Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Mutation screening based on the mechanical properties of DNA molecules tethered to a solid surface.

ABSTRACT: We report a rapid gene mutation screening method by making use of the mechanical properties of single-strand DNA (ssDNA) tethered to a solid surface. With proper temperature control, ssDNA in solution undergoes intrabase pairing and forms a specific complex 3D structure. By tethering such ssDNA strands to a solid surface, a DNA film can be formed. The mechanical properties of such DNA films, probed by devices such as a quartz crystal resonator, are directly related to the specific structure of the ssDNA which is characteristic of its base sequence and thus can be used as the basis for mutation screening. Using this approach, we have detected a single base mutation among 545 bases in the P53 gene. This result suggests promising potential of employing the mechanical properties of DNA strands for rapid screening of mutations.

SUBMITTER: Yeri AS

PROVIDER: S-EPMC2806934 | biostudies-literature | 2010 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Mutation screening based on the mechanical properties of DNA molecules tethered to a solid surface.

Yeri Ashish S AS Gao Lizeng L Gao Di D

The journal of physical chemistry. B 20100101 2

We report a rapid gene mutation screening method by making use of the mechanical properties of single-strand DNA (ssDNA) tethered to a solid surface. With proper temperature control, ssDNA in solution undergoes intrabase pairing and forms a specific complex 3D structure. By tethering such ssDNA strands to a solid surface, a DNA film can be formed. The mechanical properties of such DNA films, probed by devices such as a quartz crystal resonator, are directly related to the specific structure of t ...[more]

PMID: 20030306

Similar Datasets

Silicon Surface Tethered Polymer as Artificial Solid Electrolyte Interface.

Project description:We have developed a proof of concept electrode design to covalently graft poly(methyl methacrylate) brushes directly to silicon thin film electrodes via surface-initiated atom transfer radical polymerization. This polymer layer acts as a stable artificial solid electrolyte interface that enables surface passivation despite large volume changes during cycling. Thin polymer layers (75?nm) improve average first cycle coulombic efficiency from 62.4% in bare silicon electrodes to 76.3%. Average first cycle reversible capacity was improved from 3157 to 3935 mAh g-1, and average irreversible capacity was reduced from 2011 to 1020 mAh g-1. Electrochemical impedance spectroscopy performed on silicon electrodes showed that resistance from solid electrolyte interface formation increased from 79 to 1508 ? in untreated silicon thin films over 26 cycles, while resistance growth was lower - from 98 to 498 ? - in silicon films functionalized with PMMA brushes. The lower increase suggests enhanced surface passivation and lower electrolyte degradation. This work provides a pathway to develop artificial solid electrolyte interfaces synthesized under controlled reaction conditions.

| S-EPMC6070503 | biostudies-literature

Precise sequential DNA ligation on a solid substrate: solid-based rapid sequential ligation of multiple DNA molecules.

Project description:Ligation, the joining of DNA fragments, is a fundamental procedure in molecular cloning and is indispensable to the production of genetically modified organisms that can be used for basic research, the applied biosciences, or both. Given that many genes cooperate in various pathways, incorporating multiple gene cassettes in tandem in a transgenic DNA construct for the purpose of genetic modification is often necessary when generating organisms that produce multiple foreign gene products. Here, we describe a novel method, designated PRESSO (precise sequential DNA ligation on a solid substrate), for the tandem ligation of multiple DNA fragments. We amplified donor DNA fragments with non-palindromic ends, and ligated the fragment to acceptor DNA fragments on solid beads. After the final donor DNA fragments, which included vector sequences, were joined to the construct that contained the array of fragments, the ligation product (the construct) was thereby released from the beads via digestion with a rare-cut meganuclease; the freed linear construct was circularized via an intra-molecular ligation. PRESSO allowed us to rapidly and efficiently join multiple genes in an optimized order and orientation. This method can overcome many technical challenges in functional genomics during the post-sequencing generation.

| S-EPMC3859325 | biostudies-literature

Ionic permeability and mechanical properties of DNA origami nanoplates on solid-state nanopores.

Project description:While DNA origami is a popular and versatile platform, its structural properties are still poorly understood. In this study we use solid-state nanopores to investigate the ionic permeability and mechanical properties of DNA origami nanoplates. DNA origami nanoplates of various designs are docked onto solid-state nanopores where we subsequently measure their ionic conductance. The ionic permeability is found to be high for all origami nanoplates. We observe the conductance of docked nanoplates, relative to the bare nanopore conductance, to increase as a function of pore diameter, as well as to increase upon lowering the ionic strength. The honeycomb lattice nanoplate is found to have slightly better overall performance over other plate designs. After docking, we often observe spontaneous discrete jumps in the current, a process which can be attributed to mechanical buckling. All nanoplates show a nonlinear current-voltage dependence with a lower conductance at higher applied voltages, which we attribute to a physical bending deformation of the nanoplates under the applied force. At sufficiently high voltage (force), the nanoplates are strongly deformed and can be pulled through the nanopore. These data show that DNA origami nanoplates are typically very permeable to ions and exhibit a number of unexpected mechanical properties, which are interesting in their own right, but also need to be considered in the future design of DNA origami nanostructures.

| S-EPMC4151284 | biostudies-literature

Structure and properties of tethered bilayer lipid membranes with unsaturated anchor molecules.

Project description:The self-assembled monolayers (SAMs) of new lipidic anchor molecule HC18 [Z-20-(Z-octadec-9-enyloxy)-3,6,9,12,15,18,22-heptaoxatetracont-31-ene-1-thiol] and mixed HC18/?-mercaptoethanol (?ME) SAMs were studied by spectroscopic ellipsometry, contact angle measurements, reflection-absorption infrared spectroscopy, and electrochemical impedance spectroscopy (EIS) and were evaluated in tethered bilayer lipid membranes (tBLMs). Our data indicate that HC18, containing a double bond in the alkyl segments, forms highly disordered SAMs up to anchor/?ME molar fraction ratios of 80/20 and result in tBLMs that exhibit higher lipid diffusion coefficients relative to those of previous anchor compounds with saturated alkyl chains, as determined by fluorescence correlation spectroscopy. EIS data shows the HC18 tBLMs, completed by rapid solvent exchange or vesicle fusion, form more easily than with saturated lipidic anchors, exhibit excellent electrical insulating properties indicating low defect densities, and readily incorporate the pore-forming toxin ?-hemolysin. Neutron reflectivity measurements on HC18 tBLMs confirm the formation of complete tBLMs, even at low tether compositions and high ionic lipid compositions. Our data indicate that HC18 results in tBLMs with improved physical properties for the incorporation of integral membrane proteins (IMPs) and that 80% HC18 tBLMs appear to be optimal for practical applications such as biosensors where high electrical insulation and IMP/peptide reconstitution are imperative.

| S-EPMC3753044 | biostudies-literature

QMugs, quantum mechanical properties of drug-like molecules.

Project description:Machine learning approaches in drug discovery, as well as in other areas of the chemical sciences, benefit from curated datasets of physical molecular properties. However, there currently is a lack of data collections featuring large bioactive molecules alongside first-principle quantum chemical information. The open-access QMugs (Quantum-Mechanical Properties of Drug-like Molecules) dataset fills this void. The QMugs collection comprises quantum mechanical properties of more than 665 k biologically and pharmacologically relevant molecules extracted from the ChEMBL database, totaling ~2 M conformers. QMugs contains optimized molecular geometries and thermodynamic data obtained via the semi-empirical method GFN2-xTB. Atomic and molecular properties are provided on both the GFN2-xTB and on the density-functional levels of theory (DFT, ωB97X-D/def2-SVP). QMugs features molecules of significantly larger size than previously-reported collections and comprises their respective quantum mechanical wave functions, including DFT density and orbital matrices. This dataset is intended to facilitate the development of models that learn from molecular data on different levels of theory while also providing insight into the corresponding relationships between molecular structure and biological activity.

| S-EPMC9174255 | biostudies-literature

Predicting the effect of binding molecules on the shape and mechanical properties of structured DNA assemblies.

Project description:Chemo-mechanical deformation of structured DNA assemblies driven by DNA-binding ligands has offered promising avenues for biological and therapeutic applications. However, it remains elusive how to effectively model and predict their effects on the deformation and mechanical properties of DNA structures. Here, we present a computational framework for simulating chemo-mechanical change of structured DNA assemblies. We particularly quantify the effects of ethidium bromide (EtBr) intercalation on the geometry and mechanical properties of DNA base-pairs through molecular dynamics simulations and integrated them into finite-element-based structural analysis to predict the shape and properties of DNA objects. The proposed model captures various structural changes induced by EtBr-binding such as shape variation, flexibility modulation, and supercoiling instability. It enables a rational design of structured DNA assemblies with tunable shapes and mechanical properties by binding molecules.

| S-EPMC11291742 | biostudies-literature

Phytochrome-based extracellular matrix with reversibly tunable mechanical properties

Project description:Interrogation and control of cellular fate and function using optogenetics is providing revolutionary insights into biology. Optogenetic control of cells is achieved by coupling genetically encoded photoreceptors to cellular effectors and enables unprecedented spatiotemporal control of signaling processes. Here, a fast and reversibly switchable photoreceptor is used to tune the mechanical properties of polymer materials in a fully reversible, wavelength-specific, and dose- and space-controlled manner. By integrating engineered cyanobacterial phytochrome 1 into a polyethylene glycol matrix, hydrogel materials responsive to light in the cell-compatible red/far-red spectrum are synthesized. These materials are applied to study in human mesenchymal stem cells how different mechano-signaling pathways respond to changing mechanical environments, and to control the migration of primary immune cells in 3D. This optogenetics-inspired matrix allows addressing fundamental questions of how cells react to dynamic mechanical environments. Further, remote control of such matrices could create new opportunities for tissue engineering or provide a basis for optically stimulated drug depots.

2019-01-16 | GSE125130 | GEO

DNA-based patterning of tethered membrane patches.

Project description:Solid-supported lipid bilayers are useful model systems for mimicking cellular membranes; however, the interaction of the bilayer with the surface can disrupt the function of integral membrane proteins and impede topological transformations such as membrane fusion. As a result, a variety of tethered or cushioned lipid bilayer architectures have been described, which retain the proximity to the surface, enabling surface-sensitive techniques, but physically distance the bilayer from the surface. We have recently developed a method for spatially separating a lipid bilayer from a solid support using DNA lipids. In this system, a DNA strand is covalently attached to a glass slide or SiO2 wafer, and giant unilamellar vesicles (GUVs) displaying the complement rupture to form a planar lipid bilayer tethered above the surface. However, the location of the patch is random, determined by where the DNA-GUV initially binds to its complement. To allow greater versatility and control, we sought a way to pattern tethered membrane patches. We present a method for creating spatially distinct tethered membrane patches on a glass slide using microarray printing. Surface-reactive DNA sequences are spotted onto the slide, incubated to covalently link the DNA to the surface, and DNA-GUVs patches are formed selectively on the printed DNA. By interfacing the bilayers with microfluidic flow cells, materials can be added on top of or fused into the membrane to change the composition of the bilayers. With further development, this approach would enable rapid screening of different patches in protein binding assays and would enable interfacing patches with electrical detectors.

| S-EPMC3815428 | biostudies-literature

Cytosine methylation alters DNA mechanical properties.

Project description:DNA methylation plays an essential role in transcriptional control of organismal development in epigenetics, from turning off a specific gene to inactivation of entire chromosomes. While the biological function of DNA methylation is becoming increasingly clear, the mechanism of methylation-induced gene regulation is still poorly understood. Through single-molecule force experiments and simulation we investigated the effects of methylation on strand separation of DNA, a crucial step in gene expression. Molecular force assay and single-molecule force spectroscopy revealed a strong methylation dependence of strand separation. Methylation is observed to either inhibit or facilitate strand separation, depending on methylation level and sequence context. Molecular dynamics simulations provided a detailed view of methylation effects on strand separation, suggesting the underlying physical mechanism. According to our study, methylation in epigenetics may regulate gene expression not only through mechanisms already known but also through changing mechanical properties of DNA.

| S-EPMC3203585 | biostudies-literature

DNA profiling using solid-state nanopores: detection of DNA-binding molecules.

Project description:We present a novel single-molecule method for rapidly evaluating small-molecule binding to individual DNA molecules using nanopores fabricated in ultrathin silicon membranes. A measurable shift in the residual ion current through a approximately 3.5 nm pore results from threading of a dye-intercalated DNA molecule, as compared to the typical residual current of native DNA. The average level of the residual current can be used to directly quantify the fraction of bound molecules to DNA, providing a new way to determine binding isotherms. Spatial sensitivity is also demonstrated by designing a two-segment DNA molecule that contains small-molecule binding sites in one of its two segments. Translocations of such molecules exhibit two current levels upon incubation with a DNA-binding dye, caused by selectively bound dye in one of the DNA segments. Our results, as shown here with four different dyes, coincide well with bulk fluorescence measurements performed under identical conditions. The nanopore approach for "reading-out" molecular binding along a DNA molecule, combined with the miniscule amounts of DNA required and the potential for scalability using nanopore arrays, provide a novel platform for future applications in analytical drug screening.

| S-EPMC2871189 | 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