Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Versatile kit of robust nanoshapes self-assembling from RNA and DNA modules.

ABSTRACT: DNA and RNA have emerged as a material for nanotechnology applications that take advantage of the nucleic acids' ability to encode folding and programmable self-assembly through mainly base pairing. The two types of nucleic acid have rarely been used in combination to enhance structural diversity or for partitioning of functional and architectural roles. Here, we report a design and screening strategy to integrate combinations of RNA motifs as architectural joints and DNA building blocks as functional modules for programmable self-assembly of a versatile toolkit of polygonal nucleic acid nanoshapes. Clean incorporation of diverse DNA modules with various topologies attest to the extraordinary robustness of the RNA-DNA hybrid framework. The design and screening strategy enables systematic development of RNA-DNA hybrid nanoshapes as programmable platforms for applications in molecular recognition, sensor and catalyst development as well as protein interaction studies.

SUBMITTER: Monferrer A

PROVIDER: S-EPMC6363791 | biostudies-literature | 2019 Feb

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Versatile kit of robust nanoshapes self-assembling from RNA and DNA modules.

Monferrer Alba A Zhang Douglas D Lushnikov Alexander J AJ Hermann Thomas T

Nature communications 20190205 1

DNA and RNA have emerged as a material for nanotechnology applications that take advantage of the nucleic acids' ability to encode folding and programmable self-assembly through mainly base pairing. The two types of nucleic acid have rarely been used in combination to enhance structural diversity or for partitioning of functional and architectural roles. Here, we report a design and screening strategy to integrate combinations of RNA motifs as architectural joints and DNA building blocks as func ...[more]

PMID: 30723214

Similar Datasets

Self-assembling cages from coiled-coil peptide modules.

Project description:An ability to mimic the boundaries of biological compartments would improve our understanding of self-assembly and provide routes to new materials for the delivery of drugs and biologicals and the development of protocells. We show that short designed peptides can be combined to form unilamellar spheres approximately 100 nanometers in diameter. The design comprises two, noncovalent, heterodimeric and homotrimeric coiled-coil bundles. These are joined back to back to render two complementary hubs, which when mixed form hexagonal networks that close to form cages. This design strategy offers control over chemistry, self-assembly, reversibility, and size of such particles.

| S-EPMC6485442 | biostudies-literature

Self-assembling RNA square.

Project description:The three-dimensional structures of noncoding RNA molecules reveal recurring architectural motifs that have been exploited for the design of artificial RNA nanomaterials. Programmed assembly of RNA nanoobjects from autonomously folding tetraloop-receptor complexes as well as junction motifs has been achieved previously through sequence-directed hybridization of complex sets of long oligonucleotides. Due to size and complexity, structural characterization of artificial RNA nanoobjects has been limited to low-resolution microscopy studies. Here we present the design, construction, and crystal structure determination at 2.2 Å of the smallest yet square-shaped nanoobject made entirely of double-stranded RNA. The RNA square is comprised of 100 residues and self-assembles from four copies each of two oligonucleotides of 10 and 15 bases length. Despite the high symmetry on the level of secondary structure, the three-dimensional architecture of the square is asymmetric, with all four corners adopting distinct folding patterns. We demonstrate the programmed self-assembly of RNA squares from complex mixtures of corner units and establish a concept to exploit the RNA square as a combinatorial nanoscale platform.

| S-EPMC3080994 | biostudies-literature

Self-Assembling Glycopeptide Conjugate as a Versatile Platform for Mimicking Complex Polysaccharides.

Project description:Polysaccharides are a class of carbohydrates that play pivotal roles in living systems such as being chemical messengers in many vital biological pathways. However, the complexity and heterogeneity of these natural structures have posed daunting challenges on their production, characterization, evaluation, and applications. While there have been various types of synthetic skeletons that could mimic some biological aspects of polysaccharides, a safer and more easily accessed system is still desired to avoid the unnatural components and difficulties in modifying the structures. In this work, conveniently accessible self-assembling glycopeptide conjugates are developed, where the natural O-glycosidic linkages and phosphoryl modifications assist the self-assembly and concurrently reduce the risk of toxicity. The generated nanoparticles in aqueous solution offer a multivalent display of structurally controllable carbohydrates as mimics of polysaccharides, among which a mannosylated version exhibits immunostimulatory effects in both cellular assays and vaccination of mice. The obtained results demonstrate the potential of this glycopeptide conjugate-derived platform in exploiting the intriguing properties of carbohydrates in a more structurally maneuverable fashion.

| S-EPMC7435236 | biostudies-literature

XRCC1 - Strategies for coordinating and assembling a versatile DNA damage response.

Project description:X-ray cross complementing protein 1 (XRCC1) is a DNA repair scaffold that supports base excision repair and single strand break repair, and is also a participant in other repair pathways. It also serves as an important co-transporter for several other repair proteins, including aprataxin and PNKP-like factor (APLF), and DNA Ligase 3α (LIG3). By combining highly specialized regions that help to organize specific repair functions with recruitment of additional enzymes whose contribution is dependent on the details of the damaged site, XRCC1 is able to handle an expanded range of problems that may arise as the repair progresses or in connection with other repair pathways with which it interfaces. This review discusses the interplay between these functions and considers some possible interactions that underlie its reported repair activities.

| S-EPMC7587305 | biostudies-literature

Vesicle Tubulation with Self-Assembling DNA Nanosprings.

Project description:A major goal of nanotechnology and bioengineering is to build artificial nanomachines capable of generating specific membrane curvatures on demand. Inspired by natural membrane-deforming proteins, we designed DNA-origami curls that polymerize into nanosprings and show their efficacy in vesicle deformation. DNA-coated membrane tubules emerge from spherical vesicles when DNA-origami polymerization or high membrane-surface coverage occurs. Unlike many previous methods, the DNA self-assembly-mediated membrane tubulation eliminates the need for detergents or top-down manipulation. The DNA-origami design and deformation conditions have substantial influence on the tubulation efficiency and tube morphology, underscoring the intricate interplay between lipid bilayers and vesicle-deforming DNA structures.

| S-EPMC5924453 | biostudies-literature

Clotting Mimicry from Robust Hemostatic Bandages Based on Self-Assembling Peptides.

Project description:Uncontrolled bleeding from traumatic wounds is a major factor in deaths resulting from military conflict, accidents, disasters and crime. Self-assembling peptide nanofibers have shown superior hemostatic activity, and herein, we elucidate their mechanism by visualizing the formation of nanofiber-based clots that aggregate blood components with a similar morphology to fibrin-based clots. Furthermore, to enhance its direct application to a wound, we developed layer-by-layer assembled thin film coatings onto common materials used for wound dressings-gauze and gelatin sponges. We find these nanofibers elute upon hydration under physiological conditions and generate nanofiber-based clots with blood. After exposure to a range of harsh temperature conditions (-80 to 60 °C) for a week and even 5 months at 60 °C, these hemostatic bandages remain capable of releasing active nanofibers. In addition, the application of these nanofiber-based films from gauze bandages was found to accelerate hemostasis in porcine skin wounds as compared to plain gauze. The thermal robustness, in combination with the self-assembling peptide's potent hemostatic activity, biocompatibility, biodegradability, and low cost of production, makes this a promising approach for a cheap yet effective hemostatic bandage.

| S-EPMC4580967 | biostudies-literature

Peptide-amphiphile nanofibers: a versatile scaffold for the preparation of self-assembling materials.

Project description:Twelve derivatives of peptide-amphiphile molecules, designed to self-assemble into nanofibers, are described. The scope of amino acid selection and alkyl tail modification in the peptide-amphiphile molecules are investigated, yielding nanofibers varying in morphology, surface chemistry, and potential bioactivity. The results demonstrate the chemically versatile nature of this supramolecular system and its high potential for manufacturing nanomaterials. In addition, three different modes of self-assembly resulting in nanofibers are described, including pH control, divalent ion induction, and concentration.

| S-EPMC122734 | biostudies-literature

The Robust Self-Assembling Tubular Nanostructures Formed by gp053 from Phage vB_EcoM_FV3.

Project description:The recombinant phage tail sheath protein, gp053, from Escherichia coli infecting myovirus vB_EcoM_FV3 (FV3) was able to self-assemble into long, ordered and extremely stable tubular structures (polysheaths) in the absence of other viral proteins. TEM observations revealed that those protein nanotubes varied in length (~10⁻1000 nm). Meanwhile, the width of the polysheaths (~28 nm) corresponded to the width of the contracted tail sheath of phage FV3. The formed protein nanotubes could withstand various extreme treatments including heating up to 100 °C and high concentrations of urea. To determine the shortest variant of gp053 capable of forming protein nanotubes, a set of N- or/and C-truncated as well as poly-His-tagged variants of gp053 were constructed. The TEM analysis of these mutants showed that up to 25 and 100 amino acid residues could be removed from the N and C termini, respectively, without disturbing the process of self-assembly. In addition, two to six copies of the gp053 encoding gene were fused into one open reading frame. All the constructed oligomers of gp053 self-assembled in vitro forming structures of different regularity. By using the modification of cysteines with biotin, the polysheaths were tested for exposed thiol groups. Polysheaths formed by the wild-type gp053 or its mutants possess physicochemical properties, which are very attractive for the construction of self-assembling nanostructures with potential applications in different fields of nanosciences.

| S-EPMC6357053 | biostudies-literature

The wending rhombus: Self-assembling 3D DNA crystals.

Project description:In this perspective, we provide a summary of recent developments in self-assembling three-dimensional (3D) DNA crystals. Starting from the inception of this subfield, we describe the various advancements in structure that have led to an increase in the diversity of macromolecular crystal motifs formed through self-assembly, and we further comment on the future directions of the field, which exploit noncanonical base pairing interactions beyond Watson-Crick. We then survey the current applications of self-assembling 3D DNA crystals in reversibly active nanodevices and materials engineering and provide an outlook on the direction researchers are taking these structures. Finally, we compare 3D DNA crystals with DNA origami and suggest how these distinct subfields might work together to enhance biomolecule structure solution, nanotechnological motifs, and their applications.

| S-EPMC9808540 | biostudies-literature

In vitro transcription of self-assembling DNA nanoparticles.

Project description:Nucleic acid nanoparticles are playing an increasingly important role in biomolecular diagnostics and therapeutics as well as a variety of other areas. The unique attributes of self-assembling DNA nanoparticles provide a potentially valuable addition or alternative to the lipid-based nanoparticles that are currently used to ferry nucleic acids in living systems. To explore this possibility, we have assessed the ability of self-assembling DNA nanoparticles to be constructed from complete gene cassettes that are capable of gene expression in vitro. In the current report, we describe the somewhat counter-intuitive result that despite extensive crossovers (the stereochemical analogs of Holliday junctions) and variations in architecture, these DNA nanoparticles are amenable to gene expression as evidenced by T7 RNA polymerase-driven transcription of a reporter gene in vitro. These findings, coupled with the vastly malleable architecture and chemistry of self-assembling DNA nanoparticles, warrant further investigation of their utility in biomedical genetics.

| S-EPMC10415316 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data