Terminal labeling and addition of homopolymer tracts to duplex DNA fragments by terminal deoxynucleotidyl transferase.

abstract：:Selenoproteins contain the amino acid selenocysteine which is encoded by a UGA Sec codon. Recoding UGA Sec requires a complex mechanism, comprising the cis-acting SECIS RNA hairpin in the 3'UTR of selenoprotein mRNAs, and trans-acting factors. Among these, the SECIS Binding Protein 2 (SBP2) is central to the mechanism...

journal_title：Nucleic acids research

authors： Takeuchi A,Schmitt D,Chapple C,Babaylova E,Karpova G,Guigo R,Krol A,Allmang C

更新日期：2009-04-01 00:00:00

abstract：:We present a new coarse grained method for the simulation of duplex DNA. The algorithm uses a generalized multi-harmonic model that can represent any multi-normal distribution of helical parameters, thus avoiding caveats of current mesoscopic models for DNA simulation and representing a breakthrough in the field. The ...

journal_title：Nucleic acids research

authors： Walther J,Dans PD,Balaceanu A,Hospital A,Bayarri G,Orozco M

更新日期：2020-03-18 00:00:00

abstract：:We have previously reported the human cDNA encoding MSSP-1, a sequence-specific double- and single-stranded DNA binding protein [Negishi, Nishita, Saëgusa, Kakizaki, Galli, Kihara, Tamai, Miyajima, Iguchi-Ariga and Ariga (1994) Oncogene, 9, 1133-1143]. MSSP-1 binds to a DNA replication origin/transcriptional enhancer ...

journal_title：Nucleic acids research

authors： Takai T,Nishita Y,Iguchi-Ariga SM,Ariga H

更新日期：1994-12-25 00:00:00

abstract：:Holliday junctions (four-way DNA junctions), formed during homologous recombination, are bound and resolved by junction-specific endonucleases to yield recombinant duplex DNA products. The junction-resolving enzymes are a structurally diverse class of proteins that nevertheless have many properties in common; in parti...

journal_title：Nucleic acids research

authors： White MF,Lilley DM

更新日期：1998-12-15 00:00:00

abstract：:The Blocks Database contains multiple alignments of conserved regions in protein families which can be searched by e-mail (blocks@blocks.fhcrc.org) and World Wide Web (http://blocks.fhcrc.org/ ) servers to classify protein and nucleotide sequences. Recent enhancements to the servers include: (i) improved calculation o...

journal_title：Nucleic acids research

authors： Henikoff JG,Pietrokovski S,Henikoff S

更新日期：1997-01-01 00:00:00

abstract：:In the battle against viruses, antiviral peptides (AVPs) had demonstrated the immense potential. Presently, more than 15 peptide-based drugs are in various stages of clinical trials. Emerging and re-emerging viruses further emphasize the efforts to accelerate antiviral drug discovery efforts. Despite, huge importance ...

journal_title：Nucleic acids research

authors： Thakur N,Qureshi A,Kumar M

更新日期：2012-07-01 00:00:00

abstract：:Replication Factor C (RF-C) of Saccharomyces cerevisiae is a complex that consists of several different polypeptides ranging from 120- to 37 kDa (Yoder and Burgers, 1991; Fien and Stillman, 1992), similar to human RF-C. We have isolated a gene, RFC2, that appears to be a component of the yeast RF-C. The RFC2 gene is l...

journal_title：Nucleic acids research

authors： Noskov V,Maki S,Kawasaki Y,Leem SH,Ono B,Araki H,Pavlov Y,Sugino A

更新日期：1994-05-11 00:00:00

abstract：:The nucleotide sequence of the Anacystis nidulans 23S rRNA gene, including the 5'- and 3'-flanking regions has been determined. The gene is 2876 nucleotides long and shows higher primary sequence homology to the 23S rRNAs of plastids (84.5%) than to that of E. coli (79%). The predicted rRNA transcript also shares many...

journal_title：Nucleic acids research

authors： Douglas SE,Doolittle WF

更新日期：1984-04-11 00:00:00

abstract：:Nucleosomes, a basic structural unit of eukaryotic chromatin, play a significant role in regulating gene expression. We have developed a web tool based on DNA sequences known from empirical and theoretical studies to influence DNA bending and flexibility, and to exclude nucleosomes. NXSensor (available at http://www.s...

journal_title：Nucleic acids research

authors： Luykx P,Bajić IV,Khuri S

更新日期：2006-07-01 00:00:00

abstract：:The side chains of the 20 types of amino acids, owing to a large extent to their different physical properties, have characteristic distributions in interior/surface regions of individual proteins and in interface/non-interface portions of protein surfaces that bind proteins or nucleic acids. These distributions have ...

journal_title：Nucleic acids research

authors： Tjong H,Qin S,Zhou HX

更新日期：2007-07-01 00:00:00

abstract：:Mutational analysis of the 5'-untranslated leader sequence (omega) of tobacco mosaic virus (TMV) was carried out to determine those sequences necessary for the translational enhancement associated with omega. Five deletion mutants, a single base substitution, and a 25 base replacement mutant were tested for alteration...

journal_title：Nucleic acids research

authors： Gallie DR,Sleat DE,Watts JW,Turner PC,Wilson TM

更新日期：1988-02-11 00:00:00

abstract：:RNA editing in protozoan parasites is a mitochondrial RNA processing reaction in which exclusively uridylate residues are inserted into, and less frequently deleted from, pre-mRNAs. Molecules central to the process are so-called guide RNAs (gRNAs) which function as templates in the reaction. For a detailed molecular u...

journal_title：Nucleic acids research

authors： Hermann T,Schmid B,Heumann H,Göringer HU

更新日期：1997-06-15 00:00:00

abstract：:Computational analysis of biosynthetic gene clusters (BGCs) has revolutionized natural product discovery by enabling the rapid investigation of secondary metabolic potential within microbial genome sequences. Grouping homologous BGCs into Gene Cluster Families (GCFs) facilitates mapping their architectural and taxonom...

journal_title：Nucleic acids research

authors： Kautsar SA,Blin K,Shaw S,Weber T,Medema MH

更新日期：2021-01-08 00:00:00

abstract：:The analysis of chromatin fine structure and transcription factor occupancy of differentially expressed genes by in vivo footprinting and ligation-mediated-PCR (LMPCR) is a powerful tool to understand the impact of chromatin on gene expression. However, as with all PCR-based techniques, the accuracy of the experiments...

journal_title：Nucleic acids research

authors： Ingram R,Gao C,Lebon J,Liu Q,Mayoral RJ,Sommer SS,Hoogenkamp M,Riggs AD,Bonifer C

更新日期：2008-02-01 00:00:00

abstract：:Well defined biomacromolecular patterns such as binding sites, catalytic sites, specific protein or nucleic acid sequences, etc. precisely modulate many important biological phenomena. We introduce PatternQuery, a web-based application designed for detection and fast extraction of such patterns. The application uses a...

journal_title：Nucleic acids research

authors： Sehnal D,Pravda L,Svobodová Vařeková R,Ionescu CM,Koča J

更新日期：2015-07-01 00:00:00

abstract：:Genomic DNA methylation profiles exhibit substantial variation within the human population, with important functional implications for gene regulation. So far little is known about the characteristics and determinants of DNA methylation variation among healthy individuals. We performed bioinformatic analysis of high-r...

journal_title：Nucleic acids research

authors： Bock C,Walter J,Paulsen M,Lengauer T

更新日期：2008-06-01 00:00:00

abstract：:Equilibrative nucleoside transporters (ENTs) are a recently characterized and poorly understood group of membrane proteins that are important in the uptake of endogenous nucleosides required for nucleic acid and nucleoside triphosphate synthesis. Despite their central importance in cellular metabolism and nucleoside a...

journal_title：Nucleic acids research

authors： Sankar N,Machado J,Abdulla P,Hilliker AJ,Coe IR

更新日期：2002-10-15 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：:Pathogenic bacteria encounter host-imposed manganese (Mn) limitation during infection. Herein we report that in the human pathogen Streptococcus pyogenes, the adaptive response to Mn limitation is controlled by a DtxR family metalloregulator, MtsR. Genes upregulated by MtsR during Mn limitation include Mn (mtsABC) and...

journal_title：Nucleic acids research

authors： Do H,Makthal N,Chandrangsu P,Olsen RJ,Helmann JD,Musser JM,Kumaraswami M

更新日期：2019-08-22 00:00:00

abstract：:The cloned 18 S ribosomal RNA gene from Saccharomyces cerevisiae have been sequenced, using the Maxam-Gilbert procedure. From this data the complete sequence of 1789 nucleotides of the 18 S RNA was deduced. Extensive homology with many eucaryotic as well as E. coli ribosomal small subunit rRNA (S-rRNA) has been observ...

journal_title：Nucleic acids research

authors： Rubtsov PM,Musakhanov MM,Zakharyev VM,Krayev AS,Skryabin KG,Bayev AA

更新日期：1980-12-11 00:00:00

abstract：:Genomic DNA of calf thymus contains 1.5 times as much 5-methylcytosine as similar sperm DNA, but the major EcoRI repeat fragment from satellite I of thymus contains ten times as much 5-methylcytosine as the corresponding fragment from sperm DNA. Restriction enzyme analyses of the total DNA and the satellite I fragment...

journal_title：Nucleic acids research

authors： Sturm KS,Taylor JH

更新日期：1981-09-25 00:00:00

abstract：:DNA mismatches are highly polymorphic and dynamic in nature, albeit poorly characterized structurally. We utilized the antitumour antibiotic CoII(Chro)2 (Chro = chromomycin A3) to stabilize the palindromic duplex d(TTGGCGAA) DNA with two G:G mismatches, allowing X-ray crystallography-based monitoring of mismatch polym...

journal_title：Nucleic acids research

authors： Satange R,Chuang CY,Neidle S,Hou MH

更新日期：2019-09-19 00:00:00

abstract：:Argonaute (Ago) proteins function in RNA silencing as components of the RNA-induced silencing complex (RISC). In lower organisms, the small interfering RNA and miRNA pathways diverge due in part to sorting mechanisms that direct distinct small RNA (sRNA) duplexes onto specific Ago-RISCs. However, such sorting mechanis...

journal_title：Nucleic acids research

authors： Yamakawa N,Okuyama K,Ogata J,Kanai A,Helwak A,Takamatsu M,Imadome K,Takakura K,Chanda B,Kurosaki N,Yamamoto H,Ando K,Matsui H,Inaba T,Kotani A

更新日期：2014-04-01 00:00:00

abstract：:The U1A protein is a sequence-specific RNA binding protein found in the U1 snRNP particle where it binds to stem/loop II of U1 snRNA. U1A contains two 'RNP' or 'RRM' (RNA Recognition Motif) domains, which are common to many RNA-binding proteins. The N-terminal RRM has been shown to bind specifically to the U1 RNA stem...

journal_title：Nucleic acids research

authors： Hall KB,Stump WT

更新日期：1992-08-25 00:00:00

abstract：:Specific DNA restriction endonuclease fragments can be identified after electrophoresis in agarose gels by hybridization in the gel (in situ) to radioactive homologous RNA. RNA-DNA hybrids are detected by autoradiography of the gel. Comparison of band patterns of the autoradiogram and the ethidium bromide stained gel ...

journal_title：Nucleic acids research

authors： Shinnick TM,Lund E,Smithies O,Blattner FR

更新日期：1975-10-01 00:00:00

abstract：:Increasing experimental evidence shows a prominent role of histone modifications in the coordinated control of gene expression in the human malaria parasite Plasmodium falciparum. The search for the histone-mark-reading machinery that translates histone modifications into biological processes, such as formation of het...

journal_title：Nucleic acids research

authors： Pérez-Toledo K,Rojas-Meza AP,Mancio-Silva L,Hernández-Cuevas NA,Delgadillo DM,Vargas M,Martínez-Calvillo S,Scherf A,Hernandez-Rivas R

更新日期：2009-05-01 00:00:00

abstract：:The extent of base pairing in Escherichia coli and Bacillus stearothermophilus 5S RNAs was determined by infrared spectroscopy. From the infrared spectra taken at 20 degrees and 52 degrees C it is concluded that E. coli and B. stearothermophlius 5S RNAs possess a large number of base pairs (Table I). Comparison of our...

journal_title：Nucleic acids research

authors： Appel B,Erdmann VA,Stulz J,Ackerman T

更新日期：1979-10-25 00:00:00

abstract：:Effective transcript profiling in animal systems requires isolation of homogenous tissue or cells followed by faithful mRNA amplification. Linear amplification based on cDNA synthesis and in vitro transcription is reported to maintain representation of mRNA levels, however, quantitative data demonstrating this as well...

journal_title：Nucleic acids research

authors： Baugh LR,Hill AA,Brown EL,Hunter CP

更新日期：2001-03-01 00:00:00

abstract：:Alternative splicing of pre-mRNA generates protein diversity. Dysfunction of splicing machinery and expression of specific transcripts has been linked to cancer progression and drug response. Exon microarray technology enables genome-wide quantification of expression levels of the majority of exons and facilitates the...

journal_title：Nucleic acids research

authors： Chen P,Lepikhova T,Hu Y,Monni O,Hautaniemi S

更新日期：2011-10-01 00:00:00

abstract：:Rap1 is an essential DNA-binding factor from the yeast Saccharomyces cerevisiae involved in transcription and telomere maintenance. Its binding to DNA targets Rap1 at particular loci, and may optimize its ability to form functional macromolecular assemblies. It is a modular protein, rich in large potentially unfolded ...

journal_title：Nucleic acids research

authors： Matot B,Le Bihan YV,Lescasse R,Pérez J,Miron S,David G,Castaing B,Weber P,Raynal B,Zinn-Justin S,Gasparini S,Le Du MH

更新日期：2012-04-01 00:00:00