PAP-LMPCR for improved, allele-specific footprinting and automated chromatin fine structure analysis.

abstract：:A C-->U mutation (rdn5) in the conserved sarcin/ricin domain of yeast 25S rRNA has been shown to cause translational suppression and paromomycin resistance. It also separates the killing from the misreading effect of this antibiotic. We confirm these findings and provide in vitro evidence that rdn5 causes a 3-fold inc...

journal_title：Nucleic acids research

authors： Panopoulos P,Dresios J,Synetos D

更新日期：2004-10-11 00:00:00

abstract：:Non-coding RNAs (ncRNAs) have diverse essential biological functions in all organisms, and in eukaryotes, two such classes of ncRNAs are the small nucleolar (sno) and small nuclear (sn) RNAs. In this study, we have identified and characterized a collection of sno and snRNAs in Giardia lamblia, by exploiting our discov...

journal_title：Nucleic acids research

authors： Hudson AJ,Moore AN,Elniski D,Joseph J,Yee J,Russell AG

更新日期：2012-11-01 00:00:00

abstract：:The transcription factor HIV-TF1, which binds to a region about 60 bp upstream from the enhancer of the human immunodeficiency virus-1 (HIV-1), was purified from human B cells. HIV-TF1 had a molecular weight of 39,000. Binding of HIV-TF1 to the HIV long terminal repeat (LTR) activated transcription from the HIV promot...

journal_title：Nucleic acids research

authors： Maekawa T,Sudo T,Kurimoto M,Ishii S

更新日期：1991-09-11 00:00:00

abstract：:Alfalfa mosaic virus RNA 4, the subgenomic messenger for viral coat protein, was partially digested with RNase T1 or RNase A and the sequence of a number of fragments was deduced by in vitro labeling with polynucleotide kinase and application of RNA sequencing techniques. From overlapping fragments, the complete prima...

journal_title：Nucleic acids research

authors： Brederode FT,Koper-Zwarthoff EC,Bol JF

更新日期：1980-05-24 00:00:00

abstract：:The CRISPR/Cas adaptive immune system provides resistance against phages and plasmids in Archaea and Bacteria. CRISPR loci integrate short DNA sequences from invading genetic elements that provide small RNA-mediated interference in subsequent exposure to matching nucleic acids. In Streptococcus thermophilus, it was pr...

journal_title：Nucleic acids research

authors： Sapranauskas R,Gasiunas G,Fremaux C,Barrangou R,Horvath P,Siksnys V

更新日期：2011-11-01 00:00:00

abstract：:Sensory photoreceptors have enabled non-invasive and spatiotemporal control of numerous biological processes. Photoreceptor engineering has expanded the repertoire beyond natural receptors, but to date no generally applicable strategy exists towards constructing light-regulated protein actuators of arbitrary function....

journal_title：Nucleic acids research

authors： Richter F,Fonfara I,Bouazza B,Schumacher CH,Bratovič M,Charpentier E,Möglich A

更新日期：2016-11-16 00:00:00

abstract：:We describe a new, broadly applicable methodology for screening in parallel interactions of RNA-binding proteins (RBPs) with large numbers of microRNA (miRNA) precursors and for determining their affinities in native form in the presence of cellular factors. The assays aim at identifying pre-miRNAs that are potentiall...

journal_title：Nucleic acids research

authors： Towbin H,Wenter P,Guennewig B,Imig J,Zagalak JA,Gerber AP,Hall J

更新日期：2013-02-01 00:00:00

abstract：:DNA from healthy Malaysian newborns was studied on gene maps after digestion with different restriction endonucleases. Of 65 newborns, two were found to be carriers of two different variants of triplicated alpha-globin loci. In variant no. 1, found in an Malay, the three alpha-globin genes are in an elongated DNA frag...

journal_title：Nucleic acids research

authors： Lie-Injo LE,Herrera AR,Kan YW

更新日期：1981-08-11 00:00:00

abstract：:Bacillus subtilis OhrR is a dimeric repressor that senses organic peroxides and regulates the expression of the OhrA peroxiredoxin. Derepression results from oxidation of an active site cysteine which ultimately results in formation of a mixed disulfide with a low molecular weight thiol, a cyclic sulfenamide, or overo...

journal_title：Nucleic acids research

authors： Eiamphungporn W,Soonsanga S,Lee JW,Helmann JD

更新日期：2009-03-01 00:00:00

abstract：:Translesion synthesis (TLS) employs low fidelity polymerases to replicate past damaged DNA in a potentially error-prone process. Regulatory mechanisms that prevent TLS-associated mutagenesis are unknown; however, our recent studies suggest that the PCNA-binding protein Spartan plays a role in suppression of damage-ind...

journal_title：Nucleic acids research

authors： Kim MS,Machida Y,Vashisht AA,Wohlschlegel JA,Pang YP,Machida YJ

更新日期：2013-02-01 00:00:00

abstract：:We present a multi-laboratory effort to describe the structural and dynamical properties of duplex B-DNA under physiological conditions. By processing a large amount of atomistic molecular dynamics simulations, we determine the sequence-dependent structural properties of DNA as expressed in the equilibrium distributio...

journal_title：Nucleic acids research

authors： Dans PD,Balaceanu A,Pasi M,Patelli AS,Petkevičiūtė D,Walther J,Hospital A,Bayarri G,Lavery R,Maddocks JH,Orozco M

更新日期：2019-12-02 00:00:00

abstract：:Mammalian DNA (cytosine-5) methyltransferase 1 (DNMT1) is essential for maintenance methylation. Phosphorylation of Ser143 (pSer143) stabilizes DNMT1 during DNA replication. Here, we show 14-3-3 is a reader protein of DNMT1pSer143. In mammalian cells 14-3-3 colocalizes and binds DNMT1pSer143 post-DNA replication. The ...

journal_title：Nucleic acids research

authors： Estève PO,Zhang G,Ponnaluri VK,Deepti K,Chin HG,Dai N,Sagum C,Black K,Corrêa IR Jr,Bedford MT,Cheng X,Pradhan S

更新日期：2016-02-29 00:00:00

abstract：:Minichromosome maintenance (MCM) proteins facilitate replication by licensing origins and unwinding the DNA double strand. Interestingly, the number of MCM hexamers greatly exceeds the number of firing origins suggesting additional roles of MCMs. Here we show a hitherto unanticipated function of MCM2 in cilia formatio...

journal_title：Nucleic acids research

authors： Casar Tena T,Maerz LD,Szafranski K,Groth M,Blätte TJ,Donow C,Matysik S,Walther P,Jeggo PA,Burkhalter MD,Philipp M

更新日期：2019-01-10 00:00:00

abstract：:DNA, isolated from age-synchronous senescent populations of Caenorhabditis elegans has been quantitatively and qualitatively analyzed for the presence of 5-methylcytosine. High performance liquid chromatography on two wild-type and several mutant strains of C. elegans failed to detect any 5-methylcytosine. The restric...

journal_title：Nucleic acids research

authors： Simpson VJ,Johnson TE,Hammen RF

更新日期：1986-08-26 00:00:00

abstract：:Classical simulations of protein flexibility remain computationally expensive, especially for large proteins. A few years ago, we developed a fast method for predicting protein structure fluctuations that uses a single protein model as the input. The method has been made available as the CABS-flex web server and appli...

journal_title：Nucleic acids research

authors： Kuriata A,Gierut AM,Oleniecki T,Ciemny MP,Kolinski A,Kurcinski M,Kmiecik S

更新日期：2018-07-02 00:00:00

abstract：:In bacteria, promoter identification by RNA polymerase is mediated by a dissociable σ factor. The housekeeping σ(70) factor of Escherichia coli recognizes two well characterized DNA sequence elements, known as the '-10' and '-35' hexamers. These elements are separated by 'spacer' DNA, the sequence of which is generall...

journal_title：Nucleic acids research

authors： Singh SS,Typas A,Hengge R,Grainger DC

更新日期：2011-07-01 00:00:00

abstract：:The Superimposé webserver performs structural similarity searches with a preference towards 3D structure-based methods. Similarities can be detected between small molecules (e.g. drugs), parts of large structures (e.g. binding sites of proteins) and entire proteins. For this purpose, a number of algorithms were implem...

journal_title：Nucleic acids research

authors： Bauer RA,Bourne PE,Formella A,Frömmel C,Gille C,Goede A,Guerler A,Hoppe A,Knapp EW,Pöschel T,Wittig B,Ziegler V,Preissner R

更新日期：2008-07-01 00:00:00

abstract：:We describe the first polyA-containing processed pseudogene reported in the chicken. It includes a 0.52 kb open reading frame which could encode a 175 amino acid protein. The putative protein shows extensive homology to the ras oncogene superfamily, being most closely related to the yeast protein YP2. It is one of the...

journal_title：Nucleic acids research

authors： Alsip GR,Konkel DA

更新日期：1986-03-11 00:00:00

abstract：:The Transcription Regulatory Regions Database (TRRD) is a curated database designed for accumulation of experimental data on extended regulatory regions of eukaryotic genes, the regulatory elements they contain, i.e., transcription factor binding sites, promoters, enhancers, silencers, etc., and expression patterns of...

journal_title：Nucleic acids research

authors： Kolchanov NA,Ananko EA,Podkolodnaya OA,Ignatieva EV,Stepanenko IL,Kel-Margoulis OV,Kel AE,Merkulova TI,Goryachkovskaya TN,Busygina TV,Kolpakov FA,Podkolodny NL,Naumochkin AN,Romashchenko AG

更新日期：1999-01-01 00:00:00

abstract：:The transcription activator-like effectors (TALEs) and the RNA-guided clustered regularly interspaced short palindromic repeat (CRISPR) associated protein (Cas9) utlilize distinct molecular mechanisms in targeting site recognition. The two proteins can be modified to carry additional functional domains to regulate exp...

journal_title：Nucleic acids research

authors： Gao X,Tsang JC,Gaba F,Wu D,Lu L,Liu P

更新日期：2014-11-10 00:00:00

abstract：:MPromDb (Mammalian Promoter Database) is a curated database that strives to annotate gene promoters identified from ChIP-seq results with the goal of providing an integrated resource for mammalian transcriptional regulation and epigenetics. We analyzed 507 million uniquely aligned RNAP-II ChIP-seq reads from 26 differ...

journal_title：Nucleic acids research

authors： Gupta R,Bhattacharyya A,Agosto-Perez FJ,Wickramasinghe P,Davuluri RV

更新日期：2011-01-01 00:00:00

abstract：:The accurate calculation of protein/nucleic acid-ligand interactions or condensed phase properties by force field-based methods require a precise description of the energetics of intermolecular interactions. Despite the progress made in force fields, small molecule parameterization remains an open problem due to the m...

journal_title：Nucleic acids research

authors： Dodda LS,Cabeza de Vaca I,Tirado-Rives J,Jorgensen WL

更新日期：2017-07-03 00:00:00

abstract：:We present the LGA (Local-Global Alignment) method, designed to facilitate the comparison of protein structures or fragments of protein structures in sequence dependent and sequence independent modes. The LGA structure alignment program is available as an online service at http://PredictionCenter.llnl.gov/local/lga. D...

journal_title：Nucleic acids research

authors： Zemla A

更新日期：2003-07-01 00:00:00

abstract：:Transcription factor IIIA (TFIIIA) and p43 zinc finger protein form distinct complexes with 5S ribosomal RNA in Xenopus oocytes. Additionally, TFIIIA binds the internal promoter of the 5S RNA gene and supports assembly of a transcription initiation complex. Both proteins have nine tandemly repeated zinc fingers with a...

journal_title：Nucleic acids research

authors： Ryan RF,Darby MK

更新日期：1998-02-01 00:00:00

abstract：:One challenge in engineering organisms is taking responsibility for their behavior over many generations. Spontaneous mutations arising before or during use can impact heterologous genetic functions, disrupt system integration, or change organism phenotype. Here, we propose restructuring the genetic code itself such t...

journal_title：Nucleic acids research

authors： Calles J,Justice I,Brinkley D,Garcia A,Endy D

更新日期：2019-11-04 00:00:00

abstract：:A general procedure, based on a new activated alkyne linker, for the preparation of peptide-oligonucleotide conjugates (POCs) on solid support has been developed. With this linker, conjugation is effective at room temperature (RT) in millimolar concentration and submicromolar amounts. This is made possible since the u...

journal_title：Nucleic acids research

authors： Wenska M,Alvira M,Steunenberg P,Stenberg A,Murtola M,Strömberg R

更新日期：2011-11-01 00:00:00

abstract：:CeR-2 RNA is one of the newly identified Caenorhabditis elegans noncoding RNAs (ncRNAs). The characterization of CeR-2 by RNomic studies has failed to classify it into any known ncRNA family. In this study, we examined the spatiotemporal expression patterns of CeR-2 to gain insight into its function. CeR-2 is expresse...

journal_title：Nucleic acids research

authors： Hokii Y,Sasano Y,Sato M,Sakamoto H,Sakata K,Shingai R,Taneda A,Oka S,Himeno H,Muto A,Fujiwara T,Ushida C

更新日期：2010-09-01 00:00:00

abstract：:5' strand resection at DNA double strand breaks (DSBs) is critical for homologous recombination (HR) and genomic stability. Here we develop a novel method to quantitatively measure single-stranded DNA intermediates in human cells and find that the 5' strand at endonuclease-generated break sites is resected up to 3.5 k...

journal_title：Nucleic acids research

authors： Zhou Y,Caron P,Legube G,Paull TT

更新日期：2014-02-01 00:00:00

abstract：:A multipurpose plasmid, pUR 250, has been constructed. It contains seven unique cloning sites (Hind III, Xba I, Sal I, Acc I, Hinc II, BamH I and EcoR I) in a small region of its lac Z gene part. Insertion of foreign DNA into the plasmid can be easily detected. Plasmid DNA isolated from a clone by a rapid method can b...

journal_title：Nucleic acids research

authors： Rüther U

更新日期：1982-10-11 00:00:00

abstract：:The transcriptional activity of the p53 tumor suppressor protein is crucial for the regulation of cell growth, apoptosis and tumor progression. The first identified p53 relative, p73, was reported to be monoallelically expressed in normal tissues. In some tumors, loss of heterozygosity was associated with overexpressi...

journal_title：Nucleic acids research

authors： Vikhanskaya F,D'Incalci M,Broggini M

更新日期：2000-01-15 00:00:00