boundary conditions, with and without an applied electric field. When appropriate, comparisons are made with the exact solutions. Ways to increase the performance of the algorithm as well as how to avoid various pitfalls are discussed.

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Liquid Crystal Ordering of Four-Base-Long DNA Oligomers with Both G–C and A–T Pairing

Cited by 13 publications

References 28 publications

Liquid Crystal Coacervates Composed of Short Double-Stranded DNA and Cationic Peptides

Liquid Crystal Coacervates Composed of Short Double-Stranded DNA and Cationic Peptides

Phase separations, liquid crystal ordering and molecular partitioning in mixtures of PEG and DNA oligomers

The Genetic Algorithm: Using Biology to Compute Liquid Crystal Director Configurations

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