Protein and dna sequences. Medical search. Frequent questions

See how the University of Washington used HiFi sequencing to uncover a key finding about ALS and the human genome. (pacb.com)
Enteritidis strains isolated from egg and chicken samples, then used Whole Genome Sequence (WGS) data to model the structures of their protein products. (pacb.com)
Repeated sequences (also known as repetitive elements, repeating units or repeats) are short or long patterns of nucleic acids (DNA or RNA) that occur in multiple copies throughout the genome. (wikipedia.org)
Some of these repeated sequences are necessary for maintaining important genome structures such as telomeres or centromeres. (wikipedia.org)
While some repeated DNA sequences are important for cellular functioning and genome maintenance, other repetitive sequences can be harmful. (wikipedia.org)
Overall, repeated sequences are an important area of focus because they can provide insight into human diseases and genome evolution. (wikipedia.org)
In the 2000s, the data from full eukaryotic genome sequencing enabled the identification of different promoters, enhancers, and regulatory RNAs which are all coded by repetitive regions. (wikipedia.org)
Tandem repeats are repeated sequences which are directly adjacent to each other in the genome. (wikipedia.org)
As part of that project, researchers in Brazil formed a consortium, called the ZiBRA project, in collaboration with Instituto Evandro Chagas and Fundação Oswaldo Cruz public health laboratories in Brazil, to bring mobile, full-genome sequencing to monitor Zika. (genengnews.com)
The ability for any lab to sequence the genome of a pathogen quickly and cost-effectively is a game-changer for public health. (genengnews.com)
A larger version of the MinION instrument, the GridION, is even being used to sequence the genome of the tulip-at 34 Gb, it is one of the largest genomes around. (genengnews.com)
That combination of speed, portability, and affordability puts real-time, whole-genome sequencing within reach of any scientist in the world. (genengnews.com)
Programmed genome rearrangements in Oxytricha produce transcriptionally active extrachromosomal circular DNA. (shengsci.com)
Extrachromosomal circular DNA (eccDNA) is both a driver of eukaryotic genome instability and a product of programmed genome rearrangements, but its extent had not been surveyed in Oxytricha, a ciliate with elaborate DNA elimination and translocation during development. (shengsci.com)
We're now dealing with the amount of data that astrophysicists deal with, all because of the genome sequencing revolution," said ORNL researcher Ada Sedova. (eurekalert.org)
They have modeled the full proteomes - all the proteins coded in an organism's genome - for four microbes, each with approximately 5,000 proteins. (eurekalert.org)
Recent work by the international ENCODE (Encyclopedia of DNA Elements) Project (1, 2) suggested that a large percentage of non-coding DNA, which makes up an estimated 95% of the human genome, has a function in gene regulation. (evolutionnews.org)
Sarah Gregory] Today, I'm talking with Dr. Kelly Oakeson about bioinformatics and genome sequencing in a public health lab. (cdc.gov)
I also do whole genome sequencing. (cdc.gov)
Kelly Oakeson] Well, whole genome sequence data provides a very high-resolution tool for everything from identifying what types of microbes or viruses you might have in any given sample to determining antimicrobial resistance and identifying clusters of related microbes in the case of a foodborne illness outbreak. (cdc.gov)

DNA-dependent transcription of adenovirus genes in a soluble whole-cell extract. (wikidata.org)
DNA sequences and predicted protein structures of prot6E and sefA genes for Salmonella ser. (pacb.com)
In search of the genes that enable sphagnum moss to tolerate rising temperatures, ORNL scientists start by comparing its DNA sequences to the model organism Arabidopsis, a thoroughly investigated plant species in the mustard family. (eurekalert.org)
The DNA that makes up genes contains the instructions to synthesise proteins, but it's wrong to think that, for a given gene, these instructions are always the same for all parts of the organisms . (evolutionnews.org)
Indeed, FANTOM5's survey of 95 percent of protein-coding genes found near universal coverage by promoters, based on the first few bases of RNA transcripts. (evolutionnews.org)
Gene expression refers to how often or when proteins are created from the instructions within your genes. (cdc.gov)
While genetic changes can alter which protein is made, epigenetic changes affect gene expression to turn genes "on" and "off. (cdc.gov)
Non-coding RNA may also recruit proteins to modify histones to turn genes "on" or "off. (cdc.gov)
Epigenetics allows the muscle cell to turn "on" genes to make proteins important for its job and turn "off" genes important for a nerve cell's job. (cdc.gov)
In a study of 450 CRC diagnosed under 50 years via the Ohio Colorectal Cancer Prevention Initiative, germline DNA analysis for mutations in 25 cancer susceptibility genes was done in addition to assessing microsatellite instability and/or immunohistochemistry for MMR deficiency. (cdc.gov)
In hereditary nonpolyposis colorectal cancer (HNPCC), an inherited mutation in one of the DNA mismatch repair (MMR) genes appears to be a critical factor. (medscape.com)
MMR genes normally produce proteins that identify and correct sequence mismatches that may occur during DNA replication. (medscape.com)
As the sequencing and gene annotation projects of entire genomes of many species are headed towards completion (see, e.g. [13] ), massive mapping efforts in biology are now focused on how the genes interact. (lu.se)
They interact with specific intracellular receptor proteins in the target tissues and alter the expression of genes to corticosteroids. (bvsalud.org)
Even if the DNA sequence - the set of genes - is the same in all cells, only certain genes are expressed, i.e. only information from certain genes is copied (transcribed) and used to build protein structures or regulate processes. (lu.se)
Gene expression generally produces proteins, but there are also non-coding genes that produce RNA molecules (rRNA, tRNA). (lu.se)
DNA methylation is a chemical process that regulates the function of the genes. (lu.se)
It is not only the genes that code for proteins that are methylated, but also parts of the DNA that code for regulatory functions (RNA molecules), which can have a greater effect than genes. (lu.se)

Sarah Gregory] I understand that the ability of this sequencing to work optimally is dependent on bioinformatics. (cdc.gov)
So, bioinformatics combines computer science and biology in order to make heads or tails out of all of this sequence data we're making. (cdc.gov)
I think a general lack of understanding as to what bioinformatics is and how important it is, especially when dealing with next generation sequence data. (cdc.gov)

Circular maps of plasmid genomes from two PacBio platform-sequenced Salmonella ser. (pacb.com)
Our revolutionary sequencing technologies combine the completeness of long reads with the accuracy of short reads to provide the most comprehensive view of genomes, transcriptomes, and epigenomes. (pacb.com)
they found out that more than half of the eukaryotic genomes were repetitive DNA through their experiments on reassociation of DNA. (wikipedia.org)
Researchers are using the Summit supercomputer at ORNL and tools developed by Google's DeepMind and Georgia Tech to speed the accurate identification of protein structures and functions across the entire genomes of organisms. (eurekalert.org)
The FANTOM5 promoter atlas is a natural extension of earlier maps of active transcripts and promoters complementing the sequencing of mammalian genomes. (evolutionnews.org)
Diane Burgess and Michael Freeling sampled the genomes of a wide variety of plant species (e.g., rice, banana, cacao, the model plant Arabidopsis , and other flowering plants, both monocots and dicots) and found " numerous conserved non-coding sequences " (CNSs). (evolutionnews.org)
Mobile DNA elements and the dynamics of genomes. (lu.se)

Noncoding" sequences are not translated into proteins, and nucleic acids with such motifs need not deviate from the typical shape (e.g. the "B-form" DNA double helix). (wikipedia.org)
RNA is a single-stranded nucleic acid involved in the transfer of genetic information from DNA to protein. (primorigen.com)
DNA is a double-stranded nucleic acid that stores genetic information in the form of a sequence of nucleotides. (primorigen.com)
The T4 Gene 32 Protein is a single-stranded nucleic acid binding protein that has the function of stabilizing single-stranded regions of DNA. (qiagen.com)

Thus, integrative massively parallel protein synthesis as well as multiplex functional measurements are needed to fully decipher the protein functional landscape. (harvard.edu)
Control of eukaryotic messenger RNA synthesis by sequence-specific DNA-binding proteins. (wikidata.org)
What is protein synthesis and why is it important? (primorigen.com)
Protein synthesis is the process by which cells build proteins from amino acids . (primorigen.com)
Protein synthesis is defined as the process by which cells build proteins. (primorigen.com)
The importance of protein synthesis can be seen in its impact on gene expression, gene regulation, and diseases. (primorigen.com)
Transcription is the first stage of protein synthesis, and it involves the synthesis of messenger RNA (mRNA) from a DNA template. (primorigen.com)
Translation is the second stage of protein synthesis, and it involves the synthesis of a protein from an mRNA template. (primorigen.com)
Post-translational modifications are the final stage of protein synthesis, and they involve the modification of proteins after they have been synthesized. (primorigen.com)
Codon usage can differ between organisms and can affect the rate of protein synthesis. (primorigen.com)
RNA and DNA are essential molecules in protein synthesis. (primorigen.com)
There are three main types of RNA involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). (primorigen.com)
The DNA sequence is transcribed into RNA during protein synthesis, and it serves as a template for mRNA synthesis. (primorigen.com)
Protein synthesis occurs in different organelles in eukaryotic cells, including the nucleus, ribosomes, and endoplasmic reticulum. (primorigen.com)
In prokaryotic cells, protein synthesis occurs in the cytoplasm. (primorigen.com)
The emission profiles present at each cluster over subsequent rounds of synthesis enable the elucidation of DNA sequences, in a process known as sequencing-by-synthesis. (biologists.com)
Prot ein display on a Ma ssively- P aralleled Array) that combines sequencing-by-synthesis with protein function assays to enable quantitative protein function assays with a massively high throughput. (biologists.com)
Cells continuously monitor protein synthesis to prevent accumulation of aberrant polypeptides. (shengsci.com)
DNA synthesis occurred on either circular or linear plasmids coupled to the beads, but only DNA synthesis on the circular plasmid was inhibited by geminin and a. (shengsci.com)
The T4 Gene 32 Protein has exhibited an ability to enhance the performance of several DNA synthesis-related activities in secondary-structure rich regions, including PCR amplification and DNA sequencing. (qiagen.com)
The T4 Gene 32 Protein also stimulates the rate of synthesis of T4 DNA Polymerase on primed-single-stranded substrates showing a 5-10-fold increase in synthesis rate. (qiagen.com)
The ability of T4 Gene 32 Protein to enhance the performance of several DNA synthesis-related activities is based on its essential function in the replication of bacteriophage T4. (qiagen.com)
in particular, what varies is the point in the "string" of code at which protein synthesis starts . (evolutionnews.org)
The complexes may induce transcription of messenger RNA, leading to the synthesis of new proteins. (bvsalud.org)

I utilize it to screen therapeutically relevant protein binding motifs against thousands of proteins from the human proteome. (harvard.edu)
A team of scientists led by the Department of Energy's Oak Ridge National Laboratory and the Georgia Institute of Technology is using supercomputing and revolutionary deep learning tools to predict the structures and roles of thousands of proteins with unknown functions. (eurekalert.org)
DNA is the molecule that encodes the genetic instructions enabling a cell to produce the thousands of proteins it typically needs. (evolutionnews.org)

The knowledge about DNA-binding residues, binding specificity and binding affinity helps to not only understand the recognition mechanism of protein-DNA complex, but also give clues for protein function annotation. (nature.com)
Therefore, a reliable identification of DNA-binding sites in DNA-binding protein is important for protein function annotation, in silico modeling of transcription regulation and site-directed mutagenesis. (nature.com)
UGENE provides customizable tools for visualization, analysis, annotation of genetic sequences. (bestfreewaredownload.com)
Search a DNA sequence to match either a DNA query, or a protein translation, or an annotation. (cnet.com)

The nucleus is the site of DNA replication and transcription, and it is where mRNA is synthesized. (primorigen.com)
Eukaryotic High-Mobility Group B (HMGB) proteins alter DNA elasticity while facilitating transcription, replication and DNA repair. (shengsci.com)
We describe an improved model of DNA replication in Xenopus egg extracts, in which a circular plasmid immobilized on paramagnetic beads is used as a template. (shengsci.com)
In this article, we reconcile this inconsistency by showing that, in a defined in vitro system with plasmid DNA templates, a variety of sequence-specific DNA-binding proteins, such as the bacteriophage λ O replication initiator or the E. coli lactose or galactose repressors, strikingly stimulate transcription-coupled DNA supercoiling. (johnshopkins.edu)
The native Gene 32 Protein from bacteriophage T4 (T4gp32) is a single-stranded DNA binding protein that is required for T4 DNA replication, recombination and repair. (qiagen.com)
Gp32 binds transiently and cooperatively to ssDNA template sequences as these entities are exposed by the processive helicase operating within the replication complex. (qiagen.com)
This binding puts these ssDNA sequences into optimal conformations for interacting with DNA polymerases and other replication proteins. (qiagen.com)

Proteins are complex molecules made up of amino acids arranged in a specific sequence, and they perform a wide range of functions in biological systems. (primorigen.com)
In Illumina sequencing, DNA fragments are added to sequencing flow cells, where they bind to flow cell oligonucleotides and via bridge amplification, produce clusters of identical DNA molecules. (biologists.com)
Deep sequencing of RNA molecules cross-linked to immunoprecipitated protein particles (CLIP-seq) revealed. (shengsci.com)
Many non-coding sequences produce RNA molecules that regulate gene expression by turning them on and off. (evolutionnews.org)
Nanosecond to microsecond protein dynamics probed by magnetic relaxation dispersion of buried water molecules. (lu.se)
Among these proteins, annexin is known to inhibit phospholipase A2 and thus block the production of mediators and arachidonic acid metabolites such as the COX-2 enzyme, leukotrienes and prostaglandins, cytokines, interleukins, adhesion molecules and enzymes such as collagenase 24,25 . (bvsalud.org)

Distinct structural bases for sequence-specific DNA binding by mammalian BEN domain proteins. (bvsalud.org)
Here, we characterize several mammalian BEN domain (BD) factors, including from two NACC family BTB-BEN proteins and from BEND3, which has four BDs. (bvsalud.org)
Together, these studies expand the DNA recognition activities of BEN factors and provide structural insights into sequence-specific DNA binding by mammalian BEN proteins . (bvsalud.org)
Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. (nih.gov)

In many organisms, a significant fraction of the genomic DNA is repetitive, with over two-thirds of the sequence consisting of repetitive elements in humans. (wikipedia.org)
In the meantime, new genomic research could be changing clinical and public health approaches to reducing the burden of colorectal cancer from LS and in general, by shifting the laboratory testing approach toward tumor next generation sequencing. (cdc.gov)

DNA from additional tooth samples of these persons was extracted, and more markers mapped on the Y. pestis high copy number plasmid pPCP1 were included. (cdc.gov)
Y. pestis strain CO92 plasmid pPCP1 sequence AL109969.1) on the Y. pestis pla gene (encoding plasminogen activator). (cdc.gov)
The miniF plasmid C protein: sequence, purification and DNA binding. (shengsci.com)
The C protein has been purified from cells carrying the Ptrp-C plasmid, and a preliminary study of C protein-DNA binding properties has been carried out. (shengsci.com)
Double-stranded endonuclease activity was determined in a 50 μL reaction containing 0.5 μg of plasmid DNA and 10 μL of protein solution incubated for 4 hours at 37°C. (qiagen.com)
Share: export a plasmid map as an image, or export an annotated DNA sequence to GenBank format and freely share data with your colleagues or customers using the universally accessible SnapGene format. (cnet.com)

Using a competition assay on agarose gels we found that the p53 consensus sequences in longer DNA fragments are better targets than the same sequences in shorter DNAs. (nih.gov)
Several studies implicated that longer DNA targets are broken down to small fragments during extensive food processing causing failure of PCR-based identification methods [ 23 , 26 , 28 , 31 ]. (hindawi.com)
The DNA containing the target gene(s) is split into fragments using restriction enzymes . (encyclopedia.com)
These fragments are then inserted into cloning vectors , such as bacterial plasmids or bacteriophages, which transfer the recombinant DNA to suitable host cells, such as the bacterium E. coli. (encyclopedia.com)
Alternatively, complementary DNA is inserted into the vectors, or 'naked' DNA fragments can be taken up directly by a host bacterium from its medium (this is less efficient than vector transfer). (encyclopedia.com)

However, all of these methods involve PCR amplification of target DNA that is typically more than hundred base-pair long [ 25 - 30 ]. (hindawi.com)
Improved yields and quality of templates may be achieved with the use of DNA-binding proteins in amplification and sequencing reactions. (qiagen.com)

Methods for gene identification and analysis of gene structure: cloning, PCR, restriction mapping, in situ hybridisation, DNA sequencing. (lu.se)

Complete sequencing and characterization of 21,243 full-length human cDNAs. (nih.gov)

We have determined the nucleotide sequence of the C gene. (shengsci.com)

Development of an Analytical Assay for Electrochemical Detection and Quantification of Protein-Bound 3-Nitrotyrosine in Biological. (aidstar-one.com)

For example, many DNA binding proteins that have affinity for specific DNA binding sites bind DNA in only its double-helical form. (wikipedia.org)
For this, we would make use of datasets about containing DNA-binding proteins and the DNA sequences they bind to. (stackexchange.com)
Myc proteins are basic helix-loop-helix/ leucine-zipper proteins that bind to specific DNA sequences. (uu.nl)
In the nucleus, these complexes bind to specific DNA sequences and alter their expression. (bvsalud.org)
Certain transcription factors do not bind when the DNA is methylated while others only bind when the DNA is methylated. (lu.se)

In contrast, animals that received a sham DNA vaccine (n = 12) had no detectable neutralizing antibodies against IDV, and viral RNA was readily detectable in respiratory tract tissues after intranasal challenge [3 x 10(5) TCID50] with IDV D/OK (n = 6) or D/660 (n = 6). (cdc.gov)

Note: all of the sequences from the links immediately above are simple linear readouts of the amino acid sequences of the proteins indicated. (whozoo.org)

Isolates were sequenced using Illumina technologies. (pacb.com)
From sequence to function: Current Illumina high-throughput sequencing technology adapted to carry out functional screening on a huge variety of proteins. (biologists.com)
Illumina high-throughput sequencing technologies have been widely utilised to tackle many biological problems. (biologists.com)
To generate protein arrays, the authors first created a library of DNA constructs encoding their polypeptides of interest, which are then clustered and sequenced on an Illumina MiSeq, with the cluster positions recorded (Figure 1A). (biologists.com)
As the position of the clusters remain the same from the initial Illumina MiSeq to the final functional assays, DNA sequence, which determines protein sequence, can be directly correlated with protein function. (biologists.com)

Bullock and Fersht 8 have shown that mutations of DNA-binding residues, such as those on the tumor repressor protein P53, may predispose individuals to cancer. (nature.com)
Protein sequence information mainly consists of amino acid residue composition, biochemical features of amino acid residues and evolutionary information in terms of position-specific scoring matrices (PSSM). (nature.com)
Yan and his coworkers 11 trained a Naïve Bayes classifier by using only sequence information, such as the identities of the target residue and its sequence neighboring residues. (nature.com)
The crystal structures of the conserved ETS domain of SAP-1 bound to DNA sequences from the E74 and c-fos promoters reveal that a set of conserved residues contact a GGA core DNA sequence. (rcsb.org)
Discrimination for sequences outside this core is mediated by DNA contacts from conserved and nonconserved protein residues and sequence-dependent DNA structural properties characteristic of A-form DNA structure. (rcsb.org)
Protein folding is the process of arranging amino acid residues to form a functional protein. (primorigen.com)

Amino acids are the building blocks of proteins, and peptide bonds link them together to form long chains. (primorigen.com)
Ribosomes decode the mRNA, which links the amino acids together by peptide bonds to form a protein. (primorigen.com)
The authors then carried out in vitro transcription and translation with stalling of both the E. coli RNA Polymerase and ribosome, such that both the transcript and peptide remain associated with the DNA template. (biologists.com)
To test the technology with protein binding assays, the authors utilised the well-characterised FLAG peptide/M2 antibody system. (biologists.com)
After DNA sequencing and peptide generation, the M2 antibody was introduced, before the introduction of a fluorescent secondary antibody and imaging, similarly to an ELISA. (biologists.com)
Viral DNA and a viral peptide are cofactors of adenovirus virion proteinase activity. (microbiologyresearch.org)
All recognized mutations for AD are associated with increased deposition of amyloid-beta (Abeta), a peptide fragment comprising 39-43 amino acids that derive from the catabolism of the amyloid precursor protein (APP) molecule. (medscape.com)

Immunoglobulin gene transcription is activated by downstream sequence elements. (wikidata.org)
SAP-1 is a member of the Ets transcription factors and cooperates with SRF protein to activate transcription of the c-fos protooncogene. (rcsb.org)
Transcription by RNA polymerase can stimulate localized DNA supercoiling in Escherichia coli. (johnshopkins.edu)
Our data are most consistent with a model in which specific DNA-binding proteins facilitate a twin-domain mechanism to enhance DNA supercoiling during transcription. (johnshopkins.edu)
Leng, F & McMacken, R 2002, ' Potent stimulation of transcription-coupled DNA supercoiling by sequence-specific DNA-binding proteins ', Proceedings of the National Academy of Sciences of the United States of America , vol. 99, no. 14, pp. 9139-9144. (johnshopkins.edu)
Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and sequence-specific DNA binding activity. (nih.gov)
A total of 1,050 swine fecal samples from 88 pig farms were collected and tested by reverse transcription-PCR for sapoviruses, and positive findings were confirmed by sequencing. (lu.se)
Transcription factors are a group of proteins that are needed for a gene to start being copied to RNA, i.e. for transcription to start. (lu.se)

RNA polymerase reads the DNA sequence and produces a complementary RNA sequence. (primorigen.com)
In vivo, there is extensive experimental support for a "twin-domain" model in which positive DNA supercoils are generated ahead of a translocating RNA polymerase complex and negative supercoils are formed behind it. (johnshopkins.edu)
We demonstrate further that this stimulation requires the presence in the DNA template of a recognition sequence for the relevant DNA-binding protein and depends on the production of long RNA chains by an RNA polymerase. (johnshopkins.edu)
It represents an advance in an order of magnitude in the wide range of cell types and the amount of data produced per sample, and using single-molecule sequencing avoided polymerase chain reaction (PCR), digestion and cloning bias. (evolutionnews.org)

Second, I measure thousands of combinatorial mutations to the green fluorescent protein (GFP) and investigate our ability to predict those mutations using machine learning. (harvard.edu)
Through novel experimental and computational methods, I am able to predict the effect of mutations and determine a method for protein function exploration across distant sequence space. (harvard.edu)
However, SWISS-MODEL was unable to clearly model the protein structure of these two mutations. (pacb.com)
By studying double mutants more closely, the authors found pairs of mutations that exhibited positive cooperativity, and noted that most strong positively-cooperative pairs are in close proximity in the protein (Cα-Cα distances of less than 13 Å). (biologists.com)
New mutations -- or changes in the DNA -- are theoretically one way these kinds of uncommon scenarios can happen. (thetech.org)
The increased cancer risk is due to inherited mutations that degrade the self-repair capability of DNA. (medscape.com)
Spontaneous mutations happen as a result of apparently chance errors in the formation of DNA during cell division. (lu.se)
When a cell divides, the mutations are passed on to the daughter cells, but only mutations that occur in the DNA of the gametes are passed on to the next generation. (lu.se)

An analysis of the number of binding sites in the spatial context of the target site indicates that the interactions between binding sites next to each other are important for protein-DNA recognition and their binding ability. (nature.com)
The rules governing sequence-specific DNA-protein recognition are under a long-standing debate regarding the prevalence of base versus shape readout mechanisms to explain sequence specificity and of the conformational selection versus induced fit binding paradigms to explain binding-related conformational changes in DNA. (irbbarcelona.org)
Finally, comparison with our previous invertebrate BEN structures, along with additional structural predictions using AlphaFold2 and RoseTTAFold, reveal distinct strategies for target DNA recognition by different types of BEN domain proteins . (bvsalud.org)

When histones are loosely packed, more DNA is exposed or not wrapped around a histone and can be accessed by proteins that 'read' the gene, so the gene is turned "on. (cdc.gov)
The protein structure that surrounds the DNA, chromatin, largely comprises histone proteins and can be open or closed and thus allow or prevent factors binding to the DNA. (lu.se)
Epigenetic modifications of the histone proteins, such as acetylation or methylation, affect how tightly the DNA is packed around the histones and thus how accessible the DNA sequence is. (lu.se)
As well as DNA methylation, there are also other epigenetic mechanisms such as modification of histone proteins. (lu.se)

Recombination is important as a source of genetic diversity, as a mechanism for repairing damaged DNA, and a necessary step in the appropriate segregation of chromosomes in meiosis. (wikipedia.org)
Using a combination of atomistic simulations on a subset of representative sequences and mesoscopic simulations at the protein-DNA interactome level, we demonstrate the prevalence of the shape readout model in determining sequence-specificity and of the conformational selection paradigm in defining the general mechanism for binding-related conformational changes in DNA. (irbbarcelona.org)
Our results suggest that the DNA uses a double mechanism to adapt its structure to the protein: it moves along the easiest deformation modes to approach the bioactive conformation, while final adjustments require localised rearrangements at the base pair step and backbone level. (irbbarcelona.org)
Single-molecule kinetics reveal microscopic mechanism by which High-Mobility Group B proteins alter DNA flexibility. (shengsci.com)
Localization of DNA supercoils by nucleoprotein complexes may serve as a general mechanism for modulating DNA transactions that are sensitive to DNA superhelicity. (johnshopkins.edu)

Protein-DNA interactions are involved in many fundamental biological processes essential for cellular function. (nature.com)
Although the repetitive DNA sequences were conserved and ubiquitous, their biological role was yet unknown. (wikipedia.org)
In biology, a sequence motif is a nucleotide or amino-acid sequence pattern that is widespread and usually assumed to be related to biological function of the macromolecule. (wikipedia.org)
The assay was a viable alternative approach of qPCR for detecting, quantifying and counting copy number of shorter size DNA sequences to address a wide ranging biological problem in food industry, diagnostic laboratories and forensic medicine. (hindawi.com)
No studies so far practically explored the sequence and mismatch detecting power of the fluorophore-labeled-oligo-nanoparticle conjugates in heterogeneous biological samples. (hindawi.com)
Kelly Oakeson] Yeah, so Next Generation Sequencing generates a lot of sequence data that need to be translated into meaningful biological information. (cdc.gov)
Time scales of water dynamics at biological interfaces: peptides, proteins and cells. (lu.se)

Recently, the new sequencing technologies have allowed new discoveries for Life Sciences. (udemy.com)

Bioinformatic analyses of DNA- and protein sequences. (lu.se)

Taken together, this thesis lays the groundwork for making the high-throughput measurements needed to dissect a protein's function, enabling a future of complex protein design. (harvard.edu)
Modeling studies of a SAP-1/SRF/DNA complex suggest that SRF may modulate SAP-1 binding to DNA by interacting with its ETS domain. (rcsb.org)
These data support the hypothesis that N-Myc affects neuroblastoma gene expression through the formation of a DNA-binding heterodimeric complex with Max in vivo. (uu.nl)
their complex 3D shapes guide how they interact with other proteins to do the work of the cell. (eurekalert.org)
The analysis of domain structure of this protein suggested that it might be involved in correct assembly of thecytochrome bcl complex. (researchgate.net)
Others, and in particular the life science industry, assert that DNA and proteins are simply chemical compounds, albeit complex ones. (lu.se)
The physical basis of model-free analysis of NMR relaxation data from proteins and complex fluids. (lu.se)

Annotate: automatically annotate common features, or manually annotate coding sequences and other features, design and annotate primers for PCR, sequencing, or mutagenesis, and identify open reading frames (ORFs) with a single mouse click. (cnet.com)
Design and test primers for this sequence using Primer-BLAST. (nih.gov)
Catechol 2,3-dioxygenase (C23O) gene was found andamplified with the designed primers from the total DNA of C-14-1. (researchgate.net)

Unlike genetic changes, epigenetic changes are reversible and do not change your DNA sequence, but they can change how your body reads a DNA sequence. (cdc.gov)
Epigenetic changes mainly take place through chemical modification of DNA (DNA methylation) and histones, the proteins around which the DNA helix winds itself. (lu.se)

Comparison with the related PU.1/DNA and GABPalpha/beta/DNA complexes provides general insights into DNA discrimination between Ets proteins. (rcsb.org)
More precisely, we suggest that some nucleoprotein complexes, perhaps those that contain sharply bent DNA, can form barriers that impede the diffusion and merger of independent chromosomal supercoil domains. (johnshopkins.edu)
In particular, X-ray structures of BEN domain DNA complexes are only known for Drosophila factors bearing a single BEN domain, which lack direct vertebrate orthologs. (bvsalud.org)

Hybrid biomaterials composed of functionalized nanoparticles, covalently linked to biomolecules such as peptides, proteins, and polynucleotides, are especially interesting for their size-dependent properties and dimensional similarities to biomacromolecules [ 1 - 8 ]. (hindawi.com)

Some repetitive elements are neutral and occur when there is an absence of selection for specific sequences depending on how transposition or crossing over occurs. (wikipedia.org)
Nanoscaffolding and nanoquenching properties of thiol-capped gold nanocrystals (GNCs), covalently linked to fluorophore-lebeled oligonucleotide through metal-sulfur bond, were extensively studied for decades to detect specific sequences and single-nucleotide mismatches [ 1 - 3 , 21 , 22 ]. (hindawi.com)

There are many different types of proteins synthesized by cells, including enzymes, structural proteins, hormones, and transport proteins. (primorigen.com)
The role of adenovirus structural proteins in the regulation of adenovirus infection. (microbiologyresearch.org)

The T4 Gene 32 Protein is intended for molecular biology applications. (qiagen.com)

The genetic code, written in triplets of nucleotides called codons, determines how the nucleotide sequence of DNA is translated into a protein's amino acid sequence. (primorigen.com)

For example, RNA-Seq enables the study of gene expression changes, Hi-C considers chromatin architecture and ChIP-seq examines binding of DNA-binding proteins. (biologists.com)
Epigenetics of a tandem DNA repeat: chromatin DNaseI sensitivity and opposite methylation changes in cancers. (shengsci.com)
DNA methylation and chromatin DNaseI sensitivity were analyzed in and adjacent to D4Z4 repeat arrays, which consist of 1 to approximately 100 tandem 3.3-kb units at subtelomeric 4q and 10q. (shengsci.com)

One of the most important functions of the tumor suppressor p53 protein is its sequence-specific binding to DNA. (nih.gov)
Universal Screening for Lynch Syndrome: Can Tumor Sequencing Have a Larger Public Health Impact on Treatment and Prevention of Colorectal Cancer? (cdc.gov)
A universal tumor sequencing test can identify LS patients as well as guide treatment of CRC patients who do not have LS. (cdc.gov)
A recent study compared the performance of tumor next-generation sequencing to the current multistep approach (using microsatellite instability (MSI) testing and/or immunohistochemistry (IHC) for MMR proteins). (cdc.gov)
As part of the multicenter, population-based Ohio Colorectal Cancer Prevention Initiative, tumor DNA was sequenced for 419 consecutive CRC cases undergoing standard universal tumor screening and germline genetic testing, and 46 patients with CRC known to have LS due to a germline mutation in a mismatch repair gene. (cdc.gov)

Other information about this group: The nucleotide (DNA/RNA) and protein sequences have been sourced through the European Nucleotide Archive (ENA) and Universal Protein Resource (UniProt), databases that contains comprehensive sets of nucleotide (DNA/RNA) and protein sequences from all organisms that have been published by the International Research Community. (edu.au)
How can we harness proteins to achieve goals such as making needed chemicals, medicines and sustainable fuels, or to engineer organisms that can help mitigate the effects of climate change? (eurekalert.org)
But in many organisms, there is much more DNA in a cell than is needed to code for all the necessary proteins . (evolutionnews.org)

Over the past decade, there has been an explosion of data and information regarding protein sequence and function. (harvard.edu)
This data collection contains all currently published nucleotide (DNA/RNA) and protein sequences from Australian Mollusca, commonly known as molluscs, mollusks. (edu.au)
The contents of this collection is dynamic and will change over time as more data is deposited into the European Nucleotide Archive (ENA) and Universal Protein Resource (UniProt). (edu.au)
In vitro selection data revealed sequence-specific binding activities of isolated BEN domains from all of these factors. (bvsalud.org)
Gene Codes announces the release of Sequencher 5.1 DNA analysis software for Sanger or NGS data sets. (genecodes.com)
With advances in DNA sequencing technology, data are available for about 350 million protein sequences - a number that continues to climb. (eurekalert.org)
We want to be able to use high-performance computing to take that sequencing data and come up with useful inferences to narrow the field for experiments. (eurekalert.org)
Sarah Gregory] Ok, so what does sequence data in a public health lab do for us? (cdc.gov)
It allows us to quickly generate huge amounts of data and DNA sequence in a very short period of time. (cdc.gov)
This hands on course will give you additional experience in analyzing next generation sequencing data. (lu.se)

The multiple sequence alignment of 16 subunit VII homologues showsthat Bmuccr is very hydrophilic, has a characteristic charge distribution, and has a high helical content. (researchgate.net)

Several experimental techniques have been proposed to identify the DNA-binding sites and investigate the interaction modes between proteins and DNAs. (nature.com)

We obtained a high-resolution structure of BEND3-BD4 bound to its preferred binding site , which reveals how BEND3 identifies cognate DNA targets and shows differences with one of its non- DNA -binding BEN domains (BD1). (bvsalud.org)

Results on the PDNA-62 and the PDNA-224 datasets demonstrate that features extracted from spatial context provide more information than those from sequence context and the combination of them gives more performance gain. (nature.com)

DNA methylation works by adding a chemical group to DNA. (cdc.gov)
DNA methylation at millions of sites were measured in a newborn, 26-year-old, and 103-year-old. (cdc.gov)
The level of DNA methylation decreases with age. (cdc.gov)
A newborn had the highest DNA methylation, the 103-year-old had the lowest DNA methylation, and the 26-year-old had a DNA methylation level between the newborn and 103-year-old ( 1 ). (cdc.gov)
For example, at certain parts of the AHRR gene, smokers tend to have less DNA methylation than non-smokers. (cdc.gov)
After quitting smoking, former smokers can begin to have increased DNA methylation at this gene. (cdc.gov)

Short coding motifs, which appear to lack secondary structure, include those that label proteins for delivery to particular parts of a cell, or mark them for phosphorylation. (wikipedia.org)

Discoveries of deleterious repetitive DNA-related diseases stimulated further interest in this area of study. (wikipedia.org)
Their deep learning-driven approaches infer protein structure and function from DNA sequences, accelerating new discoveries that could inform advances in biotechnology, biosecurity, bioenergy and solutions for environmental pollution and climate change. (eurekalert.org)

Kelly Oakeson] Next Generation Sequencing is a very high throughput, massively parallel method for sequencing DNA. (cdc.gov)

Tandem repeats and interspersed repeats are further categorized into subclasses based on the length of the repeated sequence and/or the mode of multiplication. (wikipedia.org)
Tandem repeats may vary in the number of nucleotides comprising the repeated sequence, as well as the number of times the sequence repeats. (wikipedia.org)
When the repeating sequence is only 2-10 nucleotides long, the repeat is referred to as a short tandem repeat (STR) or microsatellite. (wikipedia.org)

image: This protein drives key processes for sulfide use in many microorganisms that produce methane, including Thermosipho melanesiensis. (eurekalert.org)
They believe that any form of patenting DNA, or of the natural processes it is involved in, is utterly wrong, since any DNA and the information it contains is the embodiment of the code of life and should be regarded part of the common heritage of mankind. (lu.se)

However, despite all this knowledge, our ability to determine the effect of even a single mutation on protein function remains limited. (harvard.edu)
Protein mutation effects are challenging to predict primarily due to the sheer complexity of proteins, which grows at \(20^n \), where n is the length of the protein. (harvard.edu)
Other companies are interested in sequencing to understand antimicrobial resistance, identify airborne pathogens and bioterror threats, and elucidate the relationship between a gene mutation and disease. (genengnews.com)
The chance of a mutation happening in a specific spot in your DNA is around 2x10 -8 … literally a 1 in 50 million chance! (thetech.org)

Our results are consistent with a model of the p53-DNA interactions involving one-dimensional migration of the p53 protein along the DNA for distances of about 1000 bp while searching for its target sites. (nih.gov)
Kornberg 7 has presented that the interactions between DNA and histones are involved in chromosome packaging in the cell nucleus. (nature.com)
Deciphering protein–protein interactions. (crossref.org)
We developed a new single-molecule method to probe non-specific DNA interactions for two HMGB homologs: the human HMGB2 box A domain and yeast Nhp6Ap, along with chimeric mutants replacin. (shengsci.com)
Adenovirus protein- protein interactions: hexon and protein VI. (microbiologyresearch.org)

These repeats fold into highly organized G quadruplex structures which protect the ends of chromosomal DNA from degradation. (wikipedia.org)
Understanding a protein's structure and function based on lengthy strings of nucleotides - written as the letters A, C, T and G - that make up DNA has long been a bottleneck in the life sciences as researchers relied on educated guesses and painstaking laboratory experiments to validate structures. (eurekalert.org)
Because of the need for extensive experimental work to determine three dimensional structures, scientists have only solved the structures for about 170,000 of those proteins. (eurekalert.org)
Being able to see the structures of proteins adds another layer that can help scientists home in on the most promising gene candidates for experiments. (eurekalert.org)
Gene expression is the process of several steps through which the information in a gene's DNA sequence is transferred to the structures and functions of a cell. (lu.se)

When the repeating sequence is 10-60 nucleotides long, the repeat is referred to as a minisatellite. (wikipedia.org)
Click at the position you wish to insert the sequence, or select 1 or more nucleotides if you wish to replace a region with the feature. (snapgene.com)

Today, the structural and regulatory roles of repetitive DNA sequences remain an active area of research. (wikipedia.org)
Outside of gene exons, there exist regulatory sequence motifs and motifs within the "junk", such as satellite DNA. (wikipedia.org)

They are typically trained from a set of input features, which can be generally divided into three categories: protein sequence information, protein structure information and a combination of the two categories. (nature.com)
The model for the protein structure of this mutant gene was clearly different from that of the other isolates studied herein. (pacb.com)
Repeated sequences are categorized into different classes depending on features such as structure, length, location, origin, and mode of multiplication. (wikipedia.org)
McClintock's work set the stage for the discovery of repeated sequences because transposition, centromere structure, and telomere structure are all possible through repetitive elements, yet this was not fully understood at the time. (wikipedia.org)
that is a stereotypical element of the overall structure of the protein. (wikipedia.org)
The unique structure and function of a protein are determined by the sequence of amino acids in it. (primorigen.com)
Some people believe for multiple reasons that DNA, and in particular human DNA, is much more than a mere chemical structure. (lu.se)

Ribosomes are the site of translation, and they are composed of rRNA and protein. (primorigen.com)
according to morphological, physiological and its 16S rRNA gene sequence. (researchgate.net)

The presence of repeated sequence DNA makes it easier for areas of homology to align, thereby controlling when and where recombination occurs. (wikipedia.org)

See also consensus sequence. (wikipedia.org)
Usually, however, the first letter is I, and both [RK] choices resolve to R. Since the last choice is so wide, the pattern IQxxxRGxxxR is sometimes equated with the IQ motif itself, but a more accurate description would be a consensus sequence for the IQ motif. (wikipedia.org)
Previous studies have identified DYKxxDxx to be the consensus sequence of the M2 epitope. (biologists.com)
Upon studying the mutant affinity landscapes, the authors note that they largely recapitulate the expected consensus sequence (DYKxxDxx), and even find a "superFLAG" sequence that has a LoD 7.9x lower (meaning higher binding affinity) than that of the wild-type FLAG. (biologists.com)

Anatomy16

Organisms22

Diseases2

Chemicals and Drugs73

Analytical, Diagnostic and Therapeutic Techniques and Equipment30

Phenomena and Processes126

Disciplines and Occupations6

Anthropology, Education, Sociology and Social Phenomena2

Technology, Industry, Agriculture2

Information Science12

Health Care4

Genome20

Genes18

Bioinformatics3

Genomes7

Nucleic4

Synthesis24

Thousands of proteins3

Annotation4

Replication7

Molecules6

Mammalian4

Genomic2

Plasmid6

Fragments5

Amplification2

Situ1

Characterization1

Determined the nucleotide1

Detection and Quantification1

Bind5

Antibodies1

Amino acid sequences1

Illumina5

Residues6

Peptide7

Transcription8

Polymerase4

Mutations8

Recognition3

Histone4

Mechanism5

Biological7

Allowed new discoveries1

Bioinformatic1

Complex7

Primers3

Epigenetic changes2

Complexes3

Peptides1

Specific sequences2

Structural proteins2

Molecular Biology1

Nucleotide sequence1

Chromatin3

Tumor5

Organisms3

Data10

Alignment1

DNAs1

Targets1

Datasets1

Methylation6

Secondary structure1

Discoveries2

Massively1

Tandem3

Processes2

Mutation4

Interactions5

Structures5

Nucleotides2

Regulatory2

Structure7

RRNA2

Homology1

Consensus sequence4