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DNA, Single-Stranded (1):
Recent article
DNA, Single-Stranded
ISME Journal (5)5 2011
Abstract
We describe two complete ssDNA phage genomes that were reconstructed from a viral metagenome from 80 m depth at the Bermuda Atlantic Time-series Study (BATS) site in the northwestern Sargasso Sea and examine their spatial and temporal distributions. Both genomes (SARssφ1 and SARssφ2) exhibited s...
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PMID: 21124487
PDF is available here.
PDF is available here.
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Cell Cycle (10)8 2011
Abstract
Cell Cycle (10)4 2011
Abstract
We address these issues by purifying and defining the DNA-binding activity of Smc5. We show that Smc5 binds strongly and specifically to single-stranded DNA (ssDNA). Remarkably, this DNA-binding activity is independent of Smc6 and is observed with the monomeric form of Smc5. We further show that Smc...
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PMID: 21293191
PDF is available here.
PDF is available here.
Oligonucleotides (21)2 2011
Abstract
Oligonucleotide- and polynucleotide-based gene modification strategies were developed as an alternative to transgene-based and classical gene targeting-based gene therapy approaches for treatment of genetic disorders. Unlike the transgene-based strategies, oligo/polynucleotide gene t...
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PMID: 21417933
PDF is available here.
PDF is available here.
Abstract
I digestion of chromatin in cultured cells results in loss of nuclear Pkp-1, suggesting that Pkp-1 associates specifically with nuclear components. In addition, in vitro assays revealed that the amino-terminal head domains of Pkps-1 and -2 were sufficient to bind single-stranded DNA. Induction of DN...
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PMID: 20613778
PDF is available here.
PDF is available here.
Analyst (Cambridge UK) (135)11 2010
Abstract
A simple approach based on electrochemical impedance spectroscopy of a DNA hybridization sensor for breast cancer is reported by immobilizing a BRCA1 related 19 mer oligonucleotides ssDNA sequence on a glassy carbon electrode modified with a poly 5-carboxyindole conducting polymer. Differential puls...
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PMID: 20859573
PDF is available here.
PDF is available here.
Analyst (Cambridge UK) (135)11 2010
Abstract
A novel approach for selectively encapsulating Cy5 dye molecules via DNA hybridization in cationic phosphorus dendrimers (G(4)(+))/polystyrenesulfonate (PSS) microcapsules has been developed. The hybridization between Cy5 labeled single strand DNA (ssDNA) targets and complementary ssDNA probes was p...
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PMID: 20844779
PDF is available here.
PDF is available here.
Analyst (Cambridge UK) (135)11 2010
Abstract
Herein, a sensitive and selective sensor for mercury(II) and glutathione based on the aggregation-induced emission (AIE) of a tetraphenylethene derivative stimulated by Hg(2+)-DNA complexes is reported. Aggregation complexes of AIE probes, quaternized tetraphenylethene salt and anti-Hg(2+) aptamer s...
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PMID: 20877906
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (285)43 2010
Abstract
We recently determined the structure of a previously unrecognized pol-prim domain (p68N) that docks on Tag, identified the p68N surface that contacts Tag, and demonstrated its vital role in primosome function. Here, we identify the p68N-docking site on Tag by using structure-guided mutagenesis of th...
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PMID: 20685648
PDF is available here.
PDF is available here.
Abstract
Nanomedicine (5)8 2010
Abstract
Carbon nanotubes as a unique and novel class of nanomaterials have shown considerable promise in cancer therapy and diagnosis amidst the myriad of nanocarriers. The presence of a large surface area enables the engineering of the surface of nanotubes, thus making them biocompatible, a...
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PMID: 21039202
PDF is available here.
PDF is available here.
Abstract
We purified the recombinant Stn1p in Escherichia coli and found that the purified protein could specifically interact with single-stranded telomeric DNA in vitro. Co-fractionation of co-overexpressed Stn1p and Ten1p in insect cells revealed their stable association. A Stn1p/Ten1p binary complex was...
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PMID: 20576529
PDF is available here.
PDF is available here.
Abstract
We have investigated the role of two selected amino acids, glycine and arginine, on damage induced to a short chain of single stranded DNA, the tetramer GCAT, during 1 eV electron exposure. At this energy, DNA has a high cross section for DNA damage via exclusively dissociative electron attachment....
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PMID: 20563347
PDF is available here.
PDF is available here.
Abstract
We discovered that PcrA preferentially translocates on the DNA lagging strand instead of unwinding the template duplex. PcrA anchors itself to the template duplex using the 2B subdomain and reels in the lagging strand, extruding a single-stranded loop. Static disorder limited previous ensemble studi...
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PMID: 20723756
PDF is available here.
PDF is available here.
Abstract
We describe a link between transposition of IS608 and ISDra2, both members of the IS200/IS605 family, which uses obligatory single-stranded DNA intermediates, and the host replication fork. Replication direction through the IS plays a crucial role in excision: activity is maximal when the "top" IS s...
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PMID: 20691900
PDF is available here.
PDF is available here.
Abstract
We have successfully isolated a pool of DNA aptamers, named SELH3, which binds to Leishmania infantum H3 with high affinity and specificity. Thus, it appears that this novel anti-H3 aptamer population may be of potential application as a diagnostic system for leishmaniosis....
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PMID: 20545478
PDF is available here.
PDF is available here.
Abstract
We improved the target RNA-primed RCA technique for direct detection and analysis of RNA in vitro and in situ. Previously we showed that the 3' --> 5' single-stranded RNA exonucleolytic activity of Phi29 DNA polymerase converts the target RNA into a primer and uses it for RCA initiation. However, in...
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PMID: 20584897
PDF is available here.
PDF is available here.
Biochemical Journal (430)1 2010
Abstract
These results suggest a distinction between the determinants of G4 DNA binding and the ssDNA interactions required for helicase action and that hPif1 may act on G4 substrates by binding alone or as a resolvase. Human Pif1 could therefore have a role in processing G4 structures that arise in the sing...
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PMID: 20524933
PDF is available here.
PDF is available here.
Abstract
We examined TraI helicase single-stranded DNA (ssDNA) recognition to complement previous explorations of relaxase ssDNA binding. Here, we show that TraI helicase-associated ssDNA binding is independent of and located N-terminal to all helicase motifs. The helicase-associated site binds ssDNA oligonu...
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PMID: 20435720
PDF is available here.
PDF is available here.
Abstract
Multi-spectroscopic methods including resonance light scattering (RLS), ultraviolet spectra (UV), fluorescence spectra, (1)H NMR spectroscopy, coupled with thermo-denaturation experiments were firstly used to study the interaction of antitumor drug tamoxifen (TMX) with calf thymus (ctDNA) in acetate...
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PMID: 20392665
PDF is available here.
PDF is available here.
Nanotechnology (21)25 2010
Abstract
A specific colorimetric DNA detection method based on oligonucleotide functionalized gold-silver-alloy nanoparticles (AuAg-alloy-nanoprobes) is presented. The AuAg-alloy-nanoprobes were then used for the specific detection of a DNA sequence from TP53-a gene involved in cancer development. The AuAg-a...
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PMID: 20508311
PDF is available here.
PDF is available here.
Analytical Biochemistry (401)2 2010
Abstract
The preparation of DNA-tagged liposomes containing an encapsulated prosthetic group tracer, pyrroloquinoline quinone (PQQ), and their application to the development of a sandwich-type hybridization assay for the visual detection of single-stranded DNA are described. Capture DNA is conjugated to the...
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PMID: 20206593
PDF is available here.
PDF is available here.
DNA Repair (9)6 2010
Abstract
We and others have identified several cell cycle checkpoint and DNA repair proteins that influence common fragile site stability. However, the initial events underlying fragile site breakage remain poorly understood. We demonstrate here that aphidicolin-induced gaps and breaks at fragile sites are p...
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PMID: 20413351
PDF is available here.
PDF is available here.
Nucleic Acids Research (38)11 2010
Abstract
EndoTT encoded by tte0829 of Thermoanaerobacter tengcongensis binds and cleaves single-stranded (ss) and damaged double-stranded (ds) DNA in vitro as well as binding dsDNA. In the presence of a low concentration of NaCl, EndoTT cleaved ss regions of damaged dsDNA efficiently but did not cleave DNA t...
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PMID: 20172959
PDF is available here.
PDF is available here.
Nanotechnology (21)20 2010
Abstract
Using unimolecular copper(II)-dependent self-cleaving deoxyribozymes (DNAzymes), a label-free colorimetric biosensor for copper(II) ions (Cu2+) has been developed based on the sequence-length-dependent adsorption of single-stranded deoxyribonucleic acid (ssDNA) on unmodified gold nanoparticles (AuNP...
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PMID: 20418604
PDF is available here.
PDF is available here.
Abstract
We detected the hybridization of HPV PCR products during temperature change process by a self-designed adjustable metal-clamping piezoelectric sensor. The study mainly involves sensor adjustment, probe immobilization and ice bath sample addition (at different concentrations and different volumes). T...
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PMID: 20303735
PDF is available here.
PDF is available here.
Abstract
A novel protocol for the gold nanoparticles (AuNPs) modification on the electrode surface was proposed, which was based on the self-assembly of AuNPs on the mercapto-diazoaminobenzene monolayer modified electrode. The mercapto-diazoaminobenzene monolayer was obtained by covalent immobilization of 4-...
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PMID: 20207131
PDF is available here.
PDF is available here.
Abstract
Single stranded DNA aptamers that can bind to ibuprofen, a widely used anti-inflammation drug, were selected from random DNA library of 10(15) nucleotides by FluMag-SELEX process. Five different sequences were selected and their enantioselectivity and affinity were characterized. Three out of five a...
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PMID: 20456958
PDF is available here.
PDF is available here.
Abstract
We study the thermally driven denaturation of a double-stranded polymer in the presence of a stretching force via Monte-Carlo simulations. When one strand only is stretched, the denaturation transition is first order, while when both strands are stretched, melting is second order. By revisiting the...
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PMID: 20866280
PDF is available here.
PDF is available here.
PLoS Pathogens (6)5 2010
Abstract
We decided to look at the nature and frequency of HBV editing in cirrhotic samples taken during removal of a primary hepatocellular carcinoma. Forty-one cirrhotic tissue samples (10 alcoholic, 10 HBV(+), 11 HBV(+)HCV(+) and 10 HCV(+)) as well as 4 normal livers were studied. Compared to normal liver...
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PMID: 20523896
PDF is available here.
PDF is available here.
Molecular Immunology (47)9 2010
Abstract
We show for the first time ever how one mAb (mAb-5) has polyreactive (protease, DNase, and RNase) catalytic activities (catAbs). Amino acid sequence analysis of the encoded variable-genes showed that the light chains of the hybridomas expressed the germline family genes V kappa 1A, bb1.1 and V kappa...
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PMID: 20356628
PDF is available here.
PDF is available here.
Abstract
A new label-free, optical method was developed to detect sequence-specific DNA based on supramolecular self-assembly. A cationic phenylene ethynylene oligomer with two pairs of positively charged side chains (OPE-2) can form a J-dimer or J-aggregate with negatively charged DNA by a combination of el...
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PMID: 20030336
PDF is available here.
PDF is available here.
Abstract
We investigate with X-ray photoelectron spectroscopy the suitability of UV/ozonolysis previously employed to remove alkanethiols from gold, for removing 40-mer, single- and double-stranded synthetic DNA. We find that while UV/O(3) can indeed remove thiolated DNA from gold slides, the treatment times...
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PMID: 20000594
PDF is available here.
PDF is available here.
Analyst (Cambridge UK) (135)5 2010
Abstract
We report a novel method for biological thiols detection using ssDNA/silver nanoparticles system. The adsorbing ssDNA supplies silver nanoparticles high density charge to rescue nanoparticles from aggregation induced by salt. However, homocysteine (cysteine or glutathione) is conjugated more powerfu...
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PMID: 20405067
PDF is available here.
PDF is available here.
Abstract
We reported a method to fabricate fluorescent probes preferentially end-linked to Au nanorods. In comparison with organic dyes, the single nanocomplexes provide significant improvement in signal brightness. The bioconjugated nanoantenna structure implicates an approach that is more convenient and ame...
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PMID: 20364827
PDF is available here.
PDF is available here.
Journal of Molecular Biology (398)1 2010
Abstract
Quantitative analysis of the interactions of the Escherichia coli primosomal PriB protein with a single-stranded DNA was done using quantitative fluorescence titration, photocrosslinking, and analytical ultracentrifugation techniques. Stoichiometry studies were done with a series of etheno-derivativ...
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PMID: 20156448
PDF is available here.
PDF is available here.
Chemical Communications (46)15 2010
Abstract
We succeeded for the first time in achieving single-molecule imaging of DNA duplexes vertically oriented on surfaces, with an in situ scanning tunneling microscope (STM), and demonstrated that this observation clearly revealed the surface hybridization behavior for both perfectly matched and mismatc...
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PMID: 20449314
PDF is available here.
PDF is available here.
Abstract
We investigate the construction of a novel ssDNA expression vector in this study. In order to improve the expression efficiency, the mmlv-rt gene and ODN-PMT (an oligodeoxynucleotide including other essential sequences for generating ssDNA) were cloned into a single plasmid under the control of 2 se...
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PMID: 20059315
PDF is available here.
PDF is available here.
The Journal of Chemical Physics (132)13 2010
Abstract
We previously demonstrated that individual molecules of single-stranded DNA can be driven electrophoretically through a single Staphylococcus aureus alpha-hemolysin ion channel. Polynucleotides thread through the channel as extended chains and the polymer-induced ionic current blockades exhibit stab...
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PMID: 20387958
PDF is available here.
PDF is available here.
Methods in Molecular Biology (587)587 2010
Abstract
ATP-driven translocation of helicases along DNA can be assayed in several ways. Reagentless biosensors, based on fluorophore-protein adducts, provide convenient ways for real-time assays of both the separation of dsDNA and the hydrolysis of ATP. Single-stranded DNA can be assayed using a modified si...
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PMID: 20225139
PDF is available here.
PDF is available here.
Methods in Molecular Biology (587)587 2010
Abstract
We have shown for the first time that MLE catalyzes the unwinding of both DNA and RNA and that MLE helicase activity is essential for its in vivo function. Also, we have provided evidence that MLE stimulates the transcriptional activity of roX2 on the X chromosome. We have also found that MLE intera...
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PMID: 20225159
PDF is available here.
PDF is available here.
Methods in Molecular Biology (627)627 2010
Abstract
We have shown a positive relation between the length of the used carbon spacer and the general performance of the DNA biosensor. In this chapter an extended protocol for the controlled immobilization and subsequent hybridization of DNA is described....
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PMID: 20217621
PDF is available here.
PDF is available here.
Current protocols in nucleic acid chemistry / edited by Serge L. Beaucage ... [et al.] (Chapter 9) 2010
Abstract
This unit describes the selection of aptamers from a single-stranded RNA pool that bind to small molecule targets. Aptamers generated by this type of selection experiment can potentially function as receptors for small molecules in numerous applications, including medical diagnostics...
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PMID: 20201029
PDF is available here.
PDF is available here.
Chemical Communications (46)8 2010
Abstract
We now present the first example in which triplet repeat DNAs adopt the i-motif structure at neutral pH by molecular crowding. Crowding stabilized the i-motif and the pK(a) of N3 of cytosine was raised in such a microenvironment. Molecular crowding is known to accelerate the formation of the multi-s...
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PMID: 20449283
PDF is available here.
PDF is available here.
Abstract
Homologous recombination (HR) is a major pathway for the repair of double strand breaks, which is of primary importance for genomic stability and survival of all organisms. The crucial step in HR is the formation of the nucleoprotein filament composed by a single stranded DNA chain surrounded by the...
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PMID: 19916564
PDF is available here.
PDF is available here.
Abstract
We investigated the cruciform structures formation of various inverted repeats in p53-responsive sequences from p21, RGC, mdm2 and GADD45 promoters under negative superhelical stress, and analyzed the effects of these DNA topology changes on p53-DNA binding. We demonstrated using three different met...
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PMID: 20026061
PDF is available here.
PDF is available here.
Abstract
We identify four small molecules that disrupt complexes formed between Escherichia coli SSB and Exonuclease I (ExoI), a well-studied SSB-interacting enzyme. Each compound disrupts ExoI/SSB-Ct peptide complexes and abrogates SSB stimulation of ExoI nuclease activity. Structural and biochemical studie...
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PMID: 20018747
PDF is available here.
PDF is available here.
Abstract
We show x-ray crystal structures for a set of NS3h complexes, including ground-state and transition-state ternary complexes captured with ATP mimics (ADP.BeF(3) and ). These structures provide, for the first time, three conformational snapshots demonstrating the molecular basis of action for a SF2 h...
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PMID: 20080715
PDF is available here.
PDF is available here.
Abstract
We attempted to select aptamers for covalently-stabilized oligomeric Abeta40(21) generated using photo-induced cross-linking of unmodified proteins (PICUP)(22,23). Similar to previous findings(17,19,20), these aptamers reacted with fibrils of Abeta and several other amyloidogenic proteins likely rec...
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PMID: 20616783
PDF is available here.
PDF is available here.
BMC Microbiology (10) 2010
Abstract
We report the characterization of single-stranded DNA binding proteins (SSBs) from the thermophilic bacteria Thermotoga maritima (TmaSSB) and Thermotoga neapolitana (TneSSB). They are the smallest known bacterial SSB proteins, consisting of 141 and 142 amino acid residues with a calculated molecular...
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PMID: 20950419
PDF is available here.
PDF is available here.
Upgrading SELEX technology by using lambda exonuclease digestion for single-stranded DNA generation.
Abstract
We demonstrate the considerable benefits of ssDNA production by lambda exonuclease digestion for in vitro selection of DNA aptamers. We believe that the generation of ssDNA aptamers using this method will greatly improve the success rate of SELEX experiments concerning the recovery of target-specifi...
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PMID: 20110867
PDF is available here.
PDF is available here.
Abstract
The minichromosome maintenance (MCM) complex is thought to function as the replicative helicase in archaea, separating the two strands of chromosomal DNA during replication. The catalytic activity resides within the C-terminal region of the MCM protein, while the N-terminal portion plays an importan...
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PMID: 21151660
PDF is available here.
PDF is available here.
Extremophiles (14)1 2010
Abstract
We have found that Cdc6/Orc1 binds to oriC and unwinds duplex DNA in the hyperthermophilic archaeon Pyrococcus furiosus, by means of a P1 endonuclease assay. A primer extension analysis further revealed that this localized unwinding occurs in the oriC region at a specific site, which is 12-bp long a...
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PMID: 19787415
PDF is available here.
PDF is available here.
Extremophiles (14)1 2010
Abstract
We have found that Cdc6/Orc1 binds to oriC and unwinds duplex DNA in the hyperthermophilic archaeon Pyrococcus furiosus, by means of a P1 endonuclease assay. A primer extension analysis further revealed that this localized unwinding occurs in the oriC region at a specific site, which is 12-bp long a...
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PMID: 19787415
PDF is available here.
PDF is available here.
Extremophiles (14)1 2010
Abstract
We have found that Cdc6/Orc1 binds to oriC and unwinds duplex DNA in the hyperthermophilic archaeon Pyrococcus furiosus, by means of a P1 endonuclease assay. A primer extension analysis further revealed that this localized unwinding occurs in the oriC region at a specific site, which is 12-bp long a...
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PMID: 19787415
PDF is available here.
PDF is available here.
Extremophiles (14)1 2010
Abstract
We have found that Cdc6/Orc1 binds to oriC and unwinds duplex DNA in the hyperthermophilic archaeon Pyrococcus furiosus, by means of a P1 endonuclease assay. A primer extension analysis further revealed that this localized unwinding occurs in the oriC region at a specific site, which is 12-bp long a...
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PMID: 19787415
PDF is available here.
PDF is available here.
Extremophiles (14)1 2010
Abstract
We have found that Cdc6/Orc1 binds to oriC and unwinds duplex DNA in the hyperthermophilic archaeon Pyrococcus furiosus, by means of a P1 endonuclease assay. A primer extension analysis further revealed that this localized unwinding occurs in the oriC region at a specific site, which is 12-bp long a...
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PMID: 19787415
PDF is available here.
PDF is available here.
Extremophiles (14)1 2010
Abstract
We have found that Cdc6/Orc1 binds to oriC and unwinds duplex DNA in the hyperthermophilic archaeon Pyrococcus furiosus, by means of a P1 endonuclease assay. A primer extension analysis further revealed that this localized unwinding occurs in the oriC region at a specific site, which is 12-bp long a...
|
PMID: 19787415
PDF is available here.
PDF is available here.
Extremophiles (14)1 2010
Abstract
We have found that Cdc6/Orc1 binds to oriC and unwinds duplex DNA in the hyperthermophilic archaeon Pyrococcus furiosus, by means of a P1 endonuclease assay. A primer extension analysis further revealed that this localized unwinding occurs in the oriC region at a specific site, which is 12-bp long a...
|
PMID: 19787415
PDF is available here.
PDF is available here.
Extremophiles (14)1 2010
Abstract
We have found that Cdc6/Orc1 binds to oriC and unwinds duplex DNA in the hyperthermophilic archaeon Pyrococcus furiosus, by means of a P1 endonuclease assay. A primer extension analysis further revealed that this localized unwinding occurs in the oriC region at a specific site, which is 12-bp long a...
|
PMID: 19787415
PDF is available here.
PDF is available here.