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The ease with which racemic mixtures crystallize compared with the equivalent chiral systems is routinely taken advantage of to produce crystals of small molecules. However, biological macromolecules such as DNA and proteins are naturally chiral, and thus the limited range of chiral space groups available hampers the crystallization of such molecules. Inspiring work over the past 15 years has shown that racemic mixtures of proteins, which were made possible by impressive advances in protein chemical synthesis, can indeed improve the success rate of protein crystallization experiments. More recently, the racemic crystallization approach was extended to include nucleic acids as a possible aid in the determination of enantiopure DNA crystal structures. Here, findings are reported that suggest that the benefits may extend beyond this. Two racemic crystal structures of the DNA sequence d(CCCGGG) are described which were found to fold into A‐form DNA. This form differs from the Z‐form DNA conformation adopted by the chiral equivalent in the solid state, suggesting that the use of racemates may also favour the emergence of new conformations. Importantly, the racemic mixture forms interactions in the solid state that differ from the chiral equivalent (including the formation of racemic pseudo‐helices), suggesting that the use of racemic DNA mixtures could provide new possibilities for the design of precise self‐assembled nanomaterials and nanostructures. [ABSTRACT FROM AUTHOR]

We present a new structure of a DNA dodecamer obtained in the presence of Ni2+ ions. The DNA forms Ni‐guanine cross‐links between neighboring molecules. Our results show that an adequate dosage of Ni2+ may help to form well‐defined DNA nanostructures. We also compare our structure with other dodecamers which present unique features and also crystallize in trigonal unit cells, strongly influenced by the counterions associated with DNA. In all cases, the DNA duplexes form parallel pseudo‐helical columns in the crystal, similar to DNA‐protamine and native DNA fibers. [ABSTRACT FROM AUTHOR]

This manuscript reports a strategy for controlling the crystallization kinetics and improving the quality of engineered self‐assembled 3D DNA crystals. Growing large, high‐quality biomacromolecule crystals is critically important for determining the 3D structures of biomacromolecules. It often presents a great challenge to structural biologists. Herein, we introduce a rationally designed agent to modulate the crystallization process. Under such conditions, fewer, but larger, crystals that yield diffraction patterns of modestly higher resolution are produced compared with the crystals from conditions without the modulating agent. We attribute the improvement to a smaller number of nuclei and slow growth rate of crystallization. This strategy is expected to be generally applicable for crystallization of other biomacromolecules. [ABSTRACT FROM AUTHOR]

Crystals of left‐handed Z‐DNA [d(CGCGCG)]2 diffract X‐rays to beyond 1 Å resolution, feature a small unit cell (∼18 × 31 × 44 Å) and are well hydrated, with around 90 water molecules surrounding the duplex in the asymmetric unit. The duplex shows regular hydration patterns in the narrow minor groove, on the convex surface and around sugar–phosphate backbones. Therefore, Z‐DNA offers an ideal case to test the benefits of low‐temperature neutron diffraction data collection to potentially determine the donor–acceptor patterns of first‐ and second‐shell water molecules. Nucleic acid fragments pose challenges for neutron crystallography because water molecules are located on the surface rather than inside sequestered spaces such as protein active sites or channels. Water molecules can be expected to display dynamic behavior, particularly in cases where water is not part of an inner shell and directly coordinated to DNA atoms. Thus, nuclear density maps based on room‐temperature diffraction data with a resolution of 1.6 Å did not allow an unequivocal determination of the orientations of water molecules. Here, cryo‐neutron diffraction data collection for a Z‐DNA crystal on the Macromolecular Neutron Diffractometer at the Spallation Neutron Source at Oak Ridge National Laboratory and the outcome of an initial refinement of the structure are reported. A total of 12 diffraction images were recorded with an exposure time of 3.5 h per image, whereby the crystal was static for each diffraction image with a 10° ϕ rotation between images. Initial refinements using these neutron data indicated the positions and orientations of 30 water molecules within the first hydration shell of the DNA molecule. This experiment constitutes a state‐of‐the‐art approach and is the first attempt to our knowledge to determine the low‐temperature neutron structure of a DNA crystal. [ABSTRACT FROM AUTHOR]

Abstract: Programming self‐assembled designer DNA crystals with various lattices and functions is one of the most important goals for nanofabrication using nucleic acids. The resulting porous materials possess atomic precision for several potential applications that rely on crystalline lattices and cavities. Herein, we present a rationally designed and self‐assembled 3D DNA crystal lattice with hexagonal symmetry. In our design, two 21‐base oligonucleotides are used to form a duplex motif that further assembles into a 3D array. The interactions between the strands are programmed using Watson–Crick base‐pairing. The six‐fold symmetry, as well as the chirality, is directed by the Holliday junctions formed between the duplex motifs. The rationally designed DNA crystal provides a new avenue that could create self‐assembled macromolecular 3D crystalline lattices with atomic precision. In addition, the structure contains a highly organized array of well‐defined cavities that are suitable for future applications with immobilized guests. [ABSTRACT FROM AUTHOR]

A sensitive and specific electrochemical biosensor was developed for quantitative detection of HIV-related DNA by integrating toehold strand displacement reaction (TSDR) with cruciform DNA crystal. The TSDR system can be specifically triggered by HIV-related DNA generating plentiful double-stranded DNA products and releasing the target DNA to undergo an additional cycle of amplification. The hybridization reaction of double-stranded DNA products with capture probes on Au electrode surface makes the binding sites of cruciform DNA crystal available. After the attachment of cruciform DNA crystal and the employment of streptavidinylated alkaline phosphatase, a significantly amplified electrochemical signal is obtained. This strategy was applied to the highly sensitive detection of HIV-related DNA in a linear range from 1 pM to 100 nM and a detection limit as low as 0.21 pM was achieved. The proposed strategy can be accomplished without the employment of any enzymes or intensive purification. In addition, this method has good selectivity and anti-interference ability, which could be applied in complex samples with comparable analytical performance. For these advantages, the proposed strategy holds great potential for rapid and early clinical diagnosis of HIV infection. [ABSTRACT FROM AUTHOR]

In the current work, accurate quantification over 10 to 108 DNA copies has been successfully achieved for the first time by real-time electrochemical PCR. This has been made possible thanks to the combined use of a fully automated house-built electrochemical qPCR device, optimized for parallel heating and electrochemical monitoring of up to 48 PCR solutions, and the appropriate selection of a DNA intercalating redox probe retaining a strong affinity binding to ds-DNA at the PCR measurement temperature of 72 °C (corresponding to the PCR elongation step). This has also been achieved through the identification of the key parameters governing the onset electrochemical signal decrease and amplitude signal decrease as a function of the PCR cycle for a given DNA intercalating redox probe, thus allowing us to predict the electrochemical PCR kinetic plots from the values of the DNA affinity binding constant determined as a function of temperature. To the best of our knowledge, the analytical performances of the current electrochemical qPCR outperform all of those previously published, in terms of detection limit, dynamic range, reproducibility and melting curve analysis compared to that achieved on a commercialized bench-top fluorescence-based qPCR instrument. [ABSTRACT FROM AUTHOR]

The foundational goal of structural DNA nanotechnology -- the field that uses oligonucleotides as a molecular building block for the programmable self-assembly of nanostructured systems -- was to use DNA to construct three-dimensional (3D) lattices for solving macromolecular structures. The programmable nature of DNA makes it an ideal system for rationally constructing self-assembled crystals and immobilizing guest molecules in a repeating 3D array through their specific stereospatial interactions with the scaffold. In this work, we have extended a previously described motif (4 X 5) by expanding the structure to a system that links four double-helical layers; we use a central weaving oligonucleotide containing a sequence of four six-base repeats (4 X 6), forming a matrix of layers that are organized and dictated by a series of Holliday junctions. In addition, we have assembled mirror image crystals (L-DNA) with the identical sequence that are completely resistant to nucleases. Bromine and selenium derivatives were obtained for the L- and D-DNA forms, respectively, allowing phase determination for both forms and solution of the resulting structures to 3.0 and 3.05 À resolution. Both right- and left-handed forms crystallized in the trigonal space groups with mirror image 3-fold helical screw axes P32 and P31 for each motif,respectively. The structures reveal a highly organized array of discrete and well-defined cavities that are suitable for hosting guest molecules and allow us to dictate a priori the assembly of guest -- DNA conjugates with a specified crystalline hand. [ABSTRACT FROM AUTHOR]

Pioneer transcription factors recognise and bind their target sequences in inaccessible chromatin to establish new transcriptional networks throughout development and cellular reprogramming. During this process, pioneer factors establish an accessible chromatin state to facilitate additional transcription factor binding, yet it remains unclear how different pioneer factors achieve this. Here, we discover that the pluripotency-associated pioneer factor OCT4 binds chromatin to shape accessibility, transcription factor co-binding, and regulatory element function in mouse embryonic stem cells. Chromatin accessibility at OCT4-bound sites requires the chromatin remodeller BRG1, which is recruited to these sites by OCT4 to support additional transcription factor binding and expression of the pluripotency-associated transcriptome. Furthermore, the requirement for BRG1 in shaping OCT4 binding reflects how these target sites are used during cellular reprogramming and early mouse development. Together this reveals a distinct requirement for a chromatin remodeller in promoting the activity of the pioneer factor OCT4 and regulating the pluripotency network. [ABSTRACT FROM AUTHOR]

DNA crystals make it possible to organize guest molecules into specific periodic 3D patterns at the nanoscale, and thereby to create novel macroscopic objects with potentially useful functionality. Here, we describe the fluorescence and energy transfer properties of DNA crystals that are self-assembled from DNA tensegrity triangles with covalently attached Cy3 and Cy5 dyes. When compared to reference DNA strands in solution, the fluorescence measurements indicate that the dyes in the crystal experience a more homogeneous environment, resulting in a 2-fold increase in Cy3 quantum yield and single-exponential Cy3 fluorescence decays. Energy transfer in a network of coupled Cy3 and Cy5 dyes in the DNA crystal is demonstrated experimentally. Numerical simulation finds the experiments to be consistent with a Förster model of the dyes in the periodic crystalline environment, and particularly if the transition dipoles are assumed random in orientation but static on the time scale of the excitation decay. [ABSTRACT FROM AUTHOR]

Summary High-fidelity DNA synthesis requires that polymerases display a strong preference for right nucleotide insertion. When the wrong nucleotide is inserted, the polymerase deters extension from the mismatched DNA terminus. Twenty-three crystallographic structures of DNA polymerase β with terminal template-primer mismatches were determined as binary DNA and ternary pre-catalytic substrate complexes. These structures indicate that the mismatched termini adopt various distorted conformations that attempt to satisfy stacking and hydrogen-bonding interactions. The binary complex structures indicate an induced strain in the mismatched template nucleotide. Addition of a non-hydrolyzable incoming nucleotide stabilizes the templating nucleotide with concomitant strain in the primer terminus. Several dead-end ternary complex structures suggest that DNA synthesis might occur as the enzyme transitions from an open to a closed complex. The structures are consistent with an induced-fit mechanism where a mismatched terminus is misaligned relative to the correct incoming nucleotide to deter or delay further DNA synthesis. [ABSTRACT FROM AUTHOR]

In this work, we present a joint experimental and molecular dynamics simulations effort to understand and map the crystallization behavior of polyhedral nanoparticles assembled via the interaction of DNA surface ligands. In these systems, we systematically investigated the interplay between the effects of particle core (via the particle symmetry and particle size) and ligands (via the ligand length) on crystallization behavior. This investigation revealed rich phase diagrams, previously unobserved phase transitions in polyhedral crystallization behavior, and an unexpected symmetry breaking in the ligand distribution on a particle surface. To understand these results, we introduce the concept of a zone of anisotropy, or the portion of the phase space where the anisotropy of the particle is preserved in the crystallization behavior. Through comparison of the zone of anisotropy for each particle we develop a foundational roadmap to guide future investigations. [ABSTRACT FROM AUTHOR]

Structural DNA nanotechnology combines branched DNA junctions with sticky-ended cohesion to create self-assembling macromolecular architectures. One of the key goals of structural DNA nanotechnology is to construct threedimensional (3D) crystalline lattices. Here we present a new DNA motif and a strategy that has led to the assembly of a 3D lattice. We have determined the X-ray crystal structures of two related constructs to 3.1 Å resolution using brominederivatized crystals. The motif we used employs a fivenucleotide repeating sequence that weaves through a series of two-turn DNA duplexes. The duplexes are tied into a layered structure that is organized and dictated by a concert of four-arm junctions; these in turn assemble into continuous arrays facilitated by sequence-specific sticky-ended cohesion. The 3D X-ray structure of these DNA crystals holds promise for the design of new structural motifs to create programmable 3D DNA lattices with atomic spatial resolution. The two arrays differ by the use of four or six repeats of the five-nucleotide units in the repeating but statistically disordered central strand. In addition, we report a 2D rhombuslike array formed from similar components. [ABSTRACT FROM AUTHOR]

The tensegrity triangle is a robust DNA motif that can self-assemble to generate macroscopic three-dimensional crystals. However, the stability of these crystals is dependent on the high ionic conditions used for crystal growth. Here we demonstrate that a triplex-forming oligonucleotide can be used to direct the specific intercalation, and subsequent photo-cross-linking, of 4,5′,8-trimethylpsoralen to single or multiple loci within or between the tiles of the crystal. Cross-linking between the tiles of the crystal improves their thermal stability. Such an approach is likely to facilitate the removal of crystals from their mother liquor and may prove useful for applications that require greater crystal stability. [ABSTRACT FROM AUTHOR]

Summary Cpf1 is an RNA-guided endonuclease of a type V CRISPR-Cas system that has been recently harnessed for genome editing. Here, we report the crystal structure of Acidaminococcus sp. Cpf1 (AsCpf1) in complex with the guide RNA and its target DNA at 2.8 Å resolution. AsCpf1 adopts a bilobed architecture, with the RNA-DNA heteroduplex bound inside the central channel. The structural comparison of AsCpf1 with Cas9, a type II CRISPR-Cas nuclease, reveals both striking similarity and major differences, thereby explaining their distinct functionalities. AsCpf1 contains the RuvC domain and a putative novel nuclease domain, which are responsible for cleaving the non-target and target strands, respectively, and for jointly generating staggered DNA double-strand breaks. AsCpf1 recognizes the 5′-TTTN-3′ protospacer adjacent motif by base and shape readout mechanisms. Our findings provide mechanistic insights into RNA-guided DNA cleavage by Cpf1 and establish a framework for rational engineering of the CRISPR-Cpf1 toolbox. [ABSTRACT FROM AUTHOR]

The article highlights several research articles related to chemistry appeared in the 2015 issue of sister publications of the periodical. Topics discussed include electrically conductive porous metal-organic frameworks by L. Sun in "Angewandte Chemie," enhancing DNA crystal durability by chemical crosslinking by D. Zhang in "ChemBioChem" and chitooligosaccharide synthesis using an ionic tag by L. Gillard in "European Journal of Organic Chemistry."

Structure solution based on the weak anomalous signal from native (protein and DNA) crystals is increasingly being attempted as part of synchrotron experiments. Maximizing the measurable anomalous signal by collecting diffraction data at longer wavelengths presents a series of technical challenges caused by the increased absorption of X-rays and larger diffraction angles. A new beamline at Diamond Light Source has been built specifically for collecting data at wavelengths beyond the capability of other synchrotron macromolecular crystallography beamlines. Here, the theoretical considerations in support of the long-wavelength beamline are outlined and the in-vacuum design of the endstation is discussed, as well as other hardware features aimed at enhancing the accuracy of the diffraction data. The first commissioning results, representing the first in-vacuum protein structure solution, demonstrate the promising potential of the beamline. [ABSTRACT FROM AUTHOR]

Drosophila Zeste is a DNA binding protein important for chromatin-targeted regulation of gene expression. It is best studied in the context of transvection—a mechanism of interallelic gene regulation involving paired chromosomes—and repression of the expression of white by Zeste mutants. Both of these functions depend on the DNA binding and self-association properties of Zeste, but the underlying structural basis remains unknown. Here we report the crystal structure of the DNA binding domain of Zeste in complex with a 19-bp DNA duplex containing the consensus recognition sequence motif. The structure reveals a helix–turn–helix Myb/homeodomain-like fold with the Zeste-specific insertion sequence forming a short helix and a long loop. Direct base contacts by the major groove binding helix principally account for the sequence-specific recognition, and backbone contacts via the Zeste-specific insertion are mainly responsible for the length requirement and the orientation of DNA. Our structural and biochemical characterizations of the DNA binding property of Zeste uncover an altered DNA binding modality of homeodomain-like proteins, and the structural information should facilitate the unraveling of the intricate mechanism of Zeste in regulation of gene expression. [ABSTRACT FROM AUTHOR]

To understand the molecular origins of diseases caused by ultraviolet and visible light, and also to develop photodynamic therapy, it is important to resolve the mechanism of photoinduced DNA damage. Damage to DNA bound to a photosensitizer molecule frequently proceeds by one-electron photo-oxidation of guanine, but the precise dynamics of this process are sensitive to the location and the orientation of the photosensitizer, which are very difficult to define in solution. To overcome this, ultrafast time-resolved infrared (TRIR) spectroscopy was performed on photoexcited ruthenium polypyridyl-DNA crystals, the atomic structure of which was determined by X-ray crystallography. By combining the X-ray and TRIR data we are able to define both the geometry of the reaction site and the rates of individual steps in a reversible photoinduced electron-transfer process. This allows us to propose an individual guanine as the reaction site and, intriguingly, reveals that the dynamics in the crystal state are quite similar to those observed in the solvent medium. [ABSTRACT FROM AUTHOR]

This manuscript reports an effort to stabilize self-assembled DNA crystals. Owing to their weak inter-unit cohesion, self-assembled DNA crystals are fragile, which limits the potential applications of such crystals. To overcome this problem, another molecule was introduced, which binds to the cohesive sites and stabilizes the inter-unit interactions. The extra interactions greatly improve the stability of the DNA crystals. The original DNA crystals are only stable in solutions of high ionic strength (e.g., ≥1.2 M (NH4)2SO4); in contrast, the stabilized crystals can be stable at ionic strengths as low as that of a 0.02 M solution of (NH4)2SO4. The current strategy is expected to represent a general approach for increasing the stability of self-assembled DNA nanostructures for potential applications, for example, as structural scaffolds and molecular sieves. [ABSTRACT FROM AUTHOR]

The article discusses how advances in the control of the shape, bonding direction and valency of DNA-coated nanoparticles allow the synthesis of nanoparticle crystallites of increasing complexity. Topics include DNA-assisted crystallization of nanoparticle superlattices, lattices synthetized from DNA-linked nanoparticles resembling close-packed structure, use of X-ray diffraction in analyzing crystal growth, and formation of uniform single crystals from nanoparticles.

As DNA exhibits persistent structures with dimensions that exceed the range of their intermolecular forces, solid-state DNA undergoes thermal degradation at elevated temperatures. Therefore, the realization of solvent-free DNA fluids, including liquid crystals and liquids, still remains a significant challenge. To address this intriguing issue, we demonstrate that combining DNA with suitable cationic surfactants, followed by dehydration, can be a simple generic scheme for producing these solvent-free DNA fluid systems. In the anhydrous smectic liquid crystalline phase, DNA sublayers are intercalated between aliphatic hydrocarbon sublayers. The lengths of the DNA and surfactant are found to be extremely important in tuning the physical properties of the fluids. Stable liquid-crystalline and liquid phases are obtained in the −20 °C to 200 °C temperature range without thermal degradation of the DNA. Thus, a new type of DNA-based soft biomaterial has been achieved, which will promote the study and application of DNA in a much broader context. [ABSTRACT FROM AUTHOR]

Racemates increase the chances of crystallization by allowing molecular contacts to be formed in a greater number of ways. With the advent of protein synthesis, the production of protein racemates and racemic-protein crystallography are now possible. Curiously, racemic DNA crystallography had not been investigated despite the commercial availability of L- and D-deoxyribo-oligonucleotides. Here, we report a study into racemic DNA crystallography showing the strong propensity of racemic DNA mixtures to form racemic crystals. We describe racemic crystal structures of various DNA sequences and folded conformations, including duplexes, quadruplexes, and a four-way junction, showing that the advantages of racemic crystallography should extend to DNA. [ABSTRACT FROM AUTHOR]

The dynamics of protein and nucleic acid structures is as important as their average static picture. The local molecular dynamics concealed in diffraction images is expressed as so-called B factors. To find out how the crystal-derived B factors represent the dynamic behaviour of atoms and residues of proteins and DNA in their complexes, the distributions of scaled B factors from a carefully curated data set of over 700 protein-DNA crystal structures were analyzed [Schneider et al. (2014), Nucleic Acids Res. 42, 3381-3394]. Amino acids and nucleotides were categorized based on their molecular neighbourhood as solvent-accessible, solvent-inaccessible ( i.e. forming the protein core) or lying at protein-protein or protein-DNA interfaces; the backbone and side-chain atoms were analyzed separately. The B factors of two types of crystal-ordered water molecules were also analyzed. The analysis confirmed several expected features of protein and DNA dynamics, but also revealed surprising facts. Solvent-accessible amino acids have B factors that are larger than those of residues at the biomolecular interfaces, and core-forming amino acids are the most restricted in their movement. A unique feature of the latter group is that their side-chain and backbone atoms are restricted in their movement to the same extent; in all other amino-acid groups the side chains are more floppy than the backbone. The low values of the B factors of water molecules bridging proteins with DNA and the very large fluctuations of DNA phosphates are surprising. The features discriminating different types of residues are less pronounced in structures with lower crystallographic resolution. Some of the observed trends are likely to be the consequence of improper refinement protocols that may need to be rectified. [ABSTRACT FROM AUTHOR]

DNA is an attractive polymer building materialfor nanodevicesand nanostructures due to its ability for self-recognition and self-assembly.Assembly relies on the formation of base-specific interactions thatallow strands to adopt structures in a controllable fashion. MostDNA-based higher order structures such as DNA cages, 2D and 3D DNAcrystals, or origamis are based on DNA double helices stabilized byWatson–Crick complementarity. A number of nonclassical pairingpatterns are possible between or among DNA strands; these interactionsresult in formation of unusual structures that include, but are notlimited to, G-quadruplexes, i-motifs, triplexes, and parallel-strandedduplexes. These structures create greater diversity of DNA-based buildingblocks for nanomaterials and have certain advantages over conventionalduplex DNA, such as enhanced thermal stability and sensitivity tochemical stimuli. In this Account, we briefly introduce these alternativeDNA structures and describe in detail their utilization in a varietyof nanomaterials and nanomachines. [ABSTRACT FROM AUTHOR]

The directed assembly of nanoparticle building blocks is a promising method for generating sophisticated three-dimensional materials by design. In this work, we have used DNA linkers to synthesize nanoparticle superlattices that have greater complexity than simple binary systems using the process of topotactic intercalation--the insertion of a third nanoparticle component at predetermined sites within a preformed binary lattice. Five distinct crystals were synthesized with this methodology, three of which have no equivalent in atomic or molecular crystals, demonstrating a general approach for assembling highly ordered ternary nanoparticle superlattices whose structures can be predicted before their synthesis. Additionally, the intercalation process was demonstrated to be completely reversible; the inserted nanoparticles could be expelled into solution by raising the temperature, and the ternary superlattice could be recovered by cooling. [ABSTRACT FROM AUTHOR]

We report an atomic resolution X-ray crystal structure containing both enantiomers of rac-[Ru(phen)2dppz]2+ with the d(ATGCAT)2 DNA duplex (phen = phenanthroline; dppz = dipyridophenazine). The first example of any enantiomeric pair crystallized with a DNA duplex shows different orientations of the Λ and Δ binding sites, separated by a clearly defined structured water monolayer. Job plots show that the same species is present in solution. Each enantiomer is bound at a TG/CA step and shows intercalation from the minor groove. One water molecule is directly located on one phenazine N atom in the Δ-enantiomer only. [ABSTRACT FROM AUTHOR]

Highlights: [•] Synthesis, spectral and crystallographic characterization of a norbornane derivative were carried out. [•] Compound exhibits two different helical chiralities at supramolecular level. [•] P- and M-helices are constituted by the same kind of enantiomers separately. [•] Noncovalent mixed-handed DNA mimetic based on an unnatural small molecule established by weak intermolecular H-bonds. [•] The presence of weak H-bonds was verified by QTAIM and Hirshfeld surface analyses. [Copyright &y& Elsevier]

Designed self-assembled DNA crystals consist of rigidDNA motifsthat are held together by cohesive sticky-ended interactions. A prominentapplication of such systems is that they might be able to act as macromolecularhosts for macromolecular guests, thereby alleviating the crystallizationproblem of structural biology. We have recently demonstrated thatit is indeed possible to design and construct such crystals and todetermine their structures by X-ray diffraction procedures. To actas useful hosts that organize biological macromolecules for crystallographicpurposes, maximizing the resolution of the crystals will maximizethe utility of the approach. The structures reported so far have diffractedonly to about 4 Å, so we have examined two factors that mighthave impact on the resolution. We find no difference in the resolutionwhether the DNA is synthetic or PCR-generated. However, we find thatthe presence of a phosphate on the 5′-end of the strands improvesthe resolution of the crystals markedly. [ABSTRACT FROM AUTHOR]

Three-dimensional (3D) DNA crystals have been envisioned as programmable biomaterial scaffolds for creating ordered arrays of biological and nonbiological molecules. Despite having excellent programmable properties, the linearity of the Watson-Crick B-form duplex imposes limitations on 3D crystal design. Predictable noncanonical base pairing motifs have the potential to serve as junctions to connect linear DNA segments into complex 3D lattices. Here, we designed crystals based on a template structure with parallel-stranded noncanonical base pairs. Depending on pH, the structures we determined contained all but one or two of the designed secondary structure interactions. Surprisingly, a conformational change of the designed Watson-Crick duplex region resulted in crystal packing differences between the predicted and observed structures. However, the designed noncanonical motif was virtually identical to the template when crystals were grown at pH 5.5, highlighting the motif's predictability. At pH 7.0 we observed a structurally similar variation on this motif that contains a previously unobserved C- G•G-C quadruple base pair. We demonstrate that these two variants can interconvert in crystallo in response to pH perturbations. This study spotlights several important considerations in DNA crystal design, describes the first 3D DNA lattice composed of A-DNA helical sheets, and reveals a noncanonical DNA motif that has adaptive features that may be useful for designing dynamic crystals or biomaterial assemblies. [ABSTRACT FROM AUTHOR]

Metal-Assisted and Microwave-Accelerated Evaporative Crystallization (MA-MAEC), is a new approach to crystallization of drug compounds, amino acids, DNA and proteins. In this work, we report our additional findings on the effect of engineered surfaces and sample volume on the rapid crystallization of glycine. With the use of hydrophilic functionalized surfaces and the MA-MAEC technique, glycine crystals ∼1 mm in size were grown in 35 seconds with 100% selectivity for the α-form.The use of moderately hydrophobic surfaces resulted in the growth of glycine crystals only at room temperature. An increase in volume of initial glycine solution (5-100 μL) resulted in an increase in crystal size without a significant increase in total crystallization time. Raman spectroscopy and powder X-ray diffraction results demonstrated that the glycine crystals grown on engineered surfaces were structurally identical to those grown using conventional evaporative crystallization. [ABSTRACT FROM AUTHOR]

While the theoretical implications of models of DNA tile self-assembly have been extensively researched and such models have been used to design DNA tile systems for use in experiments, there has been little research testing the fundamental assumptions of those models. In this paper, we use direct observation of individual tile attachments and detachments of two DNA tile systems on a mica surface imaged with an atomic force microscope (AFM) to compile statistics of tile attachments and detachments. We show that these statistics fit the widely used kinetic Tile Assembly Model and demonstrate AEM movies as a viable technique for directly investigating DNA tile systems during growth rather than after assembly. [ABSTRACT FROM AUTHOR]

We present the structure of coiled coils found in two oligonucleotide DNA crystals. The sequences d(ATATATATAT) and d(CGATATATAT) are used. In the first case several coiled coils with different structures are found. In the second case a single structure is present. The results are compared with other coiled coil structures. They might be used in the development of new nanomaterials. [ABSTRACT FROM AUTHOR]

Abstract: Our knowledge of nucleic acid structure grew rapidly over the past decade with the determination to high resolution of larger structures of great biological significance. Advances in sample preparation, crystallization techniques, cryocrystallography, access to synchrotron radiation, and crystallographic software continue to accelerate the structure determination of nucleic acids. Crystallographic studies of DNA and RNA molecules share many considerations that we outline here. The application of crystallography to RNA is illustrated with the structure determination of the CUG repeat that is linked to type I myotonic dystrophy. [Copyright &y& Elsevier]

The LADI-III diffractometer at the Institut Laue-Langevin has been used to carry out a preliminary neutron crystallographic study of the self-complementary DNA oligonucleotide d(AGGGGCCCCT)2 in the A conformation. The results demonstrate the viability of a full neutron crystallographic analysis with the aim of providing enhanced information on the ion-water networks that are known to be important in stabilizing A-DNA. This is the first account of a single-crystal neutron diffraction study of A-DNA. The study was carried out with the smallest crystal used to date for a neutron crystallographic study of a biological macromolecule. [ABSTRACT FROM AUTHOR]

Abstract: Flower-like ZnO superstructures were synthesized using DNA as a crystal growth modifier. By employing various techniques such as X-ray diffraction (XRD), field emission scanning electron microscopy (FESEM) and transmission electron microscopy (TEM), the structures and phases of the products were established. On the basis of the time-dependent experiments, a formation model of the products was presented. Photocatalytic experiments show that the products presented a higher photocatalytic performance than the commercial ZnO nanoparticles (ZnO NPs) with an average size of 33nm. The antibacterial experiments were also carried out through determining the minimal inhibition concentration (MIC) and the minimum bactericidal concentration (MBC). Compared with commercial ZnO NPs, the products exhibited enhanced antibacterial ability against Escherichia coli and Staphylococcus aureus. [Copyright &y& Elsevier]

We present a new structure of a DNA dodecamer obtained in the presence of Ni 2+ ions. The DNA forms Ni-guanine cross-links between neighboring molecules. Our results show that an adequate dosage of Ni 2+ may help to form well-defined DNA nanostructures. We also compare our structure with other dodecamers which present unique features and also crystallize in trigonal unit cells, strongly influenced by the counterions associated with DNA. In all cases, the DNA duplexes form parallel pseudo-helical columns in the crystal, similar to DNA-protamine and native DNA fibers., (© 2020 Wiley Periodicals LLC.)

The article reflects on how a shape-changing crystal consisting of DNA-functionalized nanoparticles can be programmed to undergo a crystal-to-crystal transformation without disintegrating. Topics include development of nanostructured materials whose physical properties can be changed, and use of DNA-coated colloids in making lattice units. It also reveals that crystal-to-crystal transition can be used in forming hexagonal layers of gold nanoparticles and quantum dots.

A correction to the article "Construction and Structure Determination of a Three-dimensional DNA Crystal" that was published in the 2016 issue.

We fabricated lanthanide ion (Ln3+, e.g. Dy3+, Er3+, Eu3+, and Gd3+)-doped self-assembled double-crossover (DX) DNA crystals grown on the surface of field effect transistors (FETs) containing either a Cr, Au, or Ni electrode. Here we demonstrate the metal electrode dependent FET characteristics as a function of various Ln3+. The drain–source current (Ids), controlled by the drain–source voltage (Vds) of Ln3+-doped DX DNA crystals with a Cr electrode on an FET, changed significantly under various gate voltages (Vg) due to the relative closeness of the work function of Cr to the energy band gap of Ln3+-DNA crystals compared to those of Au and Ni. For Ln3+-DNA crystals on an FET with either a Cr or Ni electrode at a fixed Vds, Ids decreased with increasing Vg ranging from  −2 to 0 V and from 0 to  +3 V in the positive and negative regions, respectively. By contrast, Ids for Ln3+-DNA crystals on an FET with Au decreased with increasing Vg in only the positive region due to the greater electronegativity of Au. Furthermore, Ln3+-DNA crystals on an FET exhibited behaviour sensitive to Vg due to the appreciable charge carriers generated from Ln3+. Finally, we address the resistivity and the mobility of Ln3+-DNA crystals on an FET with different metal electrodes obtained from Ids–Vds and Ids–Vg curves. The resistivities of Ln3+-DNA crystals on FETs with Cr and Au electrodes were smaller than those of pristine DNA crystals on an FET, and the mobility of Ln3+-DNA crystals on an FET with Cr was relatively higher than that associated with other electrodes. [ABSTRACT FROM AUTHOR]

The article discusses the use of DNA linkers in rational design of the assembly of nanoparticle crystals. Topics discussed include advances in DNA synthesis, DNA linkers providing control of crystal stability and architecture, and advantage of DNA linkers in reprogramming the structure of a DNAâ€nanoparticle superlattice.

We studied the physical characteristics of modified-DNA (M-DNA) double crossover crystals fabricated via substrate-assisted growth with various concentrations of four different divalent metallic ions, Cu2+, Ni2+, Zn2+, and Co2+. Atomic force microscopy (AFM) was used to test the stability of the M-DNA crystals with different metal ion concentrations. The AFM images show that M-DNA crystals formed without deformation at up to the critical concentrations of 6 mM of [Cu2+], 1.5 mM of [Ni2+], 1 mM of [Zn2+], and 1 mM of [Co2+]. Above these critical concentrations, the M-DNA crystals exhibited deformed, amorphous structures. Raman spectroscopy was then used to identify the preference of the metal ion coordinate sites. The intensities of the Raman bands gradually decreased as the concentration of the metal ions increased, and when the metal ion concentrations increased beyond the critical values, the Raman band of the amorphous M-DNA was significantly suppressed. The metal ions had a preferential binding order in the DNA molecules with G–C and A–T base pairs followed by the phosphate backbone. A two-probe station was used to measure the electrical current–voltage properties of the crystals which indicated that the maximum currents of the M-DNA complexes could be achieved at around the critical concentration of each ion. We expect that the functionalized ion-doped M-DNA crystals will allow for efficient devices and sensors to be fabricated in the near future. [ABSTRACT FROM AUTHOR]

The article focuses on an experiment conducted by Evelyn Auyeung and colleagues in which they attached pieces of DNA to gold nanoparticles, and then heated a solution of these DNA functionalized nanoparticles to form micrometre-sized crystals in the form of rhombic dodecahedra.