Binding of single stranded dna dna binding proteins. Medical search. Frequent questions

Single-stranded DNA is produced during all aspects of DNA metabolism: replication, recombination, and repair. (wikipedia.org)
SSB protein domains in bacteria are important in its function of maintaining DNA metabolism, more specifically DNA replication, repair, and recombination. (wikipedia.org)
DSBs usually act as transcriptional factors to regulate the genes' expressions, while SSBs usually play roles in DNA replication, recombination, and repair, etc. (biomedcentral.com)
SSB binds with ssDNA with high affinity and low specificity, and is mainly involved in DNA replication, recombination and repair. (biomedcentral.com)
Biophysical studies showed that the orthologs of the two OB fold/one zinc finger replication protein A in Hethanosarcina acetivorans and Methanopyrus kandleri exhibit two binding modes, wrapping and stretching of DNA. (johnshopkins.edu)
Together with PCBP-1, this protein also functions as a translational coactivator of poliovirus RNA via a sequence-specific interaction with stem-loop IV of the IRES, promoting poliovirus RNA replication by binding to its 5'-terminal cloverleaf structure. (nih.gov)
It was also recently shown that PARP-1 is a sensor of unligated Okazaki fragments during DNA replication 16 and cells deficient in ribonucleotide excision repair are sensitized to PARP inhibition 17 . (nature.com)
It has a small (4500 nucleotides) genome that encoding four DNA helicases that are required for viral DNA replication and efficient packaging of single stranded DNA into virions. (utoledo.edu)
Rep78 and Rep68 also have a site specific nuclease activity, residing in an N-terminal structure, that creates a priming site in the template for DNA replication. (utoledo.edu)
The smaller replication proteins, Rep40 and Rep52, require ATP to bind DNA, show no sequence specificity in DNA binding and lack the N-terminal nuclease domains. (utoledo.edu)
DNA is the biological information that instructs cells how to exist in an ordered fashion: accurate replication is thus one of the most important events in the life cycle of a cell. (embl.de)
We are studying how genome integrity is preserved and the consequences of modifying the program of DNA replication. (umu.se)
Pur-alpha is a highly conserved, sequence-specific DNA- and RNA-binding protein involved in diverse cellular and viral functions including transcription, replication, and cell growth. (embl-heidelberg.de)
The human Pur factor binds strongly to a sequence element repeated withinzones of initiation of DNA replication in several eukaryotic cells. (embl-heidelberg.de)
A shortage of this protein may prevent normal DNA replication and repair, causing widespread damage to a person's genetic information over time. (medlineplus.gov)

HotStarTaq DNA polymerase (Qiagen). (cdc.gov)
Poly(ADP-ribose) polymerase-1 (PARP-1) is an abundant and ubiquitous nuclear protein that uses NAD + to synthesize a multibranched polyanion composed of ADP-ribose moieties, giving rise to poly(ADP-ribose) (PAR), onto itself or a variety of target proteins. (nature.com)
DNA Polymerase I, Large (Klenow) Fragment is available at Gentaur for Next week delivery. (telospub.com)
A proteolytic product of E. coli DNA Polymerase I Biomolecule/Target: Alternates names: DNA Polymerase I,DNA Polymerase I, Large Fragment,Klenow Fragment,DNA. (telospub.com)
ssDNA template is hybridized to a sequencing primer and incubated with the enzymes DNA polymerase , ATP sulfurylase , luciferase and apyrase , and with the substrates adenosine 5´ phosphosulfate (APS) and luciferin . (wikidoc.org)
DNA polymerase incorporates the correct, complementary dNTPs onto the template. (wikidoc.org)
A number of DNA polymerases have been grouped under the designation of DNA polymerase family B. Six regions of similarity (numbered from I to VI) are found in all or a subset of the B family polymerases. (embl.de)
Crystal structures of an NH2-terminal fragment of T4 DNA polymerase and its complexes with single-stranded DNA and with divalent metal ions. (embl.de)
We report the crystal structure of an NH2-terminal 388-residue fragment of T4 DNA polymerase (protein N388) refined at 2.2 A resolution. (embl.de)

We created several deletion mutants of this protein based on its conserved motifs, and from these structures functional chimeras were synthesized, supporting the hypothesis that gene duplication and recombination could lead to novel functional forms of single-stranded DNA-binding proteins. (johnshopkins.edu)
Furthermore, PARP-1 abrogation leads to increased DNA resection tracks and an increase of homologous recombination in cellulo. (nature.com)
In the presence of homologous donor DNA and pAgo," they emphasized, "homologous recombination is increased by up to 50% at targeted gene loci, suggesting that gene editing applications are feasible. (genengnews.com)
Involved in DNA nonhomologous end joining (NHEJ) required for double-strand break repair and V(D)J recombination. (lu.se)
To reduce the risk of analyzing cell line- pathway can be divided into distinct stages based on the specific features, we used several representative cell lines for recombination status of the Ig genes and on the expression each of four major stages in B cell development: pro-B, pre-B, pattern of surface markers and the presence of intracellular proteins [1- 6]. (lu.se)

Human Pur alpha, expressed as a glutathioneS-transferase fusion protein, specifically binds to the hypophosphorylatedform of Rb with an affinity as high as that of SV40 large T-antigen. (embl-heidelberg.de)
The 14/SATB1 monoclonal antibody specifically binds to the special AT-rich sequence binding protein 1 that is encoded by the SATB1 (SATB homeobox 1) gene. (bdbiosciences.com)
Early studies showed that FinO specifically binds the 3' transcriptional terminator structure of FinP in a manner that critically relies on both the GC-rich hairpin and 3' polypyrimidine tail that define the terminator 16 , and further work showed that the base of the hairpin and 3' tail are both strongly protected from ribonuclease degradation by FinO 17 . (nature.com)

While DSBs involve in binding to particular dsDNA sequences, to modulate the process of transcription, to cleave DNA molecules, or to be involved in chromosome packaging and transcription in the cell nucleus, etc. (biomedcentral.com)
We identified several putative THA8L-binding sites, enriched with purine sequences, in the group II introns. (rcsb.org)
Sequence analysis of five tryptic peptides revealed that their sequences matched corresponding sequences of the A2 protein of the heterogeneous nuclear ribonucleoprotein (hnRNP) complex. (jci.org)
Using profile analysis we constructed a database enriched in protein sequences containing one or more presumptive copies of the RNA-recognition motif (RRM). (embl.de)
We present a comprehensive table of 125 sequences containing 252 RRMs, including 22 previously unreported RRMs in 17 proteins. (embl.de)
It recognizes ATC sequences that consist of stretches of A's, T's, and C's on one DNA strand. (bdbiosciences.com)
Here, we report 2 unrelated male patients with EDI, both of whom have normal NEMO coding sequences, but exhibit a marked reduction in expression of full-length NEMO protein. (bvsalud.org)
2 alleles may have slight differences or the same DNA sequences. (msdmanuals.com)

Most unexpectedly, genes coding for similar proteins were found in the genomes of eukaryotes, including humans. (johnshopkins.edu)
THA8L resembles THA8 (thylakoid assembly 8), a protein that is required for the splicing of specific group II introns of genes involved in biogenesis of chloroplast thylakoid membranes. (rcsb.org)
Alvarez JD, Yasui DH, Niida H, Joh T, Loh DY, Kohwi-Shigematsu T. The MAR-binding protein SATB1 orchestrates temporal and spatial expression of multiple genes during T-cell development. (bdbiosciences.com)
The goal of this study was to describe the regulation of expression of these genes and proteins along with their relationship to telomere length in an animal model comparing different diets and a simulated occupational exposure. (cdc.gov)
Missense mutations in the gene encoding NEMO are associated with reduced signal-induced nuclear translocation of NF-κB proteins, resulting in defective expression of NF-κB target genes. (bvsalud.org)
Genes are arranged linearly along the DNA of chromosomes. (msdmanuals.com)
From experimentally validated target genes of these 86 miRNAs, pan-sensitive and pan-resistant genes with concordant mRNA and protein expression associated with in-vitro drug response to 19 NCCN-recommended breast cancer drugs were selected. (cdc.gov)

However, our mesophilic protein also contains a putative single-stranded DNA binding or repA domain. (genengnews.com)
NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both, RNA and single-stranded DNA (ssDNA), in yeast. (nih.gov)
The subgroup also includes NAM8, a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. (nih.gov)
Many eukaryotic proteins that are known or supposed to bind single-stranded RNA contain one or more copies of a putative RNA-binding domain of about 90 amino acids. (embl.de)
This is known as the eukaryotic putative RNA-binding region RNP-1 signature or RNA recognition motif (RRM). (embl.de)
The presence of a putative RRM in these proteins, which are implicated in a variety of cellular processes, strongly suggests that their function involves binding to RNA. (embl.de)

abstract = "The architecture of single-stranded DNA-binding proteins, which play key roles in DNA metabolism, is based on different combinations of the oligonucleotide/oligosaccharide binding (OB) fold. (johnshopkins.edu)
Our pAgo candidate nicks and cuts plasmid DNA nonspecifically in the absence of guide in in vitro assays, presumably due to the presence of single-stranded DNA that co-purifies with the protein," the abstract continued. (genengnews.com)

In this study we investigate the feasibility of applying the compatible solute, osmolyte and radiation protector Ectoine (THP(B)), as a scavenger molecule during SAXS measurements of the single-stranded DNA-binding protein Gene-V Protein (G5P/GVP). (rsc.org)
The genetic material is fundamentally the double helix of the DNA molecule. (whale.to)
Any substance that damages DNA or chromosomes, or changes genetic activity, is genotoxic because it is acting on the same material, i.e. the DNA molecule. (whale.to)
The technology actually uses the SOMAmers, which is a chemically modified single stranded DNA molecule. (dirjournal.com)
This DNA molecule is used to bind to target proteins resulting in the identification and quantifying biomarkers. (dirjournal.com)
The stochastic nature of single-molecule charge transport measurements requires collection of large data sets to capture the full complexity of a molecular system. (imperial.ac.uk)
Here we present such an approach based on multivariate pattern analysis and apply it to simulated and experimental single-molecule charge transport data. (imperial.ac.uk)
It has long been a mystery how a bacterial cell is able to import a molecule as complex as DNA. (mpg.de)
of the DNA molecule. (medlineplus.gov)
A gene, the basic unit of heredity, is a segment of DNA containing all the information necessary to synthesize a polypeptide (protein) or a functional RNA molecule. (msdmanuals.com)
A gene is a segment of DNA that provides the code to construct a protein or RNA molecule. (msdmanuals.com)

The protein encoded by this gene appears to be multifunctional. (nih.gov)
CusabioAlternative Name(s): DsDNA-binding protein A (rpbB)Gene Names: dsbAResearch Areas: Cell. (joplink.net)
A new technology based on the protein Argonaute from Natronobacterium gregoryi (NgAgo) could change how gene editing is approached. (genengnews.com)
DNA methylation is a common epigenetic marker that regulates gene expression. (biomedcentral.com)
The retinoblastoma protein, Rb, is detected in extracts of monkey CV-1cells complexed with Pur alpha, a sequence-specific single-strandedDNA-binding protein implicated in control of gene transcription and DNAreplication. (embl-heidelberg.de)
Sequence of cDNA comprising the human pur gene and sequence-specificsingle-stranded-DNA-binding properties of the encoded protein. (embl-heidelberg.de)
The ProQ/FinO family of RNA binding proteins mediate sRNA-directed gene regulation throughout gram-negative bacteria. (nature.com)
This gene provides instructions for making one member of a protein family called RecQ helicases. (medlineplus.gov)
Mutations in the RECQL4 gene prevent cells from producing any RECQL4 protein or change the way the protein is pieced together, which disrupts its usual function. (medlineplus.gov)
Nonstructural protein 1 (NS1) is a DNA-binding protein involved in gene transcription. (medscape.com)
One of the few antigens against which mammals develop protective immunity is the highly polymorphic OspC protein, encoded by the ospC gene on the cp26 plasmid. (cdc.gov)
By means of DNA sequencing of a large sample collection of the pathogen from across the United States, we studied the gene for the bacterium's highly diverse OspC protein, protective immunity against which develops in animals. (cdc.gov)

SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. (cdc.gov)
This can make the process of genome assembly more difficult, particularly for sequence containing a large amount of repetitive DNA . (wikidoc.org)
A robust and cost-effective way for measuring whole genome methylation is Methyl-CpG binding domain-based capture followed by seque. (biomedcentral.com)
Genome-wide analyses show major changes in the overall landscape of physiological and stimulus-induced R-loops with thousands of differentially altered regions, as well as binding of APOBEC3B to many of these sites. (bvsalud.org)
It is a very small (approximately 20 nm), nonenveloped virus with a single-stranded negative-sense DNA genome (see following images). (medscape.com)
The telomeres are the DNA-protein structures at the ends of eukaryotic chromosomes, which serve to protect and stabilize the genome. (lu.se)

Single-strand DNA-binding protein (SSB) is a protein found in Escherichia coli (E. coli) bacteria, that binds to single-stranded regions of deoxyribonucleic acid (DNA). (wikipedia.org)
Bound or free: interaction of the C-terminal domain of E. coli single-stranded DNA binding protein (SSB) with the tetrameric core of SSB. (cipps.org.au)
Single Stranded DNA Binding Protein, E. coli is available at Gentaur for Next week delivery. (telospub.com)
In vivo, we are able to program our pAgo candidate with 5′-phosphorylated DNA guides to cleave both plasmid and chromosomal targets to reduce survival under selective conditions in E. coli . (genengnews.com)
Inthe absence of DNA, glutathione S-transferase-Pur alpha binds to p56RB, anNH2-terminal-truncated Rb protein purified from Escherichia coli,containing the T-antigen binding domain, to form multimeric complexes. (embl-heidelberg.de)

Whereas the polypeptide serving this function in bacteria contains one OB fold, the eukaryotic functional homolog comprises a complex of three proteins, each harboring at least one OB fold. (johnshopkins.edu)

Pentatricopeptide repeat (PPR) proteins are sequence-specific RNA-binding proteins that form a pervasive family of proteins conserved in yeast, plants, and humans. (rcsb.org)
Unreported homologies in the RRM-enriched database to the metazoan SR family of splicing factors are described for an Arg-rich human nuclear protein and two yeast proteins (S. pombe mei2 and S. cerevisiae Npl3). (embl.de)

Theprotein binds preferentially to the purine-rich single strand of thiselement, PUR. (embl-heidelberg.de)
Taken together with the fact that APOBEC3B binds single-stranded DNA and RNA and preferentially deaminates DNA, these results support a mechanism in which APOBEC3B regulates R-loops and contributes to R-loop mutagenesis in cancer. (bvsalud.org)

The great progress of the structure genomics project [ 9 ] results that more and more high resolution 3D structures for DSBs and SSBs are available now, which makes it possible to investigate the common structural differences between SSB and DSB that are responsible for the binding specificity. (biomedcentral.com)
In the meantime, the investigation results can help to annotate or refine the annotation of the proteins with known structures yet unknown or not fully understood functions. (biomedcentral.com)
The larger Rep proteins, Rep78 and Rep68, assemble into stable, hexameric oligomers on specific secondary structures on the 3' and 5' termini of the single stranded viral DNA. (utoledo.edu)
Our studies are aimed at understanding how these proteins assemble on DNA structures and the specificity of their interaction with DNA. (utoledo.edu)
But, of course, we also want to identify target structures that could inhibit DNA transfer and, for example, stem the spread of antibiotic resistance," D'Imprima says. (mpg.de)
The structures of many DNA quadru- magnetization ( 11 - 13 ). (lu.se)

Studies of the thermodynamics of binding of ligands to glycyl tRNAs suggest that the formation of glycyl adenylate, an obligate intermediate on the reaction pathway, is accompanied by a significant conformation change in the protein that alters the affinity of the enzyme for tRNA. (utoledo.edu)
We report here the cloning and sequencing of a cDNA encodinga protein with strong affinity for the PUR element. (embl-heidelberg.de)
Tissue culture supernatant is purified by either protein A/G or affinity purification methods. (bdbiosciences.com)
A protein interacting with an A-T-rich region that is a positive control element within the SP6 κ promoter was purified and identified as CArG-box binding factor-A. The purified protein was shown to interact specifically with the coding strand of single-stranded DNA and, with lower affinity, with double-stranded DNA. (lu.se)
The hnRNP protein has a strong affinity for polypyrimidine-rich RNA and for single-stranded polypyrimidine-rich DNA. (bvsalud.org)

Extracellular vesicle DNA from human melanoma tissues contains cancer-specific mutations. (gu.se)
Mutations in these two positively charged patches greatly reduced THA8L RNA-binding activity. (rcsb.org)
Results Protein-altering de novo mutations in PURA were identified in four subjects. (bmj.com)
However, mutations in the gun-like structure cause the crown to disintegrate, so that the bacterial cell is no longer able to absorb DNA. (mpg.de)
Mutations are detected by lack of binding to wild-type probes and/or by binding to probes specific for commonly occurring mutations. (cdc.gov)
Because molecular beacons can use different fluorophores, real-time PCR assays can be designed in which different DNA fragments or mutations can be amplified and detected simultaneously in the same tube. (cdc.gov)
For example, a single-well assay has been developed that uses five molecular beacons to detect mutations associated with rifampin resistance in M. tuberculosis bacteria and appears to perform similarly as the line-probe assays. (cdc.gov)

DNA (deoxyribonucleic acid) is the cell's genetic material, contained in chromosomes within the cell nucleus and mitochondria. (msdmanuals.com)

Purification and partial sequencing of the nuclear autoantigen RA33 shows that it is indistinguishable from the A2 protein of the heterogeneous nuclear ribonucleoprotein complex. (jci.org)
RRMs are found in a variety of RNA binding proteins, including heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs). (embl.de)
Specific genomic DNA segments that interact with the nuclear matrix are called scaffold or matrix attachment regions (SARs or MARs). (bdbiosciences.com)
Ribonucleoproteína nuclear heterogénea que se encuentra en el NÚCLEO CELULAR y en el CITOPLASMA. (bvsalud.org)
Se ha implicado a la ribonucleoproteína nuclear heterogénea K en la regulación de la expresión genética en casi todos los niveles: TRANSCRIPCIÓN GENÉTICA, procesamiento del ARNm (PROCESAMIENTO DEL ARN POSTRANSCRIPCIONAL), transporte del ARNm, estabilidad del ARNm y traducción (TRADUCCIÓN GENÉTICA). (bvsalud.org)

Pyrosequencing is a method of DNA sequencing (determining the order of nucleotides in DNA) based on the "sequencing by synthesis" principle developed by Mostafa Ronaghi and Pål Nyrén (published in Analytical Biochemistry 1996 and Science 1998). (wikidoc.org)
Aminoacyl tRNA synthetases are a class of enzymes that ensure the fidelity of protein synthesis by attaching amino acids to their cognate tRNAs. (utoledo.edu)
Small RNA molecules are generally used as primers for chain elongation, although terminal proteins may also be used for the de novo synthesis of a DNA chain. (embl.de)
Protein synthesis, folding, and tertiary and quaternary structure ultimately determine much of the body's structure and function. (msdmanuals.com)

The RAD52-like protein ODB1 is required for the efficient excision of two mitochondrial introns spliced via first-step hydrolysis. (uni-halle.de)

Glass or quartz nanopipettes have found increasing use as tools for studying the biophysical properties of DNA and proteins, and as sensor devices. (imperial.ac.uk)

Decreased Trf1-Trf2 negatively regulates telomere length and DNA damage foci in rat liver tissue after a high-fat diet and welding fume exposure. (cdc.gov)
Telomere attrition resulting in DNA damage contributes to liver pathology. (cdc.gov)
The telomeric repeat-binding factor 1 (Trf1) and 2 (Trf2), and the protection of telomere 1 (Pot1) are involved in telomere maintenance by preventing telomere end-to-end fusion through proper folding of the telomere. (cdc.gov)
At 12 and 24 wk, the effect on shelterin proteins and telomere length was examined in peripheral blood mononuclear cells (PBMCs) and homogenized liver tissue. (cdc.gov)
Double- and single-stranded telomere DNA-binding proteins Trf1/Trf2 and Pot1, as well as telomeric DNA damage foci LambdaH2AX and 53BP1, were influenced at 12 wk and 24 wk by both diet and exposure. (cdc.gov)
In conclusion, our data suggest that disruption/down-regulation of single-stranded Pot1 and double-stranded Trf1/Trf2 expression in liver might act as an anti-apoptotic mechanism in the DNA-damage response leading to multistep liver injury by involvement in the telomere response to diet changes and WF exposure. (cdc.gov)
We therefore focus on elucidating the roles of the telomere binding proteins in this process. (lu.se)

There are two kinds of DNAs, single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA). (biomedcentral.com)
The Crystal Structure of the Herpes Simplex Virus 1 Ssdna-Binding Protein Suggests the Structural Basis For Flexible, Cooperative Single-Stranded Dna Binding. (atomistry.com)

A mutation that inhibited binding of the protein to the A-T-rich region also aborted the transcriptional stimulatory effect of the region. (lu.se)

With the development of biotechnology, a large amount of proteins have been sequenced. (biomedcentral.com)
According to Dr. Pass, the test measures 19 protein biomarkers for malignant pleural mesothelioma and can find and quantify the small amount of proteins secreted by the tumor cells. (dirjournal.com)

Click on the protein counts, or double click on taxonomic names to display all proteins containing POLBc domain in the selected taxonomic class. (embl.de)
To display all proteins with a RRM domain in a specific node, click on it. (embl.de)

On the basis of these data, we constructed a model of THA8L-RNA binding that is dependent on two forces: one is the interaction between nucleotide bases and specific amino acids in the PPR motifs (codes), and the other is the interaction between the negatively charged RNA backbone and positively charged residues of PPR motifs. (rcsb.org)
Example of a pyrogram showing the nucleotide sequence in a specific section of DNA. (wikidoc.org)
The tops represent light emission and nucleotide binding. (wikidoc.org)
Latest platform of Pyrosequencing (GS FLX from 454 Life Sciences which is owned by Roche) can generate 100 million nucleotide data in a 7 hour run with a single machine. (wikidoc.org)
This function is performed by DNA- directed DNA-polymerases ( EC 2.7.7.7 ) by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA, using a complementary DNA chain as a template. (embl.de)
Molecular beacons can discriminate between targets differing by a single nucleotide. (cdc.gov)

The encoded protein is also suggested to play a part in formation of a sequence-specific alpha-globin mRNP complex which is associated with alpha-globin mRNA stability. (nih.gov)
Currently, a limitation of the method is that the lengths of individual reads of DNA sequence are in the neighborhood of 300-500 nucleotides, shorter than the 800-1000 obtainable with chain termination methods (e.g. (wikidoc.org)
The structure of the 3'-5' exonuclease domain of protein N388 closely resembles the corresponding region in the Klenow fragment despite minimal sequence identity. (embl.de)
We present a systematic analysis of sequence motifs found in metazoan protein factors involved in constitutive pre-mRNA splicing and in alternative splicing regulation. (embl.de)

Such magnetic relaxation dispersion (MRD1) structural polymorphism of quadruplexes ( 2, 5, 6 ), but little measurements have been used to study ion binding (via 23Na is known about the energetics and kinetics of ion binding. (lu.se)

Association of human Pur alpha with the retinoblastoma protein, Rb,regulates binding to the single-stranded DNA Pur alpha recognitionelement. (embl-heidelberg.de)

In some genomic regions, the lack of protospacer adjacent motifs (PAMs) means that CRISPR is bound to lose its grip. (genengnews.com)
NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. (nih.gov)

The motif also appears in a few single stranded DNA binding proteins. (embl.de)
The R3H motif: a domain that binds single-stranded nucleic acids. (embl-heidelberg.de)
Binding of Pur alpha top56RB, the COOH-terminal portion of Rb, is inhibited by a syntheticpeptide containing the T-antigen Rb-binding motif. (embl-heidelberg.de)
The RNA recognition motif protein CP33A is a global ligand of chloroplast mRNAs and is essential for plastid biogenesis and plant development. (uni-halle.de)

This deletion, which results in a frameshift and a premature stop codon, occurs on the same haplotype background, suggesting that a single mutational event is involved in the four families. (nih.gov)
Through use of a series of deletion mutants, the DNAbinding activity of Pur alpha is localized to a series of modular aminoacid repeats. (embl-heidelberg.de)

Several PAR-binding modules orchestrate the relocation of DDR-associated factors in addition to the accumulation of intrinsically disordered proteins through an intracellular liquid demixing mechanism 11 , 12 . (nature.com)

Telomeric DNA and shelterin proteins prevent loss of essential genetic information during cell division. (cdc.gov)
Since telomerase is recruited to and elongates the single-stranded telomeric 3 ′ overhangs, the generation of 3 ′ overhangs is an essential step in the maintenance process. (lu.se)

In the crown we may have discovered a crucial switch for the recognition and binding of DNA," says Edoardo D'Imprima of the Department of Structural Biology at the Max Planck Institute in Frankfurt. (mpg.de)
Thesingle-stranded DNA Pur alpha recognition element disrupts thesecomplexes. (embl-heidelberg.de)
Here, we investigate the structural basis for RNA recognition by ProQ/FinO proteins, through the crystal structure of the ProQ/FinO domain of the Legionella pneumophila DNA uptake regulator, RocC, bound to the transcriptional terminator of its primary partner, the sRNA RocR. (nature.com)

Pur-alpha can influence viral interaction through functional associations, for example with the Tat protein and TAR RNA of HIV-1, and with large T-antigen and DNA regulatory regions of JC virus. (embl-heidelberg.de)
The capsid proteins are viral protein 1 (VP1) and viral protein 2 (VP2). (medscape.com)

PURA encodes Pur-α, a highly conserved multifunctional protein that has an important role in normal postnatal brain development in animal models. (bmj.com)
NP1 is also nonstructural and is a highly conserved protein of unknown function. (medscape.com)

The eponymous FinO protein was discovered as a regulator of F plasmid conjugation nearly 50 years ago, and acts to bind a single partner sRNA called FinP to stabilize FinP and facilitate its interactions with its antisense partner, the mRNA encoding the major F plasmid transcription factor, TraJ 5 . (nature.com)
Another plasmid-encoded ProQ/FinO family member, FopA, has also been shown to interact with a single antisense RNA 11 . (nature.com)

Rep52 and Rep40 are implicated in packaging plus and minus single stranded DNA into virions. (utoledo.edu)

This means that the structural changes of (bio-)polymers, such as proteins and DNA, can be monitored in situ to understand their sensitivity to changes in chemical environments. (rsc.org)
Now that the molecular structure determines its biological function, structural information is expected to provide insight on the binding mechanism of SSB or DSB. (biomedcentral.com)
Structural analysis revealed that THA8L contains two extensive patches of positively charged residues next to the residues that are proposed to comprise the RNA-binding codes. (rcsb.org)
SCOPe: Structural Classification of Proteins - extended. (berkeley.edu)
Structural analysis and RNA binding studies reveal that other ProQ/FinO domains also recognize related transcriptional terminators with different specificities for the length of the 3' ssRNA tail. (nature.com)

This fragment contains both the 3'-5' exonuclease active site and part of the autologous mRNA binding site (J. D. Karam, personal communication). (embl.de)
Likewise, the ProQ/FinO domain-containing protein RocC of Legionella pneumophila interacts with only one trans -acting sRNA (RocR) to repress post-transcriptionally multiple mRNA targets 6 . (nature.com)

As well as stabilizing this single-stranded DNA, SSB proteins bind to and modulate the function of numerous proteins involved in all of these processes. (wikipedia.org)

For example, the (SSB)65 binding mode, in which approximately 65 nucleotides of DNA wrap around the SSB tetramer and contact all four of its subunits, is favoured at high salt concentrations in vitro. (wikipedia.org)
At lower salt concentrations, the (SSB)35 binding mode, in which about 35 nucleotides bind to only two of the SSB subunits, tends to form. (wikipedia.org)

NgAgo may be programmed with guide DNA (red) to cut DNA (purple) at specific regions, enabling precise genetic modifications. (genengnews.com)
Genetic studies have shown that the crown is not formed by the secretin protein itself. (mpg.de)
The RECQL4 protein helps stabilize genetic information in the body's cells and plays a role in replicating and repairing DNA. (medlineplus.gov)

The dynamic turnover of PAR within seconds to minutes is executed by poly(ADP-ribose) glycohydrolase, the main PAR-degrading enzyme, which possesses both endoglycosidic and exoglycosidic activities, thereby enabling a new round of DNA damage signaling 14 . (nature.com)
Serum proteins can bind more tightly to the 17E DNAzyme complex than to the single-stranded substrate or enzyme. (uwaterloo.ca)

Protein-DNA interactions are essential for many biological processes. (biomedcentral.com)
Together, these results further our understanding of the mechanism of PPR protein-RNA interactions. (rcsb.org)

Along with PCBP-1 and hnRNPK, it is one of the major cellular poly(rC)-binding proteins. (nih.gov)
The cellular response to DNA damage involves an intricate network of enzymes responsible for sensing, signaling, and repairing damaged DNA, as well as the regulation of cell cycle checkpoints that collectively maintain genomic integrity 2 . (nature.com)

It is observed that both biological effects and epidemiological effects appear to be the same or very similar from ELF exposure and from RF/MW exposures, including calcium ion efflux, melatonin reduction, DNA strand breakage, chromosome aberrations, leukaemia, brain cancer, breast cancer, miscarriage and neurological effects. (whale.to)

Understanding the binding specificity of a DNA binding protein is helpful for the research of protein functions. (biomedcentral.com)
Though there are some researches [ 5 - 7 ] on the SSB and DSB respectively, few attentions have been paid on investigating what makes SSB and DSB have such different kind of binding specificity. (biomedcentral.com)

Since direct fluorescence monitoring is difficult due to the opacity of serum, denaturing and nondenaturing gel electrophoresis were combined for studying the interaction between serum proteins and DNAzymes. (uwaterloo.ca)

PARP-1 is the best-characterized member of the diphtheria toxin-like ADP-ribosyl transferases (ARTDs) family of proteins. (nature.com)
The purine-rich element binding (Pur) protein family protein consists PURalpha/beta/gamma in humans. (embl-heidelberg.de)
More recently, the application of RNA-seq technologies has enabled the elucidation of the biological partners and targets of several ProQ/FinO family proteins. (nature.com)
While these studies have built the case that certain ProQ/FinO family members bind to only a very limited number of partners in a highly specific manner, other family members appear to have multiple biological sRNA targets. (nature.com)
Belongs to the ATP-dependent DNA ligase family. (lu.se)

Domain analysis of this protein, which contains a single OB fold, showed that its architecture is similar to the functional homologs thought to be unique to the Crenarckaeotes. (johnshopkins.edu)

DNA/RNA-binding repeats in PUR-alpha/beta/gamma and in hypothetical proteins from spirochetes and the Bacteroides-Cytophaga-Flexibacter bacteria. (embl-heidelberg.de)

The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases. (embl.de)

Predicted to enable DNA binding activity and nuclease activity. (mcw.edu)

Analysis with a seriesof mutated oligonucleotides defines a minimal single-stranded DNAPur-binding element. (embl-heidelberg.de)
16, 17 ) for B -DNA oligonucleotides. (lu.se)

Similarly, a minimal ProQ/FinO domain protein, NMB1681, has been shown to bind a range of structured RNAs in Neisseria meningitidis 15 . (nature.com)
Two Ets proteins, PU.1 and elf-1, that have previously been shown to bind to an adjacent DNA element were shown to physically interact with CArG- box binding factor.A. An antiserum raised against the protein recognized two different forms indicating either that different splice-forms of. (lu.se)

Real-time DNA sequencing using detection of pyrophosphate release. (wikidoc.org)
High-bandwidth detection of short DNA in nanopipettes. (imperial.ac.uk)
Recently, we have demonstrated high-bandwidth detection of double-stranded (ds) DNA with microsecond time resolution in nanopipettes, using custom-designed electronics. (imperial.ac.uk)
With this understanding, the detection of DNA using the 17E DNAzyme is demonstrated in serum. (uwaterloo.ca)

Insight into how these proteins recognize their cognate RNAs initiated with FinO. (nature.com)

Degradation of both the substrate and the DNAzyme strand is very slow in serum, especially at room temperature. (uwaterloo.ca)
Source of all serum proteins is from USDA inspected abattoirs located in the United States. (bdbiosciences.com)

It has a structure of three beta-strands to a single six-stranded beta-sheet to form a protein dimer. (wikipedia.org)
However, the most common form is a protein with two OB folds and one zinc finger domain. (johnshopkins.edu)
Although the diversity shown by archaeal single-stranded DNA-binding proteins is unparalleled, the presence of their simplest form in many organisms across all domains of life is of greater evolutionary consequence. (johnshopkins.edu)
They then unfold themselves to form the DNA strands. (whale.to)
II) different residues form of the binding pocket for the 3'-terminal bases of the substrate. (embl.de)

Anatomy13

Organisms22

Diseases1

Chemicals and Drugs117

Analytical, Diagnostic and Therapeutic Techniques and Equipment29

Phenomena and Processes76

Technology, Industry, Agriculture1

Information Science4

Health Care2

Replication15

Polymerase9

Recombination5

Specifically binds3

Sequences8

Genes7

Putative6

Abstract2

Molecule11

Gene12

Genome6

Coli5

Eukaryotic1

Yeast2

Preferentially2

Structures6

Affinity5

Mutations7

Deoxyribonucleic1

Nuclear5

Synthesis4

Mitochondrial1

Biophysical1

Telomere7

SsDNA2

Mutation1

Amount of proteins2

Display all proteins2

Nucleotide6

Sequence4

Polymorphism1

Regulates1

Motifs2

Motif4

Deletion2

Intracellular1

Telomeric2

Recognition3

Viral2

Highly conserved2

Plasmid2

Virions1

Structural5

MRNA2

Modulate1

Nucleotides2

Genetic3

Enzyme2

Interactions2

Cellular2

Breakage1

Specificity2

Fluorescence1

Family5

Functional1

Hypothetical1

Consists1

Nuclease activity1

Oligonucleotides2

Shown to bind2

Detection4

Cognate1

Serum2

Form5