An assembling strategy for DNA cages with minimum strands

DNA polyhedra are artificial cage-like architectures based on interlocked and interlinked DNA double-strands. Using fewer strands to construct DNA cages shows an important role in the design of single-stranded DNA molecules. However, construction methods for DNA polyhedra from topological perspective remains not well understood. In this study, we theoretically propose an assembling strategy for DNA polyhedra with minimum strands based on computer algorithm. The results show that this efficient method could search DNA polyhedra with fewer strands faster. Our research provides new insights into design and synthesis for DNA polyhedra with required topological structures.     

Lattice model of oligonucleotide hybridization in solution. I. Model and thermodynamics

A coarse-grained lattice model of DNA oligonucleotides is proposed to investigate the general mechanisms by which single-stranded oligonucleotides hybridize to their complementary strands in solution. The model, based on a high-coordination cubic lattice, is simple enough to allow the direct simulation of DNA solutions, yet capturing how the fundamental thermodynamic processes are microscopically encoded in the nucleobase sequences. Physically relevant interactions are considered explicitly, such as interchain excluded volume, anisotropic base-pairing and base-stacking, and single-stranded bending rigidity. The model is studied in detail by a specially adapted Monte Carlo simulation method, based on parallel tempering and biased trials, which is designed to overcome the entropic and enthalpic barriers associated with the sampling of hybridization events of multiple single-stranded chains in solution. This methodology addresses both the configurational complexity of bringing together two complementary strands in a favorable orientation (entropic barrier) and the energetic penalty of breaking apart multiple associated bases in a double-stranded state (enthalpic barrier). For strands with sequences restricted to nonstaggering association and homogeneous pairing and stacking energies, base-pairing is found to dominate the hybridization over the translational and conformational entropy. For strands with sequence-dependent pairing corresponding to that of DNA, the complex dependence of the model's thermal stability on concentration, sequence, and degree of complementarity is shown to be qualitatively and quantitatively consistent both with experiment and with the predictions of statistical mechanical models.     

Electrophoretic dynamics of large DNA stars in polymer solutions and gels

We have developed a procedure for synthesizing large stable branched DNA structures that enables visualization via fluorescence microscopy. Using this procedure we have synthesized large DNA stars and observed their electrophoretic behavior in polymer solutions and gels. In dilute polyacrylamide solutions, the DNA stars move as random coils and appear to experience only brief collisions with the polymer chains in solution. The effect of polymer solution concentration on the electrophoretic mobility of stars in the dilute regime is found to be in good accord with predictions of the transient entanglement coupling (TEC) model. In semidilute polymer solutions, the star arms extend in the field direction and drag the core through the matrix. The star arms form several U-shaped conformations as they collide and engage with polyacrylamide chains. The U-shaped conformations occasionally evolve into J-shaped conformations as the star arms slide off the matrix chains they engage during electrophoretic migration. In concentrated polymer solutions, the arms of the star extend and form V-shaped structures with the core as the apex. The arms then pull the core through the matrix. These V-shaped conformations are much longer-lived than U-shaped ones and, unlike the latter, do not transform to J-shaped conformations. In polyacrylamide and agarose gels, where matrix entanglements are fixed, DNA stars become trapped when entanglements with matrix molecules prevent the core from being pulled through the matrix by the extended arms. This trapping was observed at all gel concentrations and electric fields studied.     

Synthesis and characterization of new poly(ethyleneimine)‐g‐poly(methyl methacrylate) star‐block copolymers with hyperbranched cationic core

Hyperbranched polyethyleneimine (hb‐PEI) is used as polymeric scaffold to synthesize new PEI‐g‐polymethylmethacrylate (PEI‐g‐PMMA) block copolymers, consisting of a hyperbranched, partially quarternized cationic core, and PMMA‐arms. The arms are grafted to the PEI scaffold by means of the “grafting to” method. Ammonium groups, covalently bond to the hyperbranched core, provide good adhesion to negatively charged surfaces, even in case of low‐surface charges. The PMMA strands provide compatibility of the macromolecules to PMMA matrices, hence generating potential dispersants, and compatibilizers for PMMA. A peculiar association behavior in organic solution is observed as supported by dynamic light scattering and DOSY measurements. First evidences of the applicability of the macromolecules as dispersants to prepare PMMA‐nanocomposites are given. © 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2013, 51, 3700–3715     

Separation of single-stranded DNA fragments at a 10-nucleotide resolution by stretching in microfluidic channels

We report a novel DNA separation method by tethering DNA chains to a solid surface and then stretching the DNA chains with an electric field. The anchor is such designed that the critical force to detach a DNA chain is independent of its size. Because the stretching force is proportional to the DNA net charge, a gradual increase of the electric field leads to size-based removal of the DNA strands from the surface and thus DNA separation. Here we show that this method, originally proposed for separation of long double-stranded DNA chains (>10,000 base pairs), is also applicable to single-stranded (ss) DNA fragments with less than 100 nucleotides (nt). Theoretical analysis indicates that the separation resolution is limited by the fluctuation forces on tethered DNA chains. By employing a microfluidic platform with narrow channels filled with a buffer of low ionic conductivity, we are able to apply a strong electric field to the DNA fragments with negligible Joule heating. Upon stepwise increments of the electric field, we demonstrate efficient separation of short ssDNA fragments at a 10-nt resolution.     

A mirror-image tetramolecular DNA quadruplex

L-DNA, the mirror image of natural DNA forms structures of opposite chirality. We demonstrate here that a short guanine rich L-DNA strand forms a tetramolecular quadruplex with the same properties as a D-DNA strand of identical sequence, besides an inverted circular dichroism spectra. L- and D-strands self exclude when mixed together, showing that the controlled parallel self-assembly of different G-rich strands can be obtained through L-DNA use.     

Gaussian fluctuations in tethered DNA chains

In a recent work [Gao et al., Appl. Phys. Lett. 134, 113902 (2007)], we reported a novel DNA separation method by tethering DNA chains to a solid surface and then stretching the DNA chains with an electric field. The anchor is such designed that the critical force to detach a DNA chain is independent of its length. Because the stretching force is proportional to the DNA net charge, a gradual increase of the electric field leads to size-based removal of the DNA strands from the surface and thus DNA separation. Originally proposed for separation of long double-stranded DNA chains (>10 000 bps), this method has been proven useful also for short single-stranded DNA fragments (<100 bases) for which the fluctuation force induced by the solvent becomes significant. Here we show that the fluctuation force can be approximately represented by a gaussian model for tethered DNA chains. Analytical expressions have been derived to account for the dependence of the fluctuation force on the surface confinement, the polymer chain length, and the DNA tethering potential. The theoretical predictions are found to coincide with experiment.     

Isothermal assembly of DNA origami structures using denaturing agents

DNA origami is one of the most promising recent developments in DNA self-assembly. It allows for the construction of arbitrary nanoscale patterns and objects by folding a long viral scaffold strand using a large number of short "staple" strands. Assembly is usually accomplished by thermal annealing of the DNA molecules in buffer solution. We here demonstrate that both 2D and 3D origami structures can be assembled isothermally by annealing the DNA strands in denaturing buffer, followed by a controlled reduction of denaturant concentration. This opens up origami assembly for the integration of temperature-sensitive components.     

DNA origami: the art of folding DNA

The advent of DNA origami technology greatly simplified the design and construction of nanometer-sized DNA objects. The self-assembly of a DNA-origami structure is a straightforward process in which a long single-stranded scaffold (often from the phage M13mp18) is folded into basically any desired shape with the help of a multitude of short helper strands. This approach enables the ready generation of objects with an addressable surface area of a few thousand nm(2) and with a single "pixel" resolution of about 6 nm. The process is rapid, puts low demands on experimental conditions, and delivers target products in high yields. These features make DNA origami the method of choice in structural DNA nanotechnology when two- and three-dimensional objects are desired. This Minireview summarizes recent advances in the design of DNA origami nanostructures, which open the door to numerous exciting applications.     

Structural characterization of nanoparticles from thermoresponsive poly(N-isopropylacrylamide)-DNA conjugate

Poly(N-isopropylacrylamide) (PNIPAAm) grafted with single-stranded (ss) DNA conjugate (PNIPAAm-g-DNA) self-assembles above its lower critical solution temperature to form colloidal particles. When the ssDNA within the particle hybridizes with its complementary DNA, the particles aggregate above a certain threshold of salt concentration with drastically increased turbidity in solution. Detailed structural information of the particle was obtained mainly by small-angle X-ray scattering. The influence of copolymer composition on the morphology of particle and non-crosslinking aggregation was examined. The particle consists of hydrophobic PNIPAAm core surrounded by hydrophilic DNA strands. The increase in DNA fraction brought about a significant decrease in core size, whereas the shell thickness little changed and corresponded to the length of DNA. A structural model with a sticky potential was applied to the analysis of particle aggregate. This analysis provided that the particles aggregate while the coronal layers interpenetrate each other. The interaction between the particles was quantified in terms of the sticky potential and showed a trend to be influenced by the particle size rather than the graft density of DNA strands on the particle.     

Directed self-assembly of inorganic redox complexes with artificial peptide scaffolds

An ongoing challenge in the construction of supramolecular systems is controlling the relative geometry of functional redox species for molecular electronics devices, including wires, switches, and gates. This review focuses on the use of artificial peptide strands to assemble inorganic complexes that are redox active. These approaches toward macromolecular assembly use varying oligoamide backbones and assembly motifs that grew from earlier reports of single oligolysine or proline chains containing pendant redox species that undergo photoinduced charge separation. Recently, peptide nucleic acid chains that form double-stranded duplexes analogous to DNA by hydrogen bonding of complementary base pairs have been modified to contain metal complexes. In these structures, hydrogen bonding and metal coordination combine to form crosslinks between the PNA strands. Finally, a family of structures is described that is based on an aminoethylglycine scaffold with pendant metal coordination sites, but without intervening nucleic acid base pairs. These structures form multimetallic complexes that are either single- or double-stranded, or that form hairpin loop structures. These motifs for using artificial peptide strands for self-assembly hold electron donors and acceptors in relative positions that provide structural connectivity and permit electron transfers between linked metal complexes. This is a new approach for creating polyfunctional redox architectures that could ultimately enable the construction of potentially large and complex molecular electronics devices.     

Assembly and characterization of 8-arm and 12-arm DNA branched junctions

Branched DNA molecules can be assembled into objects and networks directed by sticky-ended cohesion. The connectivity of these species is limited by the number of arms flanking the branch point. To date, the only branched junctions constructed contain six or fewer arms. We report the construction of DNA branched junctions that contain either 8 or 12 double-helical arms surrounding a branch point. The design of the 8-arm junction exploits the limits of a previous approach to thwart branch migration, but the design of the 12-arm junction uses a new to principle achieve this end. The 8-arm junction is stable with 16 nucleotide pairs per arm, but the 12-arm junction has been stabilized by 24 nucleotide pairs per arm. Ferguson analysis of these junctions in combination with 3-, 4-, 5-, and 6-arm junctions indicates a linear increase in friction constant as the number of arms increases; the 4-arm junction migrates anomalously at 4 degrees C, suggesting stacking of its domains. All strands in both the 8-arm and 12-arm junctions show similar responses to hydroxyl radical autofootprinting analysis, indicating that they lack any dominant stacking structures. The stability of the 12-arm junction demonstrates that the number of arms in a junction is not limited to the case of having adjacent identical base pairs flanking the junction. The ability to construct 8-arm and 12-arm junctions increases the number of objects, graphs, and networks that can be built from branched DNA components. In principle, the stick structure corresponding to cubic close-packing is now a possible target for assembly by DNA nanotechnology.     

MD simulations of homomorphous PNA, DNA, and RNA single strands: characterization and comparison of conformations and dynamics

MD simulations of homomorphous single-stranded PNA, DNA, and RNA with the same base sequence have been performed in aqueous solvent. For each strand two separate simulations were performed starting from a (i) helical conformation and (ii) random coiled state. Comparisons of the simulations with the single-stranded helices (case i) show that the differences in the covalent nature of the backbones cause significant differences in the structural and dynamical properties of the strands. It is found that the PNA strand maintains its nice base-stacked initial helical structure throughout the 1.5-ns MD simulation at 300 K, while DNA/RNA show relatively larger fluctuations in the structures with a few local unstacking events during -ns MD simulation each. It seems that the weak physical coupling between the bases and the backbone in PNA causes a loss of correlation between the dynamics of the bases and the backbone compared to the DNA/RNA and helps maintain the base-stacked helical conformation. The global flexibility of a single-stranded PNA helix was also found to be lowest, while RNA appears to be the most flexible single-stranded helix. The sugar pucker of several nucleotides in single-stranded DNA and RNA was found to adopt both C2'-endo and C3'-endo conformations for significant times. This effect is more pronounced for single strands in completely coiled states. The simulations with single-stranded coils as the initial structure also indicate that a PNA can adopt a more compact globular structure, while DNA/RNA of the same size adopts a more extended coil structure. This allows even a short PNA in the coiled state to form a significantly stable nonsequentially base-stacked globular structure in solution. Due to the hydrophobic nature of the PNA backbone, it interacts with surrounding water rather weakly compared to DNA/RNA.     

Molecular gears: a pair of DNA circles continuously rolls against each other

A pair of DNA nanocircles has been constructed to model gears. The nanogears can move against each other continuously. Each gear consists of a DNA duplex circle and three single-stranded teeth. The teeth on the two gears are brought together by linker strands, which are complementary to the gear teeth. The teeth are separated from each other by removal of the linker strands with a strand displacement mechanism.     

Cross-linked DNA generated by "bis-click" reactions with bis-functional azides: site independent ligation of oligonucleotides via nucleobase alkynyl chains

Template-free cross-linking of single-stranded DNA bearing octadiynyl side chains at the 7-position of 8-aza-7-deazapurine moieties with bisfunctional azides is reported employing a Cu(I)-catalyzed azide-alkyne "bis-click" reaction. Bis-adducts were formed when the bis-azide:oligonucleotide ratio was 1:1; monofunctionalization occurred when the ratio was 15:1. Four-stranded DNA consisting of two cross-linked duplexes was obtained after hydridization. Cross-linked duplexes are as stable as individual duplexes when ligation was introduced at terminal positions; ligation at a central position led to a slight duplex destabilization.     

Parallel molecular computations of pairwise exclusive-or (XOR) using DNA "string tile" self-assembly

Self-assembling DNA nanostructures are an efficient means of executing parallel molecular computations. However, previous experimental demonstrations of computations by DNA tile self-assembly only allowed for one set of distinct input to be processed at a time. Here, we report the multibit, parallel computation of pairwise exclusive-or (XOR) using DNA "string tile" self-assembly. A set of DNA tiles encoding the truth table for the XOR logical operation was constructed. Parallel tile self-assembly and ligation led to the formation of reporter DNA strands which encoded both the input and the output of the computations. These reporter strands provided a molecular look-up table containing all possible pairwise XOR calculations up to a certain input size. The computation was readout by sequencing the cloned reporter strands. This is the first experimental demonstration of a parallel computation by DNA tile self-assembly in which a large number of distinct input were simultaneously processed.     

DNA bimodified gold nanoparticles

We report a general approach to bimodify gold nanoparticles (GNPs) with two different DNA strands via DNA template reaction. Two thioctic acid modified DNA strands, one at 5' end and one at 3' end, were attached to GNPs through bivalent thiol-gold bond. By sequence design, assemblies of 5 nm GNPs chains, 10 nm GNPs chains and alternative arrangement of 5 and 10 nm GNPs could be achieved. Gel electrophoresis, transmission electron microscope (TEM), UV-vis spectra were used to characterize the assemblies. It is believed that this new kind of bimodified GNPs with two different DNA strands at different ends would enrich the toolbox of DNA-GNP conjugates and provide diverse selectivity for further assembly.     

Star-shaped oligobenzoates: non-conventional mesogens forming columnar helical mesophases

Star-shaped mesogens with a phloroglucinol or a trimesic acid core and oligobenzoate arms with up to five repeating units have been synthesised. These non-conventional mesogens form various columnar mesophases over a broad temperature range. The liquid-crystal phases were characterised by optical microscopy, differential scanning calorimetry, X-ray diffraction, dilatometry and solid-state NMR spectroscopy. In addition to the high-temperature hexagonal columnar phases, the columnar self-assemblies undulate upon cooling and consequently form higher-ordered body-centred orthorhombic columnar 3D structures. A model of E-shaped folded conformers helically displaced along the columns is proposed. Helical preorganisation in the hexagonal phase precedes the transition to the low-temperature phases. Space filling and nano-segregation compete in the self-organisation process, thus aliphatic chains and the polar oligobenzoate scaffold are not perfectly separated in these star-shaped mesogens.     

Site-specific dynamics of strands in ss- and dsDNA as revealed by time-domain fluorescence of 2-aminopurine

It is well recognized that structure and dynamics of DNA strands guide proteins toward their cognate sites in DNA. While the dynamics is controlled primarily by the nucleotide sequence, the context of a particular sequence in relation to an open end could also play a significant role. In this work we have used the fluorescent analogue of adenine, 2-aminopurine (2-AP), to extract information on site-specific dynamics of DNA strands associated with 30-70 nucleotides length. Measurement of fluorescence lifetime and anisotropy decay kinetics in various types of DNA strands in which 2-AP was located in specific positions revealed novel insights into the dynamics of strands. We find that in single-stranded (ss) DNA, the extent of motional dynamics of the bases falls off sharply from the very end toward the middle of the strand. In contrast, the flexibility of the backbone decreases more gradually in the same direction. In double-stranded (ds) DNA, the level of base-pair fraying increases toward the ends in a graded manner. Surprisingly, the same is countered by the presence of ss-overhangs emanating from dsDNA ends. Moreover, the extent of concerted motion of bases in duplex DNA increased from the end to the middle of the duplex, a result which is both striking and counterintuitive. Most surprisingly, the two complementary strands of a duplex that were unequal in length exhibited differential dynamics: the longer one with overhangs showed a distinctly higher level of flexibility than the recessed shorter strand in the same duplex. All these results, taken together, provoke newer insights in our understanding of how different bases in DNA strands are endowed with specific dynamic properties as a function of their positions. These properties are likely to be used in facilitating specific recognitions of DNA bases by proteins during various DNA-protein interaction systems.     

Stability of DNA-linked nanoparticle crystals: effect of number of strands, core size, and rigidity of strand attachment

Three-dimensional ordered lattices of nanoparticles (NPs) linked by DNA have potential applications in novel devices and materials, but most experimental attempts to form crystals result in amorphous packing. Here we use a coarse-grained computational model to address three factors that impact the stability of bcc and fcc crystals formed by DNA-linked NPs : (i) the number of attached strands to the NP surface, (ii) the size of the NP core, and (iii) the rigidity of the strand attachment. We find that allowing mobility in the attachment of DNA strands to the core NP can very slightly increase or decrease melting temperature T(M). Larger changes to T(M) result from increasing the number of strands, which increases T(M), or by increasing the core NP diameter, which decreases T(M). Both results are consistent with experimental findings. Moreover, we show that the behavior of T(M) can be quantitatively described by the model introduced previously [F. Vargas Lara and F. W. Starr, Soft Matter, 7, 2085 (2011)].