Find your PDFs fast.
Welcome to the Pubget Medical Subject Headings (MESH) browser. Click on a topic or subtopic below to explore related papers. In the gold box is the most recent paper about the current MESH term, and below are 20 related papers.
DNA, Cruciform (0):
Recent article
DNA, Cruciform
PLoS Genetics (7)5 2011
Abstract
We used a unique feature of Saccharomyces cerevisiae, return to growth (RTG), where cells undergoing meiosis can be returned to the mitotic cell cycle by a nutritional shift. By performing RTG with ndt80 mutants, which arrest in meiosis I prophase with high levels of interhomolog JMs, we could readi...
|
PMID: 21637791
PDF is available here.
PDF is available here.
| < More recent | Older article > |
Abstract
Single-molecule analyses of DNA replication have greatly advanced our understanding of mammalian replication restart. Several proteins that are not part of the core replication machinery promote the efficient restart of replication forks that have been stalled by replication inhibito...
|
PMID: 20842177
PDF is available here.
PDF is available here.
Abstract
We have performed expression screening in Escherichia coli host strains, capable of high-level expression of soluble S. cerevisiae Hop1 protein. A new protocol has been developed for expression and purification of S. cerevisiae Hop1 protein, based on the presence of hexa-histidine tag and double-str...
|
PMID: 20347988
PDF is available here.
PDF is available here.
Nucleic Acids Research (38)11 2010
Abstract
We show that the M. tuberculosis H-NS protein binds in a more structure-specific manner to DNA replication and repair intermediates, but displays lower affinity for double-stranded DNA with relatively higher GC content. Notably, M. tuberculosis H-NS was able to bind Holliday junction (HJ), the centr...
|
PMID: 20176569
PDF is available here.
PDF is available here.
Abstract
We examined the ability of the peptides to inhibit the growth of Salmonella in mammalian cells. J774A.1 macrophage-like cells and murine peritoneal macrophages were infected with Salmonella enterica serovar Typhimurium and grown in the presence or absence of peptide. We found that peptide wrwycr red...
|
PMID: 20176906
PDF is available here.
PDF is available here.
Genes to Cells (15)4 2010
Abstract
We purified human SPF45 and found that it preferentially binds to the Holliday junction, which is a key DNA intermediate in the homologous-recombination pathway. Deletion analyses revealed that the RNA recognition motif, which is located in the C-terminal region of human SPF45, is not involved in DN...
|
PMID: 20236180
PDF is available here.
PDF is available here.
Abstract
Four-way DNA (Holliday) junctions are resolved into duplex species by the action of the junction-resolving enzymes, nucleases selective for the structure of helical branchpoints. These have been isolated from bacteria and their phages, archaea, yeasts and mammals, including humans. They are all dime...
|
PMID: 20298191
PDF is available here.
PDF is available here.
Abstract
We describe the three-layer logpile (3LL), a two-dimensional DNA array which self-assembles from four synthetic oligonucleotides via a four-armed Holliday junction motif. It consists of three layers of helices, each running at 60 degrees to the others. DNA arrays can be used as periodic templates to...
|
PMID: 19722538
PDF is available here.
PDF is available here.
Biochemistry (Washington) (48)33 2009
Abstract
We suggest that the junction itself is not responsible for this unusual conformation but served as a vehicle for the study of this CG-rich sequence as a B-DNA duplex, mimicking the form that would be present in a replication complex. The existence of this unusual base lends credence to and defines a...
|
PMID: 19580331
PDF is available here.
PDF is available here.
EMBO Journal (28)6 2009
Abstract
We show that TRF2 greatly increases the rate of Holliday junction (HJ) formation and blocks the cleavage by various types of HJ resolving activities, including the newly identified human GEN1 protein. By using potassium permanganate probing and differential scanning calorimetry, we reveal that the b...
|
PMID: 19197240
PDF is available here.
PDF is available here.
Molecular Microbiology (71)5 2009
Abstract
We report that the relationship of ResT to the tyrosine recombinases extends to the ability to synapse-replicated telomeres and to catalyse the formation of a Holliday junction. We also report that ResT can use asymmetrized substrates that mimic the properties of a recombination site for a tyrosine...
|
PMID: 19170885
PDF is available here.
PDF is available here.
Abstract
We explore the feasibility of using coarse-grained models to simulate the self-assembly of DNA nanostructures. We introduce a simple model of DNA where each nucleotide is represented by two interaction sites corresponding to the sugar-phosphate backbone and the base. Using this model, we are able to...
|
PMID: 19222299
PDF is available here.
PDF is available here.
Abstract
Abstract
So-called architectural DNA binding proteins such as those of the HMGB-box family induce DNA bending and kinking. However, these proteins often display only a weak sequence preference, making the analysis of their DNA binding characteristics difficult if not impossible in a standard electrophoretic...
|
PMID: 19378185
PDF is available here.
PDF is available here.
Molecular Cell (32)5 2008
Abstract
The Holliday junction (HJ) is a central intermediate in homologous recombination. Ip et al. (2008), in a recent issue of Nature, have identified a new subclass of the Rad2/XPG family of nucleases with the hallmark of symmetrical cleavage of HJ substrates to produce nicked duplex products.
|
PMID: 19061635
PDF is available here.
PDF is available here.
Abstract
Genomic instability often underlies cancer. Analyses of proteins implicated in a cancer-predisposing condition called Bloom's syndrome illustrate the intricacies of protein interactions that ensure genomic stability.
|
PMID: 19037304
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (283)48 2008
Abstract
We found that Thermus thermophilus MutS2 (ttMutS2) harbors an endonuclease activity and that this activity is confined to the C-terminal domain, whose amino acid sequence is widely conserved in a variety of proteins with unknown function from almost all organisms ranging from bacteria to man. In thi...
|
PMID: 18838375
PDF is available here.
PDF is available here.
Biophysical Journal (95)9 2008
Abstract
We hypothesized that continuous runs over the entire sequence homology (5 bp) can occur. Direct measurements of the dependence of the fluorescence resonance energy transfer (FRET) value on the donor-acceptor (D-A) distance are required to justify this model and are the major goal of this article. To...
|
PMID: 18658216
PDF is available here.
PDF is available here.
Genes & Development (22)20 2008
Abstract
We report the isolation and characterization of a novel member of the BTB complex termed BLAP18/RMI2. BLAP18/RMI2 contains a putative OB-fold domain, and several lines of evidence suggest that it is essential for BTB complex function. First, the majority of BLAP18/RMI2 exists in complex with Topo II...
|
PMID: 18923083
PDF is available here.
PDF is available here.
Genes & Development (22)20 2008
Abstract
We report a novel component of the BLM complex, RMI2, which interacts with RMI1 through two oligonucleotide-binding (OB)-fold domains similar to those in RPA. The resulting complex, named RMI, differs from RPA in that it lacks obvious DNA-binding activity. Nevertheless, RMI stimulates the dissolutio...
|
PMID: 18923082
PDF is available here.
PDF is available here.
Journal of Physical Chemistry B (112)41 2008
Abstract
The thermal denaturation of immobile four-way DNA ("Holliday-") junctions with 17 base pair arms was studied via fluorescence spectroscopic measurements. Two arms of the molecule were labeled at the 5'-end with fluorescein and tetramethylrhodamine, respectively. Melting was monitored by the fluoresc...
|
PMID: 18811195
PDF is available here.
PDF is available here.
Molecular Cell (32)1 2008
Abstract
We have characterized the ortholog of FANCM in fission yeast Fml1 in order to understand the physiological significance of this activity. We show that Fml1 has at least two roles in homologous recombination-it promotes Rad51-dependent gene conversion at stalled/blocked replication forks and limits c...
|
PMID: 18851838
PDF is available here.
PDF is available here.
Genes & Development (22)19 2008
Abstract
Particular DNA sequences have long been known to have exceptional structures and biological properties. Famous in the medical world are the trinucleotide repeat sequences, such as (CTG)(n), and their association with more than a dozen neurodegenerative diseases. Numerous meetings have been held to d...
|
PMID: 18832065
PDF is available here.
PDF is available here.
Journal of Molecular Biology (381)4 2008
Abstract
We found that approximately 80% of strand gaps were repaired by physical strand transfer from the donor, whereas approximately 20% appear to be repaired by template switching. HR gap repair operated on both small and bulky lesions and largely depended on RecA and RecF but not on the RecBCD nuclease....
|
PMID: 18585391
PDF is available here.
PDF is available here.
Abstract
Nucleic Acids Research (36)16 2008
Abstract
We determined that the peptides bind HJ DNA and prevent the binding of RecG. Herein, we present further evidence that the peptides are competitive inhibitors of RecG binding to its substrates. We have generated structural models of interactions between WRWYCR and a junction substrate. Using the fluo...
|
PMID: 18689438
PDF is available here.
PDF is available here.
Nucleic Acids Research (36)16 2008
Abstract
We report here the isolation and characterization of two mutants of RecU (recU56 and recU71), which promote resolution of HJs, but do not promote RecA modulation. In vitro, the RecU mutant proteins (RecUK56A or RecUR71A) bind and cleave HJs and interact with RuvB. RecU interacts with RecA and inhibi...
|
PMID: 18684995
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (283)36 2008
Abstract
We visualized the binding of full-length WRN to DNA templates containing replication forks and Holliday junctions, intermediates observed during DNA replication and recombination, respectively. We show that both wild-type WRN and a helicase-defective mutant bind with exceptionally high specificity (...
|
PMID: 18596042
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (283)36 2008
Abstract
We previously showed that Rad54 promotes branch migration of Holliday junctions. Here we find that human Rad51 (hRad51) significantly stimulates the branch migration activity of hRad54. The stimulation appears to be evolutionarily conserved, as yeast Rad51 also stimulates the branch migration activi...
|
PMID: 18617519
PDF is available here.
PDF is available here.
Abstract
Molecular Cell (31)3 2008
Abstract
We show that mutants lacking both enzymes have profound defects in meiotic recombination intermediate metabolism and crossover (CO) formation. Recombination intermediates (joint molecules, JMs) accumulate in these cells, many with structures that are infrequent in wild-type cells. These JMs persist,...
|
PMID: 18691964
PDF is available here.
PDF is available here.
Molecular Cell (31)3 2008
Abstract
We show that cells lacking either enzyme frequently experience chromosome segregation problems during meiosis and that when both enzymes are absent attempted segregation fails catastrophically. In all cases, segregation appears to be impeded by unresolved JMs. Analysis of the DNA events of recombina...
|
PMID: 18691965
PDF is available here.
PDF is available here.
Biophysical Journal (95)3 2008
Abstract
We studied the effect of the sequence on Holliday junction dynamics and branch migration process. We show that a GC pair placed at the border of the homologous region almost prevents the migration into this position. At the same time, insertion of a GC pair into the middle of the AT tract does not s...
|
PMID: 18424495
PDF is available here.
PDF is available here.
Plant Journal (55)3 2008
Abstract
We demonstrate that AtRECQ2 is a (d)NTP-dependent 3'-->5' DNA helicase. We further characterized its basal properties and its action on various partial DNA duplexes. Importantly, we demonstrate that AtRECQ2 is able to disrupt recombinogenic structures: by disrupting various D-loop structures, AtRECQ...
|
PMID: 18419780
PDF is available here.
PDF is available here.
EMBO Journal (27)12 2008
Abstract
Our kinetic studies of Holliday junction branch migration catalysed by a ring-shaped helicase, T7 gp4, show that heterology of as little as a single base stalls catalysed branch migration. Using single-molecule analysis, one can locate the stall position to within a few base pairs of the heterology....
|
PMID: 18511910
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (283)23 2008
Abstract
We seek to understand the relevance of the biochemical attributes of BLAP75 in HJ processing. With the use of a series of BLAP75 protein fragments, we show that the evolutionarily conserved N-terminal third of BLAP75 mediates complex formation with BLM and Topo IIIalpha and that the DNA binding acti...
|
PMID: 18390547
PDF is available here.
PDF is available here.
Nucleic Acids Research (36)11 2008
Abstract
We have also identified combined A + B backbone-deformed conformers, e.g. with alpha/gamma switches, and a few conformers with a syn orientation of bases occurring e.g. in G-quadruplex structures. A plethora of A- and B-like conformers show a close relationship between the A- and B-form double helic...
|
PMID: 18477633
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (283)18 2008
Abstract
We have used a biotin interference assay that probes the requirement for major groove protein binding at specified DNA loci in conjunction with DNA protection, gel mobility shift, and genetic experiments to test several predictions of the models derived from the x-ray crystal structures of minimized...
|
PMID: 18319248
PDF is available here.
PDF is available here.
Molecular Cell (30)2 2008
Abstract
We structurally and biochemically analyzed DisA, a protein that controls a Bacillus subtilis sporulation checkpoint in response to DNA double-strand breaks. We find that DisA forms a large octamer that consists of an array of an uncharacterized type of nucleotide-binding domain along with two DNA-bi...
|
PMID: 18439896
PDF is available here.
PDF is available here.
Genes & Development (22)8 2008
Abstract
We have determined the crystal structure of the Mus81-Eme1 complex. Both Mus81 and Eme1 consist of a central nuclease domain, two repeats of the helix-hairpin-helix (HhH) motif at their C-terminal region, and a linker helix. While each domain structure resembles archaeal XPF homologs, the overall st...
|
PMID: 18413719
PDF is available here.
PDF is available here.
Nucleic Acids Research (36)7 2008
Abstract
We overexpressed Mus81-Mms4 in S. cerevisiae, purified the heterodimer to apparent homogeneity, and performed a classical enzymological characterization. Kinetic analysis (k(cat), K(M)) demonstrated that Mus81-Mms4 is catalytically active and identified three substrate classes in vitro. Class I subs...
|
PMID: 18281703
PDF is available here.
PDF is available here.
Abstract
We find that Mus81-Eme1 catalyzes coordinate bilateral cleavage of model Holliday-junction structures. Using a self-limiting, cruciform-containing substrate, we demonstrate that bilateral cleavage occurs sequentially within the lifetime of the enzyme-substrate complex. Coordinate bilateral cleavage...
|
PMID: 18310322
PDF is available here.
PDF is available here.
Abstract
We show that fission yeast (Rhp51) and human (hRad51) RecA homologues promote duplex-duplex DNA-strand exchange in vitro. As with RecA, a HJ is formed between the two duplex DNA molecules, and reciprocal strand exchange proceeds through branch migration of the HJ. In contrast to RecA, however, stran...
|
PMID: 18256600
PDF is available here.
PDF is available here.
Abstract
We investigated functional differences between the wild-type RuvA from Thermus thermophilus and mutants impaired the ability of complex II formation. These mutant RuvA, exclusively forming complex I, reduced activities of branch migration and ATP hydrolysis, suggesting that the octameric RuvA is ess...
|
PMID: 18068124
PDF is available here.
PDF is available here.
Molecular Cell (29)1 2008
Abstract
We show that purified FANCM binds to Holliday junctions and replication forks with high specificity and promotes migration of their junction point in an ATPase-dependent manner. Furthermore, we provide evidence that FANCM can dissociate large recombination intermediates, via branch migration of Holl...
|
PMID: 18206976
PDF is available here.
PDF is available here.
Abstract
We analyzed the substrate specificity of the Rad3 (XPD) helicase from Ferroplasma acidarmanus (FacRad3) and probed the importance of the FeS cluster for Rad3-DNA interactions. We found that the FeS cluster stabilizes secondary structure of the auxiliary domain important for coupling of single-strand...
|
PMID: 18029358
PDF is available here.
PDF is available here.
Abstract
We mutated two residues of RuvA (L125D and E126K) to prevent octamer formation. An electron microscopic analysis indicated that the mutant RuvA/RuvB/Holliday junction DNA complex formed the characteristic tripartite structure, with only one RuvA tetramer bound to one side of the Holliday junction, d...
|
PMID: 17981150
PDF is available here.
PDF is available here.
Abstract
The first alternative DNA structure--left-handed Z-DNA--was described back in 1979. The discoveries of the cruciform DNA structure, three-stranded H-DNA, four-stranded G-quartets and stably unwound DNA followed in the next decade. Each alternative structure was formed by a specific DNA sequence, whi...
|
PMID: 17981612
PDF is available here.
PDF is available here.
Abstract
Cruciforms are secondary DNA structures, serving as recognition signals at or near eukaryotic (yeast and mammalian) origins of DNA replication. The cruciform-binding protein is a member of the 14-3-3 protein family and binds to origins of DNA replication in a cell cycle-dependent manner. Five 14-3-3...
|
PMID: 18054234
PDF is available here.
PDF is available here.
Cytotherapy (10)5 2008
Abstract
Individual clones from plasmid libraries can be sequenced and assembled using custom-written software, and FLEA-PCR smears can be analyzed by capillary electrophoresis after digestion with restriction enzymes. DISCUSSION: This approach can readily analyze complex mixtures of IHJ, allowing localizati...
|
PMID: 18821360
PDF is available here.
PDF is available here.
Abstract
We have previously demonstrated that the human heterodimeric meiosis-specific MutS homologs, hMSH4-hMSH5, bind uniquely to a Holliday Junction and its developmental progenitor (Snowden, T., Acharya, S., Butz, C., Berardini, M., and Fishel, R. (2004) Mol. Cell 15, 437-451). ATP binding by hMSH4-hMSH5...
|
PMID: 17977839
PDF is available here.
PDF is available here.
Abstract
During RuvAB-mediated Holliday-junction migration two opposite arms of double-stranded DNA (dsDNA) are driven to translocate unidirectional by two respective ring-like hexameric RuvB proteins. However, how the RuvB protein, powered by ATP hydrolysis, drives unidirectional translocation of dsDNA is n...
|
PMID: 17919660
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (282)48 2007
Abstract
We report that A22 resolvase in fact has a much wider substrate specificity than previously appreciated. A22 resolvase cleaves Y-junctions, single-stranded DNA flaps, transitions from double strands to unpaired single strands ("splayed duplexes"), and DNA bulges in vitro. We also report site-directe...
|
PMID: 17890227
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (282)47 2007
Abstract
We report the purification and characterization of UvsW. Using oligonucleotide-based substrates, we confirm that UvsW unwinds branched DNA substrates, including X and Y structures, but shows little activity in unwinding linear duplex substrates with blunt or single-strand ends. Using a novel Hollida...
|
PMID: 17823128
PDF is available here.
PDF is available here.
Biochemistry (Washington) (46)44 2007
Abstract
We show that wild-type Hop1 ZnF binds significantly better to the Holliday junction compared with other recombination intermediates. Consequently, the salt titration midpoint for dissociation of the Holliday junction-ZnF complex was higher than the complexes containing flush-ended linear or tailed d...
|
PMID: 17935355
PDF is available here.
PDF is available here.
Abstract
We constructed a random spore system in which it is possible to identify a subset of NCO recombinants that can readily be accounted for by SDSA, but not by dHJ-mediated recombination. The diagnostic class of recombinants is one in which two markers on opposite sides of a double-strand break site are...
|
PMID: 17988174
PDF is available here.
PDF is available here.
Molecular Cell (28)3 2007
Abstract
We identify RAD51AP1 as a RAD51 accessory protein that specifically stimulates joint molecule formation through the combination of structure-specific DNA binding and physical contact with RAD51. At the cellular level, we show that RAD51AP1 is required to protect cells from the adverse effects of DNA...
|
PMID: 17996710
PDF is available here.
PDF is available here.
Human Genetics (122)3-4 2007
Abstract
We provide evidence that this IR forms a large non-B DNA structure containing two Holliday junctions, allowing intrastrand nucleotide pairing of the arms and interstrand pairing of the spacer region of the IR. This structure would extrude into a large double-cruciform DNA structure providing the mol...
|
PMID: 17638018
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (282)43 2007
Abstract
We show that the Holliday junction unwinding activity of BLM is greatly enhanced as a result of its association with Topo IIIalpha and BLAP75. Enhancement of this BLM activity requires both Topo IIIalpha and BLAP75. Importantly, Topo IIIalpha cannot be substituted by Escherichia coli Top3, and the H...
|
PMID: 17728255
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (282)43 2007
Abstract
We showed that IntN1 makes 7-bp staggered cuts within the NBU1 att sites, and certain mismatches within the crossover region of the attN1 site (G(-2)C attN1) or the chromosomal target site (C(-3)G attBT1-1) enhanced the in vivo integration efficiency. Here we describe an in vitro integration system...
|
PMID: 17766246
PDF is available here.
PDF is available here.