• DNA origami was patterned with either small molecules, antibodies, or larger proteins. (scilifelab.se)
  • HOX proteins execute their activity by exploiting a cooperative binding to PBX proteins and DNA. (mdpi.com)
  • Inspired by this, we are interested in understanding how DNA topology is regulated in vivo, e.g. by Topoisomerase, Recombinase and SMC proteins, and while doing so we aim to discover new soft materials. (ed.ac.uk)
  • The challenge in the post genomic era is to make full use of the vast genomic data in understanding the molecular mechanism of the function of proteins. (utmb.edu)
  • Quantification on molecular dynamics and interactions with multi-dimensional analysis and 10-nm-resolution analysis of the images enabled us to classify states of the proteins and interactions. (nii.ac.jp)
  • Whereas the different DNA repair pathways and the proteins they involve are know pretty well described, how they are regulated relative to each other in time and space remains to be deciphered. (cea.fr)
  • It seems now clear that posttranslational modification of both DNA repair and checkpoint proteins is of importance for the regulation of their activities but how these modifications are regulated and how they affect the activity of the proteins only begins to be described. (cea.fr)
  • One feature of nuclear organization is the existence of subcompartments in which specific DNA sequences and proteins associate creating microenvironments that can be more or less favorable for specific processes. (cea.fr)
  • Utilizing computational methodologies, including molecular modeling and conventional molecular dynamics simulations to understand the relationship between the three-dimensional structures, dynamics and the biological functions of DNA-binding enzymes and proteins central to Type I Diabetes. (umassmed.edu)
  • engineering proteins, nucleic acids, or nanomaterials with novel structures, dynamics, and functions for basic biology/biomedical applications and effective therapeutic approaches. (umassmed.edu)
  • Using a novel molecular dynamics method capable of capturing the motion of gyrating proteins at time intervals up to one thousand times greater than previous efforts, a team led by UC San Diego researchers has identified, for the first time, the myriad structural changes that activate and drive CRISPR-Cas9, the innovative gene-splicing technology that's transforming the field of genetic engineering. (sdsc.edu)
  • Molecular thermal motions play an essential role in many functionally important biochemical processes such as allosteric transitions, ion permeation through channels, or folding of proteins and nucleic acids. (nyu.edu)
  • Chemists have used computers for decades to model biomolecules such as proteins and DNA, says Loukas Petridis, an ORNL staff scientist. (doe.gov)
  • Our improved parametrization can be directly applied to molecular dynamics simulations of various charged biomolecular systems, including nucleic acids, proteins, and lipid bilayer membranes. (illinois.edu)
  • My research focuses on study of biologically relevant nucleic acids and proteins by the methods of molecular dynamics (MD) simulations. (ibp.cz)
  • Usually, the NOE and NMRD in B-DNA is expected to be less ``integral'' than methods can only provide bounds on the residence water molecules buried inside proteins. (lu.se)
  • While many studies have been focused on the membrane structure, the dynamics of such systems are crucial for the function of the membrane including membrane bound proteins. (lu.se)
  • Though explaining some of the fundamental biophysics of the system, these relatively short-lived simulations - conducted upward of multi-microseconds - could not clarify the conformational transitions arising from the protein's resting state to the catalytically active Cas9 state. (sdsc.edu)
  • Researchers at the Center for Molecular Biophysics at Oak Ridge National Laboratory (ORNL) and the University of Tennessee (UT) in Knoxville have long used supercomputers to model and study lignin polymers and their interactions with cellulose. (doe.gov)
  • His research is at the confluence of statistical mechanics, molecular biology, hybrid modeling and large-scale computer simulations. (foresight.org)
  • Twenty years ago at the APS March Meeting, Kurt Kremer and I presented the first numerical evidence from computer simulations that the reptation model of Edwards and de Gennes correctly describes the dynamics of entangled linear polymer melts. (aps.org)
  • Though these early simulations were limited to chains of a few $N_e$, they demonstrated the potential of computer simulations to contribute to our understanding of polymer dynamics. (aps.org)
  • Another direction in Kirmizialtin lab is to integrate computer simulations and experiments to study the complex biomolecular machinery. (nyu.edu)
  • Our results show that in the absence of DNA, the three protein forms explore a similar essential conformational space, whereas when bound to the same DNA target sequence of 25 base pairs, they diversify and restrain the subspace explored. (uniroma1.it)
  • Having a precise description of water s structure is critical to constructing accurate simulations of molecular events, including protein folding, substrate binding, macromolecular recognition, and complex formation. (phys.org)
  • The implemented routines analyze the protein environment of water molecules in molecular dynamics (MD) simulations and can differentiate between hydrogen bonded waters as well as waters in a protein environment of hydrophobic, charged, or aromatic atom groups. (acs.org)
  • PyRod adds a new perspective to structure-based screening campaigns by providing easy-to-interpret dMIFs and purely protein-based pharmacophores that are solely based on tracing water molecules in MD simulations. (acs.org)
  • This idea will be presented to stop the cancerous cell's protein synthesis and modifying DNA sequence and genetic manipulation of the cell. (nature.com)
  • He works on methods to improve protein engineering of metalloproteins using deep learning and molecular modeling. (foresight.org)
  • MASIA, in combination with homology modeling and molecular dynamics simulations, can be used to characterize functional motifs in protein families. (utmb.edu)
  • We are relating motifs identified by MASIA to the function of DNA recognition, catalysis and protein-protein interaction. (utmb.edu)
  • The object of this research is to clarify structures and their changes of DNA and protein complexes that are formed transiently and locally. (nii.ac.jp)
  • Protein Expression and Purification, molecular modelling, and molecular dynamics simulation. (umassmed.edu)
  • Protein Expression and Purification, Computational Modeling, Molecular Dynamic Simulations, X-ray Crystallography, Enzyme Activity and Enzyme Inhibition Assays, Structure Aided Drug Design. (umassmed.edu)
  • Last year, researchers from the McCammon Lab at UC San Diego used the Comet supercomputer at SDSC to perform atomistic molecular dynamics - a method that captures a more complete vision of the myriad shapes and conformations that a target protein molecule may go through - at petascale speeds (one quadrillion arithmetic calculations per second). (sdsc.edu)
  • This event brings together people with interest and expertise in quantitative studies of protein-nucleic acid interactions and dynamics in genetic and epigenetic regulation. (biophysics.org)
  • It intends to bridge statistical and bioinformatic characterization of representative protein-DNA systems with biophysical and biochemical approaches. (biophysics.org)
  • Moreover, these motions occur in mostly conserved nucleotides from structural regions (i.e., priming loop, pseudo-triloop, and U43 bulge) that biochemical and mutational studies have shown to be essential for P binding, protein-priming, pgRNA packaging, and DNA synthesis. (nist.gov)
  • We evaluated consequences of 12 intragenic variants by protein modelling and molecular dynamic studies. (springer.com)
  • Careful phenotyping is essential in interpreting consequences of RAD21 variants, and protein modeling and dynamics can be helpful in determining pathogenicity. (springer.com)
  • My primary focus is protein/RNA and protein/DNA complexes. (ibp.cz)
  • 5 , 8 , 19-21 Apart from protein/RNA and protein/DNA complexes, I have also studied neomycin-sensing riboswitch, 18 human HP1 protein, 22-23 folding pathways of guanine quadruplexes, 24-26 HIV-1 kissing loop, 27 and free energy calculations. (ibp.cz)
  • In the near future, I intend to study protein/RNA and other complexes in which local interface dynamics is prominently involved and can influence affinity and specificity of such complexes. (ibp.cz)
  • Allain, F. H. T., Chapter Fourteen - Combining NMR Spectroscopy and Molecular Dynamic Simulations to Solve and Analyze the Structure of Protein-RNA Complexes. (ibp.cz)
  • We will also set up and run molecular dynamics simulations for protein, calculating binding free energies for drug candidates with end-point methods and solvation free energies by free-energy perturbation. (lu.se)
  • We present an electrical sensor that uses rolling circle amplification (RCA) of DNA to stretch across the gap between two electrodes, interact with metal nanoparticle seeds to generate an electrically conductive nanowire, and produce electrical signals upon detection of specific target DNA sequences. (scilifelab.se)
  • With this technique, long single-stranded DNA with simple repetitive sequences are produced. (scilifelab.se)
  • The conformational behavior of the wild-type endonucleases I-DmoI and two of its mutants has been studied in the presence and in the absence of DNA target sequences by means of extended molecular dynamics simulations. (uniroma1.it)
  • NHEJ simply religates the broken ends whereas during HR a DNA break is repaired by copying homologous sequences present elsewhere in the genome. (cea.fr)
  • The formation of G-quadruplex DNA is easily conceivable in DNA sequences that are present as single strands in cells, such as the telomeric overhang. (hindawi.com)
  • It has been indeed demonstrated that the involvement of G-rich sequences in duplex architecture is compatible with their folding into quadruplex structures, thanks to the breathing of duplex DNA [ 27 ]. (hindawi.com)
  • In particular, we want to design a system that doesn't cause 'off-target' effects or non-selective cleavage of DNA sequences, that can now create unwanted collateral damage," added J. Andrew McCammon, the Joseph E. Mayer Chair of Theoretical Chemistry at UC San Diego, a Howard Hughes Medical Institute Investigator, and the study's principal investigator. (sdsc.edu)
  • Studies have revealed that the RNA guide used to direct the cleaving enzyme to its target can sometimes go astray, landing on other DNA strands with similar but not identical sequences. (sdsc.edu)
  • Molecular dynamics simulations appeared to indicate partial destabilization of the two designed sequences. (bvsalud.org)
  • Bayesian coalescent inference of past population dynamics from molecular sequences. (cdc.gov)
  • In this paper, we propose to discriminate DNA length by the capture rate of the molecules to an array of relatively large nanopores (50-130 nm) by introducing a thermal gradient by laser illumination in front of the pores balancing the force from an external electric field. (scilifelab.se)
  • The experimental data show that the capture rates of DNA molecules decrease with increasing DNA length due to the thermophoretic effect of the molecules. (scilifelab.se)
  • There were many challenges to overcome in designing and implementing QMPFF3-based molecular dynamics simulations especially to study the behavior of water molecules next to hydrophobic surfaces at atomic detail and subpicosecond time resolution. (phys.org)
  • Moreover, the drug-DNA complexes were analyzed to investigate specific drug-DNA interactions, as well as the role of the solvent water molecules in the drug-DNA binding. (ub.edu)
  • We have demonstrated that clear visualization of single molecules in cells enables their molecular quantification. (nii.ac.jp)
  • Quasi-statical unfolding of single molecules of staphylococcal nuclease and double-stranded DNA by constant-rate mechanical stretching. (nii.ac.jp)
  • Interestingly, several classes of small molecules have been developed that efficiently target G-quadruplex DNA [ 29 - 32 ]. (hindawi.com)
  • Therefore, IRAMIS implements with lasers, time-resolved spectroscopies in the range from femtosecond to the millisecond, to study the dynamics of molecular systems, like for example DNA biomolecules, or chromophore molecules for photovoltaics. (cea.fr)
  • PAM acts as an allosteric effector and triggers the interdependent conformational dynamics of the Cas9 catalytic domains (HNH and RuvC), responsible for concerted cleavage of the two DNA strands. (nih.gov)
  • We also carried out molecular dynamics simulations to provide additional insight into ε conformational dynamics. (nist.gov)
  • Their goal was to create a synthetic genetic system which mimics and surpasses the functions of the natural genetic system, and to broaden the applications of DNA both in living cells and in experimental biochemistry. (wikipedia.org)
  • Evolutionary Refinement of DNA Nanostructures Using Coarse-Grained Molecular Dynamics Simulations. (scilifelab.se)
  • Here, we implement an unsupervised software based on the coarse-grained molecular dynamics package oxDNA to simulate DNA origami structures and evaluate their rigidity. (scilifelab.se)
  • The gathered information is further processed to generate dynamic molecular interaction fields (dMIFs) for visualization and pharmacophoric features for virtual screening. (acs.org)
  • Rakesh, L, Interaction between sucrose, N-acetylcysteine and taurine in controlling insulin effects and energy shifts in body with and without the presence of diabetic drug Avandia: Molecular modeling study, J. Nanomedicine (in press), 2009. (cmich.edu)
  • For instance, the limitations of the current classical force fields (FFs) are well known, which still call for better ways to treat the metal-ligand interaction when running classical molecular dynamics simulations (Li P. & Merz K. M. Jr., Chem Rev 2017, 117, 1564). (cecam.org)
  • In the past decade, DNA nanostructures have made the leap from small assemblies of a handful of oligonucleotides to megadalton objects assembled from hundreds or thousands of component DNA strands. (scilifelab.se)
  • xDNA is more stable when compared to regular DNA when subjected to higher temperature, and while entire strands of xDNA, yDNA, xxDNA and yyDNA exist, they are currently difficult to synthesize and maintain. (wikipedia.org)
  • The extended bases xA, xC, xG, and xT are naturally fluorescent, and single strands composed of only extended bases can recognize and bind to single strands of natural DNA, making them useful tools for studying biological systems. (wikipedia.org)
  • Thus far, x-nucleobases have been added to strands of DNA using phosphoramidite derivatives, as traditional polymerases have been unsuccessful in synthesizing strands of xDNA. (wikipedia.org)
  • xDNA has a rise of 3.2Å and a twist of 32°, significantly smaller than B-DNA, which has a rise of 3.3Å and a twist of 34.2° xDNA nucleotides can occur on both strands-either alone (known as "doubly expanded DNA") or mixed with natural bases-or exclusively on one strand or the other. (wikipedia.org)
  • G-rich DNA strands are naturally involved in duplex-DNA architecture through association with their complementary C-rich DNA strands by the canonical Watson-Crick pairing [ 1 - 3 ]. (hindawi.com)
  • Indeed, given that four guanine residues can self-associate in a planar arrangement through a Hoogsteen-type hydrogen-bonding network [ 4 ] to form a structure called G-quartet, G-rich strands can adopt a peculiar three-dimensional arrangement called G-quadruplex DNA [ 5 - 9 ] resulting from the stacking of several contiguous G-quartets (Figure 1 ). (hindawi.com)
  • Dr. Gaurav Chopra and Professor Michael Levitt in the Department of Structural Biology used molecular dynamics simulations involving a state-of-the-art Quantum Mechanical Polarizable Force Field (QMPFF3) to study the hydration of buckminsterfullerene, the smallest hydrophobic nanosphere widely referred to as a buckyball or C 60 . (phys.org)
  • Konstantin Meyl adapted the scalar waves described by Nicola Tesla to biology and proposed the relationship between the scalar waves and DNA 1 . (nature.com)
  • We believe that the topology and viscoelasticity of DNA and chromatin are important - yet under-explored -- elements that regulate genome function. (ed.ac.uk)
  • Additionally, the checkpoint kinases modify the chromatin surrounding DNA damages through phosphorylation of the H2A histone (H2AX in mammals). (cea.fr)
  • On the other hand, by the presented DNA model and by obtaining DNA frequency, experimental studies of the effects of waves on DNA such as phantom effect or DNA teleportation can also be studied scientifically and precisely. (nature.com)
  • About impressionability of DNA from the wave frequency, many experimental research studies have been carried out which have opened a new branch in science, called wave genome. (nature.com)
  • Edward d'Auvergne pointed out the relax program, which looks like a useful way to connect experimental NMR spectra with molecular dynamics simulations. (openscience.org)
  • Using the restraints coming from experiments such as Cryo-EM, SAXS, and NMR Kirmizialtin lab is developing computational tools and methods using path sampling, metadynamics, and machine learning to help to sample conformations more effectively and guide MD simulations toward the direction where it meets with the experimental signal, providing more accurate description of physical processes and allowing atomic level visualization of the experimental data. (nyu.edu)
  • The docking studies and molecular dynamics simulations further corroborate the experimental findings. (bvsalud.org)
  • In collaboration with Drs. T. Izumi and S. Mitra from the Sealy Center for Molecular Science (SCMS) we are determining how apurinic/apyrimidinic endonucleases respond to subtle differences in the structure and dynamics of DNA sites damaged by low dose ionizing radiation. (utmb.edu)
  • Finally, we demonstrate detection of 10 ng of Escherichia coli genomic DNA using the sensor concept. (scilifelab.se)
  • Unrepaired or incorrectly repaired DNA damage may lead to loss of heterozygosity, mutations, deletions, genomic rearrangements and chromosome loss. (cea.fr)
  • Leptospira species molecular epidemiology in the genomic era. (cdc.gov)
  • To cap- lular phenotypes (e.g. disease) on a mechanistic level, and ture the complex network of nonlinear information process- to use genomic signals to classify disease on a molecular ing based upon multivariate inputs from inside and outside level. (lu.se)
  • xDNA (also known as expanded DNA or benzo-homologated DNA) is a size-expanded nucleotide system synthesized from the fusion of a benzene ring and one of the four natural bases: adenine, guanine, cytosine, and thymine. (wikipedia.org)
  • Later, Eric T. Kool's group finished synthesizing the remaining three expanded bases, eventually followed by yDNA ("wide" DNA), another benzo-homologated nucleotide system, and naphtho-homologated xxDNA and yyDNA. (wikipedia.org)
  • Research into xDNA replication using a Klenow fragment from DNA polymerase I shows that a natural base partner is selectively added in instances of single-nucleotide insertion. (wikipedia.org)
  • the second is a Cas9 enzyme that recognizes and slices the DNA in a precise spot, whose location or address is post-marked by a nucleotide sequence called a protospace adjacent motif, or PAM. (sdsc.edu)
  • Conformational change of HIVRT, an enzyme responsible for DNA synthesis in HIV virus, when an incoming nucleotide binds to the growing DNA strand. (nyu.edu)
  • CRISPR-Cas9 conformational activation, as revealed from Gaussian accelerated Molecular Dynamics (GaMD) simulations. (sdsc.edu)
  • Experiments with xDNA provide new insight into the behavior of natural B-DNA. (wikipedia.org)
  • Those snapshots join into movies that can show molecular behavior over a microsecond. (doe.gov)
  • They started out by examining the structure and molecular behavior of millions of atoms in lignin - and how it behaves in water and changes with subtle alterations in its sequence and structure. (doe.gov)
  • With this Dynamics workshop, our goal is to bring together leading experts in the field of membrane dynamics, with a particular focus on neutrons and X-rays, but also complementary techniques including NMR, single molecule spectroscopy and computer modeling. (lu.se)
  • However, the realization of functionalized DNA origami still suffers from imperfect production methods, in particular in the purification step, where excess material is separated from the desired functionalized DNA origami. (scilifelab.se)
  • In this article we demonstrate and optimize two purification methods that have not previously been applied to DNA origami. (scilifelab.se)
  • An international research team has developed a highly efficient novel method for simulating the dynamics of very large systems potentially containing millions of atoms, up to 1000 times more than current conventional methods. (foresight.org)
  • The research team, led by TYC member David Bowler, UCL and NIMS MANA and Tsuyoshi Miyazaki at NIMS, used high performance computing to introduce a new technique, where the time required for the calculations increases linearly with the number of atoms, to perform first-principles dynamical simulations of systems comprising more than 30,000 atoms, 100 times larger than is usual with conventional methods. (foresight.org)
  • This conformational change, which occurs along milliseconds, is captured with atomic-level precision via the use of advanced simulation methods (i.e. (sdsc.edu)
  • To overcome the time scale gap between simulations and experiments, Kirmizialtin's lab focuses on developing novel computational methods to extend the timescales of MD simulations. (nyu.edu)
  • This course covers basic theory and practical application of computational methods and programs widely used in chemistry and molecular physics, for example density functional theory, semi-empirical calculations, molecular dynamics, MM/PBSA and free-energy perturbation. (lu.se)
  • The advent of new methods to obtain large-scale surveys of various mathematical structures, such as systems of differen- gene expression in which transcript levels can be determined tial equations, graphical networks, stochastic functional re- for thousands of genes simultaneously has facilitated the ex- lations, and simulation models. (lu.se)
  • Eisenstein & Shakked, 1995) and drugs (Kopka mation about the hydration structure of DNA has et al. (lu.se)
  • 1-17 I am especially interested in biomolecular systems where a significant role of structural dynamics is known or suspected. (ibp.cz)
  • Genome integrity is constantly threatened by DNA lesions. (cea.fr)
  • The three dimensional organization of the genome in the nucleus, previously known to impact on gene expression, has recently emerged as a key regulator of DNA repair. (cea.fr)
  • By shedding light on the biophysical details governing the mechanics of CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats) activity, the study provides a fundamental framework for designing a more efficient and accurate genome-splicing technology that doesn't yield "off-target" DNA breaks currently frustrating the potential of the CRISPR-Cas9- system, particularly for clinical uses. (sdsc.edu)
  • Signals generated by the genome must be processed to the genome, regulatory models require the kind of nonlinear characterize their regulatory effects and their relationship to dynamics studied in signal processing and control. (lu.se)
  • Journal of molecular modeling. (ub.edu)
  • Presenter Stephane Redon Stephane Redon is the former head of the NANO-D research group at the INRIA Grenoble - Rhone-Alpes Research Center, that he started in January 2008 and led until October 2018, when he left to start OneAngstrom, a spin-off of Inria that commercializes the SAMSON open platform for molecular modeling. (foresight.org)
  • I am interested in studying rheological properties polymers and biopolymers and applying mathematical techniques, statistical mechanics and molecular modeling to study the properties of biological and synthetic macromolecules. (cmich.edu)
  • Numerical simulations of particulate suspensions via a discretized Boltzmann equation. (crossref.org)
  • Numerical simulation of fluid flow and transport processes in the subsurface must account for the presence of wells. (global-sci.org)
  • In DNA wireframe designs, the construction material is double-stranded DNA, which has a persistence length of around 50 nm. (scilifelab.se)
  • Knowledge of functionally important molecular motions has important implications in medicine and nanotechnology, in addition to providing insights into understanding life. (nyu.edu)
  • Anthracyclines' mechanism of action in cancer therapy is to intercalate DNA, and since DNA nanotechnology allows for such a high degree of customization, we hypothesized that this would allow us to tune the DNA nanostructures for optimal delivery of the anthracycline doxorubicin (Dox) to human breast cancer cells. (scilifelab.se)
  • Historically, proposals for molecular nanotechnology by K. Eric Drexler and others, usually referred to these days as high-throughput atomically precise manufacturing, have been based upon physical law. (foresight.org)
  • Subsequently, we use this method to characterize the mobility and diffusive dynamics of nanoscale spheres in rod matrices, while paying special attention to the length scales of the fluid which characterize the hydrodynamic screening and overall viscous motion. (aps.org)
  • In parallel, we carried out single-molecule force measurement and molecular dynamics simulations on the same subjects. (nii.ac.jp)
  • The potential of DNA structural properties in single-molecule electronics has finally been harnessed by researchers in a single-molecule junction device that shows spontaneous self-restoring ability. (innovationtoronto.com)
  • It turns out that the single-molecule conductance falls off sharply with the length of the molecule so that only extremely short stretches of DNA are useful for electrical measurements. (innovationtoronto.com)
  • Dr. Tomoaki Nishino from Tokyo Tech, Japan, who was part of this study, explains, "We investigated electron transport through the single-molecule junction of a 'zipper' DNA that is oriented perpendicular to the axis of a nanogap between two metals. (innovationtoronto.com)
  • This single-molecule junction differs from a conventional one not only in the DNA configuration but also in orientation relative to the nanogap axis. (innovationtoronto.com)
  • To their delight, they found that that the single-molecule junction with the long 90-mer DNA showed an unprecedented high conductance. (innovationtoronto.com)
  • The simulations also suggested something even more interesting: the single-molecule junction could actually restore itself i.e., go from "unzipped" to "zipped," spontaneously after an electrical failure! (innovationtoronto.com)
  • A promising method for the delivery of such genes involves the use of DNA/lipid complexes (lipoplexes). (sciencedaily.com)
  • Once recruited to DSB, these complexes get activated and induce the phosphorylation of numerous targets including transducing kinases, which subsequently phosphorylate downstream effectors to delay cell cycle and promote DNA repair. (cea.fr)
  • In parallel with the development of DNA nanostructures, software packages for the simulation of nucleic acids have seen rapid development allowing for the simulation of the dynamics of full DNA nanostructure assemblies. (scilifelab.se)
  • With present day computers coupled with efficient parallel molecular dynamics codes, it is now possible to follow the equilibrium dynamics of chains of length $10-20N_e$ from the early Rouse regime to the long time diffusive regime. (aps.org)
  • Our molecular dynamics simulations of an array of 64 parallel duplex DNA revealed considerable artifacts of cation-DNA phosphate interactions in CHARMM and AMBER parameter sets: both the DNA arrangement and the pressure inside the DNA arrays were found to be in considerable disagreement with experiment. (illinois.edu)
  • Purification of functionalized DNA origami nanostructures. (scilifelab.se)
  • Based on the results, it can be concluded that in the presence of a high concentration of HS, the isolated DNA was low quality and the additional purification procedure was necessary. (peerj.com)
  • Comparison of MD simulations of free and DNA-bound elsamicin A provided insight into the mechanism of DNA cleavage. (ub.edu)
  • Although PAM recognition is essential for cleavage, it is unknown whether and how PAM binding activates Cas9 for DNA cleavage at spatially distant sites. (nih.gov)
  • Although extensive studies of the CRISPR-Cas9 system, including X-ray crystallography and cryoelectron microscopy (cryoEM) have revealed detailed views of the system's structural and biological activity, the dynamics of Cas9 and its step-by-step acrobatics with nucleic acids during its merger and cleavage of DNA have remained fuzzy. (sdsc.edu)
  • These results will serve as a basis for the careful choice of the appropriate methodology to calculate an average of the 31P chemical shift tensors over the molecular dynamics trajectory of the oligonucleotide d(CGCGAATTCGCG)2. (muni.cz)
  • We performed targeted molecular dynamics simulation to obtain trajectory of conformational change from inactive to active form. (intechopen.com)
  • A fusion of cutting-edge methodologies, intertwining molecular dynamics simulations and the power of machine learning. (umassmed.edu)
  • Recently we have developed a new computer simulation method to simulate the dynamical and rheological properties of colloid suspensions of in a variety of complex fluids. (aps.org)
  • It is shown that the translocation can be completely turned off for the longer molecule using an appropriate bias, thus allowing a size discrimination of the DNA translocation through the nanopores. (scilifelab.se)
  • The DNA molecule is the most evolved and most complex molecule created by nature. (nature.com)
  • Deoxyribonucleic acid, more commonly known as DNA, is an evolved molecule that contains the genetic code of organisms. (nature.com)
  • In every advanced organism, the molecule called DNA (deoxyribonucleic acid, to use its full name) forms the genetic code. (innovationtoronto.com)
  • scientists have established that the intricate structures of DNA have made it possible for it to be used in new-age electronic devices with junctions comprising just a single DNA molecule. (innovationtoronto.com)
  • They have managed to achieve an unconventionally high conductivity with a long DNA molecule-based junction in a "zipper" configuration that also shows a remarkable self-restoring ability under electrical failure. (innovationtoronto.com)
  • The team used a 10-mer and a 90-mer DNA strand (which indicate the number of nucleotides, basic building blocks of DNA, comprising the molecule length) to form a zipper-like structure and attached them to either a gold surface or to the metal tip of a scanning tunneling microscope, an instrument used to image surfaces at the atomic level. (innovationtoronto.com)
  • RCA is a highly specific molecular detection mechanism based on DNA probe circularization. (scilifelab.se)
  • Here, we find evidence of a PAM-induced allosteric mechanism revealed by microsecond molecular dynamics simulations. (nih.gov)
  • Understanding and rationalizing chemical reactions, their mechanism, and the relation between molecular structure and function is key to today's science. (lu.se)
  • In this work, we study the effect of various design choices on the stiffness versus final size of nanoscale wireframe rods, given the constraints on origami designs set by the DNA origami scaffold size. (scilifelab.se)
  • Three types of functionalized DNA origami were used as model systems in this study. (scilifelab.se)
  • The basis for assessing the quantity and quality of extracted DNA was the Polymerase chain reaction (PCR) reaction since the analysis of soil DNA often relies on the use of PCR to study soil microorganisms. (peerj.com)
  • MD is one of the most powerful theoretical approaches to study the structure, molecular interactions and resulted dynamics in a unified framework. (nyu.edu)
  • The goal of this study was to identify the epidemiological and molecular characteristics of TBEV associated with fatal meningoencephalitis in Mongolia. (who.int)
  • Similar to natural bases, x-nucleotides selectively assemble into a duplex-structure resembling B-DNA. (wikipedia.org)
  • This natural 8-ring 24-membered macroheterocycle (Figure 2 ) displays high affinity for quadruplex and most importantly has no affinity for duplex DNA ( vide infra ). (hindawi.com)
  • In this system, the endonuclease Cas9 generates double strand breaks in DNA upon RNA-guided recognition of a complementary DNA sequence, which strictly requires the presence of a protospacer adjacent motif (PAM) next to the target site. (nih.gov)
  • The result is an RNA-DNA hybrid with a displaced non-target DNA strand. (sdsc.edu)
  • The resulting simulations, published in the September 8 issue of ACS Central Science , identified some of the key factors underling the complex structural changes taking place during the merger and preparation for cleaving the target DNA strand. (sdsc.edu)
  • The time series of correlation between residues during the conformational change generated by targeted molecular dynamic simulation. (intechopen.com)
  • Here, we used DNA origami flat sheets to display PD-L1 ligands at defined nanoscale distances and investigated their ability to inhibit T-cell activation in vitro. (scilifelab.se)
  • Macrocyclic scaffolds are particularly attractive for designing selective G-quadruplex ligands essentially because, on one hand, they show a poor affinity for the "standard" B-DNA conformation and, on the other hand, they fit nicely with the external G-quartets of quadruplexes. (hindawi.com)
  • cDNA synthesis was performed with SuperScript III reverse transcription (Invitrogen, https://www.thermofisher.com/us/en/home/brands/invitrogen.html) using a single primer located within the 2C and the 3 UTR. (cdc.gov)
  • Presenter Abhishek Singharoy, Arizona State University Abhishek Singharoy is an Assistant Professor in the School of Molecular Sciences at Arizona State University. (foresight.org)
  • These lipoplexes are taken up by cells in a structure called an endosome,' explains Bart Bruininks, a PhD student in the group of Siewert-Jan Marrink, Professor of Molecular Dynamics at the University of Groningen. (sciencedaily.com)
  • Evilevitch A. Hohlbauch S.V. ''Intranuclear, HSV-1 DNA ejection induces major mechanical transformations suggesting mechanoprotection of nucleus integrity. (lu.se)
  • In contrast to 2H and 17O, the 1H relaxation dispersion is dominated by labile DNA protons and therefore provides little information about DNA hydration. (lu.se)
  • To understand and combat the HIV-1 Protease drug resistance at the molecular level to design potent inhibitors. (umassmed.edu)
  • In these cases, mixed quantum-classical (QM/MM) MD simulations are required, although the quantum (QM) region, usually described using density functional theory (DFT) for its cost effective inclusion of correlation effects, is often plagued by the accuracy of the exchange correlation functionals (Roethlisberger U. & Carloni P. Lect Notes Phys 2006, 704, 449). (cecam.org)
  • June 9, 2021 During meiosis, paternal and maternal chromosomes duplicate, pair, and exchange parts of their DNA in a process called meiotic recombination. (sciencedaily.com)
  • In the assembly of DNA nanostructures, the specificity of Watson-Crick base pairing is used to control matter at the nanoscale. (scilifelab.se)
  • The molecular reasons for binding versus non-binding and the specificity toward a certain surface are analyzed by molecular dynamics simulation, using recent force field extensions for fcc metals and sheet silicates to reproduce surface and interface energies with $ (aps.org)
  • This new method will be an invaluable tool for those using predictive computational modelling and, as most simulations are stuck below 1,000 atoms, it will open the doors to studying completely new areas of physics. (foresight.org)
  • The various conformations adopted by the biomolecules by virtue of their flexibility are studied by a dual experience - theory approach, with quantum chemical simulations. (cea.fr)
  • Rarefied Gas Dynamics: Theory and Simulations, Vol. 159 of Prog. (crossref.org)