PRODOC: a resource for the comparison of tethered protein domain architectures with in-built information on remotely related domain families.

abstract：:More and more evidences demonstrate that the long non-coding RNAs (lncRNAs) play many key roles in diverse biological processes. There is a critical need to annotate the functions of increasing available lncRNAs. In this article, we try to apply a global network-based strategy to tackle this issue for the first time. ...

journal_title：Nucleic acids research

authors： Guo X,Gao L,Liao Q,Xiao H,Ma X,Yang X,Luo H,Zhao G,Bu D,Jiao F,Shao Q,Chen R,Zhao Y

更新日期：2013-01-01 00:00:00

abstract：:The Genotyping tool at the National Center for Biotechnology Information is a web-based program that identifies the genotype (or subtype) of recombinant or non-recombinant viral nucleotide sequences. It works by using BLAST to compare a query sequence to a set of reference sequences for known genotypes. Predefined ref...

journal_title：Nucleic acids research

authors： Rozanov M,Plikat U,Chappey C,Kochergin A,Tatusova T

更新日期：2004-07-01 00:00:00

abstract：:The Mouse Genome Database (MGD) focuses on the integration of mapping, homology, polymorphism and molecular data about the laboratory mouse. Detailed descriptions of genes including their chromosomal location, gene function, disease associations, mutant phenotypes, molecular polymorphisms and links to representative s...

journal_title：Nucleic acids research

authors： Blake JA,Richardson JE,Davisson MT,Eppig JT

更新日期：1999-01-01 00:00:00

abstract：:Analysis of 41 histone homologous clones from an isogenic gene library of Drosophila melanogaster showed that non-histone fragments interrupt the histone repetitive clusters at several sites. Long (L) and short (S) forms of the repeating units are distinguished by the insertion of 240 bp into the spacer between H1 and...

journal_title：Nucleic acids research

authors： Matsuo Y,Yamazaki T

更新日期：1989-01-11 00:00:00

abstract：:Differential display relies on a series of anchored primers to divide the total mRNA population into subsets of roughly equal size. However, this will only occur if the dinucleotide targeted by the anchor region of the anchored primers has a random frequency distribution [i.e. each of the 12 possible dinucleotides pre...

journal_title：Nucleic acids research

authors： Frost MR,Guggenheim JA

更新日期：1999-03-01 00:00:00

abstract：:The ability of Deinococcus radiodurans to recover from extensive DNA damage is due in part to its ability to efficiently repair its genome, even following severe fragmentation by hundreds of double-strand breaks. The single-strand annealing pathway plays an important role early during the recovery process, making use ...

journal_title：Nucleic acids research

authors： Sugiman-Marangos SN,Peel JK,Weiss YM,Ghirlando R,Junop MS

更新日期：2013-11-01 00:00:00

abstract：:Given that greater than 90% of the human genome is expressed, it is logical to assume that post-transcriptional regulatory mechanisms must be the primary means of controlling the flow of information from mRNA to protein. This report describes a robust approach that includes in silico, in vitro and in cellulo experimen...

journal_title：Nucleic acids research

authors： Beaudoin JD,Perreault JP

更新日期：2010-11-01 00:00:00

abstract：:PRMT5 is an arginine methyltransferase that accounts for the vast majority of the symmetric methylation in cells. PRMT5 exerts its function when complexed with MEP50/WDR77. This activity is often elevated in cancer cells and correlates with poor prognosis, making PRMT5 a therapeutic target. To investigate the PRMT5 si...

journal_title：Nucleic acids research

authors： Gao G,Zhang L,Villarreal OD,He W,Su D,Bedford E,Moh P,Shen J,Shi X,Bedford MT,Xu H

更新日期：2019-06-04 00:00:00

abstract：:Nucleobase analogs 5-methylisocytosine ((Me)isoC) and isoguanine (isoG) form a non-natural base pair in duplex nucleic acids with base pairing specificity orthogonal to the natural nucleobase pairs. Sequencing reactions were conducted with oligodeoxyribonucleotides (ODNs) containing d(Me)isoC and disoG using modified ...

journal_title：Nucleic acids research

authors： Ahle JD,Barr S,Chin AM,Battersby TR

更新日期：2005-06-02 00:00:00

abstract：:A truly universal nucleobase enables a host of novel applications such as simplified templates for PCR primers, randomized sequencing and DNA based devices. A universal base must pair indiscriminately to each of the canonical bases with little or preferably no destabilization of the overall duplex. In reality, many ca...

journal_title：Nucleic acids research

authors： Spring-Connell AM,Evich MG,Debelak H,Seela F,Germann MW

更新日期：2016-10-14 00:00:00

abstract：:Clustered damages are formed in DNA by ionising radiation and radiomimetic anticancer agents and are thought to be biologically severe. 7,8-dihydro-8-oxoguanine (8-oxoG), a major DNA damage resulting from oxidative attack, is highly mutagenic leading to a high level of G.C-->T.A transversions if not previously excised...

journal_title：Nucleic acids research

authors： David-Cordonnier MH,Boiteux S,O'Neill P

更新日期：2001-03-01 00:00:00

abstract：:The nucleotide sequence of 5.8S rRNA from the Chinese silkworm Philosamia cynthia ricini has been determined by gel sequencing and mobility shift methods. The complete primary structure is (sequence in text). This is one of the largest known 5.8S rRNAs. As compared to Bombyx 5.8S rRNA, it is two nucleotides longer; t...

journal_title：Nucleic acids research

authors： Feng YX,Krupp G,Gross HJ

更新日期：1982-10-25 00:00:00

abstract：:The field bean, Vicia faba L. var. minor, possesses two sub-families of 11 S legumin genes named A and B. We isolated from a genomic library a B-type gene (LeB4) and determined its primary DNA sequence. Gene LeB4 codes for a 484 amino acid residue prepropolypeptide, encompassing a signal peptide of 22 amino acid resid...

journal_title：Nucleic acids research

authors： Bäumlein H,Wobus U,Pustell J,Kafatos FC

更新日期：1986-03-25 00:00:00

abstract：:A phage-display library of random peptides is a combinatorial experimental technique that can be harnessed for studying antibody-antigen interactions. In this technique, a phage peptide library is scanned against an antibody molecule to obtain a set of peptides that are bound by the antibody with high affinity. This s...

journal_title：Nucleic acids research

authors： Mayrose I,Shlomi T,Rubinstein ND,Gershoni JM,Ruppin E,Sharan R,Pupko T

更新日期：2007-01-01 00:00:00

abstract：:The advent of jellyfish green fluorescent protein and its spectral variants, together with promising new fluorescent proteins from other classes of the Cnidarian phylum (coral and anemones), has greatly enhanced and promises to further boost the detection and localization of proteins in cell biology. It has been less ...

journal_title：Nucleic acids research

authors： Pederson T

更新日期：2001-03-01 00:00:00

abstract：:In eukaryotes, RNA-binding proteins that contain multiple K homology (KH) domains play a key role in coordinating the different steps of RNA synthesis, metabolism and localization. Understanding how the different KH modules participate in the recognition of the RNA targets is necessary to dissect the way these protein...

journal_title：Nucleic acids research

authors： Hollingworth D,Candel AM,Nicastro G,Martin SR,Briata P,Gherzi R,Ramos A

更新日期：2012-08-01 00:00:00

abstract：:The cDNA of human DNA polymerase delta was cloned. The cDNA had a length of 3.5 kb and encoded a protein of 1107 amino acid residues with a calculated molecular mass of 124 kDa. Northern blot analysis showed that the cDNA hybridized to a mRNA of 3.4 kb. Monoclonal and polyclonal antibodies to the C-terminal 20 residue...

journal_title：Nucleic acids research

authors： Yang CL,Chang LS,Zhang P,Hao H,Zhu L,Toomey NL,Lee MY

更新日期：1992-02-25 00:00:00

abstract：:The replication origin (oriC) of the Escherichia coli chromosome has been cloned and the region essential for chromosomal replication has been delimited to 245 base pairs. In previous studies the ability of recombinants between oriC and ColE1-type vectors, to transform E. coli polA- strains was used to determine which...

journal_title：Nucleic acids research

authors： Stuitje AR,Meijer M

更新日期：1983-11-25 00:00:00

abstract：:Anisotropic motions of DNA fragments in the size range 6-118 base pairs are studied by the steady-state fluorescence polarization of different excitation transitions in the intercalated ethidium cation. Calculated effective tumbling and twisting times are found to be shorter than predicted for overall motions of rigid...

journal_title：Nucleic acids research

authors： Härd T,Kearns DR

更新日期：1986-05-12 00:00:00

abstract：:The circadian clock comprises transcriptional feedback loops of clock genes. Cryptochromes are essential components of the negative feedback loop in mammals as they inhibit CLOCK-BMAL1-mediated transcription. We purified mouse CRY1 (mCRY1) protein complexes from Sarcoma 180 cells to determine their roles in circadian ...

journal_title：Nucleic acids research

authors： Hara Y,Onishi Y,Oishi K,Miyazaki K,Fukamizu A,Ishida N

更新日期：2009-03-01 00:00:00

abstract：:Double-stranded DNA viruses use ATP-powered molecular motors to package their genomic DNA. To ensure efficient genome encapsidation, these motors regulate functional transitions between initiation, translocation, and termination modes. Here, we report structural and biophysical analyses of the C-terminal domain of the...

journal_title：Nucleic acids research

authors： Mahler BP,Bujalowski PJ,Mao H,Dill EA,Jardine PJ,Choi KH,Morais MC

更新日期：2020-11-18 00:00:00

abstract：:Microbial enzymes have many known applications as biocatalysts in biotechnology, agriculture, medical and other industries. However, only a few enzymes are currently employed for such commercial applications. In this scenario, the current onslaught of metagenomic data provides a new unexplored treasure trove of genomi...

journal_title：Nucleic acids research

authors： Sharma VK,Kumar N,Prakash T,Taylor TD

更新日期：2010-01-01 00:00:00

abstract：:Oligoribonucleotides with 2'-5' linkages have been synthesized on solid support. UV melting and CD experiments indicate complementary strands associate to give complexes with melting temperatures 30 to 40 degrees C lower than for duplexes formed by 3'-5' oligoribonucleotides with the same sequence. UV melting and imin...

journal_title：Nucleic acids research

authors： Kierzek R,He L,Turner DH

更新日期：1992-04-11 00:00:00

abstract：:Hfq, a bacterial RNA-binding protein, was recently shown to contain the Sm1 motif, a characteristic of Sm and LSm proteins that function in RNA processing events in archaea and eukaryotes. In this report, comparative structural modeling was used to predict a three-dimensional structure of the Hfq core sequence. The pr...

journal_title：Nucleic acids research

authors： Sun X,Zhulin I,Wartell RM

更新日期：2002-09-01 00:00:00

abstract：:In small oocytes of Xenopus species, two sets of 5S RNA genes, oocyte-type and somatic-type, are fully activated. The 5S RNA transcripts are temporarily stored, half in association with TFIIIA to form a 7S particle, the other half in association with tRNA and two proteins (p48 and p43) to form a 42S particle. It has b...

journal_title：Nucleic acids research

authors： Barrett P,Sommerville J

更新日期：1987-11-11 00:00:00

abstract：:We have identified cDNAs encoding Mel-N1, the mouse homologue of a human nervous system-specific RNA-binding protein, Hel-N1. Two major mRNA transcripts of Mel-N1 were detected predominantly in the adult mouse brain by Northern blot analysis. To gain insight into the RNA binding specificity of Mel-N1, we performed ite...

journal_title：Nucleic acids research

authors： Abe R,Yamamoto K,Sakamoto H

更新日期：1996-06-01 00:00:00

abstract：:GenBank(®) (http://www.ncbi.nlm.nih.gov/genbank/) is a comprehensive database that contains publicly available nucleotide sequences for over 300 000 formally described species. These sequences are obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing proj...

journal_title：Nucleic acids research

authors： Benson DA,Clark K,Karsch-Mizrachi I,Lipman DJ,Ostell J,Sayers EW

更新日期：2015-01-01 00:00:00

abstract：:We report here the discovery of HMBP, a protein in nuclei of human T-helper lymphocytes and other human cell types, which binds with enhanced affinity to a promoter element in the HIV-1 long terminal repeat when that element is methylated at CpGs, the target site of the human DNA methyltransferase. This promoter eleme...

journal_title：Nucleic acids research

authors： Joel P,Shao W,Pratt K

更新日期：1993-12-11 00:00:00

abstract：:A single base change in 16S rRNA (C726 to G) has previously been shown to have a dramatic effect on protein synthesis in E. coli (1). This paper more specifically details the effects of the mutation on mRNA binding and translation-termination. The in vitro technique of toeprinting (2) was used to demonstrate that 30S ...

journal_title：Nucleic acids research

authors： Prescott CD,Göringer HU

更新日期：1990-09-25 00:00:00

abstract：:Rapid characterization of unknown biological samples is under the focus of many current studies. Here we report a method for screening of biological samples by optical mapping of their DNA. We use a novel, one-step chemo-enzymatic reaction to covalently bind fluorophores to DNA at the four-base recognition sites of a ...

journal_title：Nucleic acids research

authors： Grunwald A,Dahan M,Giesbertz A,Nilsson A,Nyberg LK,Weinhold E,Ambjörnsson T,Westerlund F,Ebenstein Y

更新日期：2015-10-15 00:00:00