Related papers: Binding branched and linear DNA structures: from i…
Colloids coated with single-stranded DNA (ssDNA) can bind selectively to other colloids coated with complementary ssDNA. The fact that DNA-coated colloids (DNACCs) can bind to specific partners opens the prospect of making colloidal…
In this paper, we explore the feasibility of using coarse-grained models to simulate the self-assembly of DNA nanostructures. We introduce a simple model of DNA where each nucleotide is represented by two interaction sites corresponding to…
We simulate the assembly of DNA copolymers from two types of short duplexes (short double strands with a single-stranded overhang at each end), as described by the oxDNA model. We find that the statistics of chain lengths can be well…
Cells operate in part by compartmentalizing chemical reactions. For example, recent work has shown that chromatin, the material that contains the cell's genome, can auto-regulate its structure by utilizing reaction products (proteins, RNA)…
DNA plays a special role in polymer science not just because of the highly selective recognition of complementary single DNA strands but also because bacteria can express DNA chains that are very long yet perfectly monodisperse. The latter…
The observation by Ke et al. [Science 338, 1177 (2012)] that large numbers of short, pre-designed DNA strands can assemble into three-dimensional target structures came as a great surprise, as no colloidal self-assembling system has ever…
An important goal of self-assembly is to achieve a preprogrammed structure with high fidelity. Here, we control the valence of DNA-functionalized emulsions to make linear and branched model polymers, or `colloidomers'. The distribution of…
The self-assembly of DNA-coated colloids into highly-ordered structures offers great promise for advanced optical materials. However, control of disorder, defects, melting, and crystal growth is hindered by the lack of a microscopic…
We study analytically the intricate phase behavior of cross-linked $AB$ diblock copolymer melts, which can undergo two main phase transitions due to quenched random constraints: Gelation, i.e., spatially random localization of polymers…
DNA is an ideal candidate to organize matter on the nanoscale, primarily due to the specificity and complexity of DNA based interactions. Recent advances in this direction include the self-assembly of colloidal crystals using DNA grafted…
Weak multivalent interactions govern a large variety of biological processes like cell-cell adhesion and virus-host interactions. These systems distinguish sharply between surfaces based on receptor density, known as superselectivity.…
DNA supercoiling, the under or overwinding of DNA, is a key physical mechanism both participating to compaction of bacterial genomes and making genomic sequences adopt various structural forms. DNA supercoiling may lead to the formation of…
Branched molecules of deoxyribonucleic acid (DNA) can self-assemble into nanostructures through complementary cohesive strand base pairing. The production of DNA nanostructures is valuable in targeted drug delivery and biomolecular…
DNA is now firmly established as a versatile and robust platform for achieving synthetic nanostructures. While the folding of single molecules into complex structures is routinely achieved through engineering basepair sequences, much less…
We study theoretically a new generic scheme of programmable self-assembly of nanoparticles into clusters of desired geometry. The problem is motivated by the feasibility of highly selective DNA-mediated interactions between colloidal…
Fractionation is necessary for self-assembly in multicomponent mixtures. Here, reversible fractionation and crystallization are realized and studied in a two-dimensional binary colloids which is supersaturated by enhancing the attraction…
We present a coarse-grained model of DNA-functionalized colloids that is computationally tractable. Importantly, the model parameters are solely based on experimental data. Using this highly simplified model, we can predict the phase…
The formation of bubbles in nucleic acids (NAs) are fundamental in many biological processes such as DNA replication, recombination, telomeres formation, nucleotide excision repair, as well as RNA transcription and splicing. These precesses…
Concentrated solutions of short blunt-ended DNA duplexes, down to 6 base pairs, are known to order into the nematic liquid crystal phase. This self-assembly is due to the stacking interactions between the duplex terminals that promotes…
DNA self-assembly is a well-understood nanotechnology to obtain extremely ordered structures from the nanometer to up to the hundred of microns scale. By contrast, DNA hydrogels rely on the disordered assembly of DNA building blocks to…