Selective detection of ribose-methylated nucleotides in RNA by a mass spectrometry-based method.

abstract：:Overlap-directed DNA assembly methods allow multiple DNA parts to be assembled together in one reaction. These methods, which rely on sequence homology between the ends of DNA parts, have become widely adopted in synthetic biology, despite being incompatible with a key principle of engineering: modularity. To answer t...

journal_title：Nucleic acids research

authors： Casini A,MacDonald JT,De Jonghe J,Christodoulou G,Freemont PS,Baldwin GS,Ellis T

更新日期：2014-01-01 00:00:00

abstract：:Mitochondrial proteins remain the subject of intense research interest due to their implication in an increasing number of different conditions including mitochondrial and metabolic disease, cancer, and neuromuscular degenerative and age-related disorders. However, the mitochondrial proteome has yet to be accurately a...

journal_title：Nucleic acids research

authors： Smith AC,Robinson AJ

更新日期：2016-01-04 00:00:00

abstract：:The aminoacylation kinetics of T7 transcripts representing defined regions of Escherichia coli serine tRNAs were determined using purified E.coli seryl-tRNA synthetase (SerRS) and the kinetic values were used to estimate the relative contribution of various tRNA(Ser) domains to recognition by SerRS. The analysis revea...

journal_title：Nucleic acids research

authors： Sampson JR,Saks ME

更新日期：1993-09-25 00:00:00

abstract：:DNA double-strand breaks are repaired by end-joining or homologous recombination. A key-committing step of recombination is DNA end resection. In resection, phosphorylated CtIP first promotes the endonuclease of MRE11-RAD50-NBS1 (MRN). Subsequently, CtIP also stimulates the WRN/BLM-DNA2 pathway, coordinating thus both...

journal_title：Nucleic acids research

authors： Howard SM,Ceppi I,Anand R,Geiger R,Cejka P

更新日期：2020-06-04 00:00:00

abstract：:A feature of Haemophilus influenzae genomes is the presence of several loci containing tracts of six or more identical tetranucleotide repeat units. These repeat tracts are unstable and mediate high frequency, reversible alterations in the expression of surface antigens. This process, termed phase variation (PV), enab...

journal_title：Nucleic acids research

authors： Bayliss CD,Sweetman WA,Moxon ER

更新日期：2005-01-14 00:00:00

abstract：:I have used a novel single-sided specific polymerase chain reaction (PCR) strategy inspired by ligation-mediated PCR to clone fragments of divergent homeobox genes from a flatworm, the planarian Polycelis nigra. Eight homeobox-containing fragments were amplified, belonging to the Hox, msh, NK-1 and NK-2 classes. Toget...

journal_title：Nucleic acids research

authors： Balavoine G

更新日期：1996-04-15 00:00:00

abstract：:The spliceosomal protein Prp1 (Prp6/U5-102 K) is necessary for the integrity of pre-catalytic spliceosomal complexes. We have identified a novel regulatory function for Prp1. Expression of mutations in the N-terminus of Prp1 leads to the accumulation of pre-catalytic spliceosomal complexes containing the five snRNAs U...

journal_title：Nucleic acids research

authors： Lützelberger M,Bottner CA,Schwelnus W,Zock-Emmenthal S,Razanau A,Käufer NF

更新日期：2010-03-01 00:00:00

abstract：:The DNA sequence of a 354 basepair EcoRI-HindIII fragment of plasmid pMB9 which has originally been derived from plasmid pSC101 has been resolved. This fragment contains a promoter for transcription directed towards the EcoRI site. Escherichia coli RNA polymerase binds to a region within the EcoRI-HindIII fragment whi...

journal_title：Nucleic acids research

authors： Pannekoek H,Maat J,van den Berg E,Noordermeer I

更新日期：1980-04-11 00:00:00

abstract：:Apolipoprotein B (apoB) is a major protein component of low density and very low density lipoproteins. Because of its large size and heterogeneity, molecular studies of apoB have been difficult, and its structure and regulation remain poorly understood. We now report the identification of human apoB cDNA clones by ant...

journal_title：Nucleic acids research

authors： Mehrabian M,Schumaker VN,Fareed GC,West R,Johnson DF,Kirchgessner T,Lin HC,Wang XB,Ma YH,Mendiaz E

更新日期：1985-10-11 00:00:00

abstract：:The three dimensional structures for representatives of nearly half of all protein families are now available in public databases. Thus, no matter which protein one investigates, it is increasingly likely that the 3D structure of a homolog will be known and may reveal unsuspected structure-function relationships. The ...

journal_title：Nucleic acids research

authors： Marchler-Bauer A,Addess KJ,Chappey C,Geer L,Madej T,Matsuo Y,Wang Y,Bryant SH

更新日期：1999-01-01 00:00:00

abstract：:This work seeks to remedy two deficiencies in the current nucleic acid nanotechnology software environment: the lack of both a fast and user-friendly visualization tool and a standard for structural analyses of simulated systems. We introduce here oxView, a web browser-based visualizer that can load structures with ov...

journal_title：Nucleic acids research

authors： Poppleton E,Bohlin J,Matthies M,Sharma S,Zhang F,Šulc P

更新日期：2020-07-09 00:00:00

abstract：:DEAD, DEAH and DExH proteins are involved in almost every facet of RNA biochemistry. Members of these protein families exhibit an RNA-dependent ATPase activity and some possess an ATP-dependent RNA helicase activity. Although genetic studies have identified specific functions for certain DEx(D)/(H)proteins from which ...

journal_title：Nucleic acids research

authors： Kossen K,Uhlenbeck OC

更新日期：1999-10-01 00:00:00

abstract：:We present a new publicly accessible web-service, RiboSoft, which implements a comprehensive hammerhead ribozyme design procedure. It accepts as input a target sequence (and some design parameters) then generates a set of ranked hammerhead ribozymes, which target the input sequence. This paper describes the implemente...

journal_title：Nucleic acids research

authors： Kharma N,Varin L,Abu-Baker A,Ouellet J,Najeh S,Ehdaeivand MR,Belmonte G,Ambri A,Rouleau G,Perreault J

更新日期：2016-02-29 00:00:00

abstract：:Protein structures often show similarities to another which would not be seen at the sequence level. Given the coordinates of a protein chain, the SALAMI server at www.zbh.uni-hamburg.de/salami will search the protein data bank and return a set of similar structures without using sequence information. The results page...

journal_title：Nucleic acids research

authors： Margraf T,Schenk G,Torda AE

更新日期：2009-07-01 00:00:00

abstract：:RNA polymerase I-catalyzed synthesis of the Schizosaccharomyces pombe approximately 37S pre-rRNAs was shown to be sensitive to regulatory sequences located several kilobases upstream of the initiation site for the rRNA gene. An in vitro transcription system for RNA polymerase I-catalyzed RNA synthesis was established ...

journal_title：Nucleic acids research

authors： Liu Z,Zhao A,Chen L,Pape L

更新日期：1997-02-01 00:00:00

abstract：:Genome-wide expression profiling is a powerful tool for implicating novel gene ensembles in cellular mechanisms of health and disease. The most popular platform for genome-wide expression profiling is the Affymetrix GeneChip. However, its selection of probes relied on earlier genome and transcriptome annotation which ...

journal_title：Nucleic acids research

authors： Dai M,Wang P,Boyd AD,Kostov G,Athey B,Jones EG,Bunney WE,Myers RM,Speed TP,Akil H,Watson SJ,Meng F

更新日期：2005-11-10 00:00:00

abstract：:The chicken c-myb gene and the v-myb oncogene transduced by avian myeloblastosis virus (AMV) encode DNA binding transcription activators. The DNA binding domain of AMV v-Myb displays a number of amino acid changes relative to c-Myb; v-Myb proteins in which one or more of three crucial residues in the DNA binding domai...

journal_title：Nucleic acids research

authors： Weston K

更新日期：1992-06-25 00:00:00

abstract：:The kinetics of PaeR7 endonuclease-catalysed cleavage reactions of fluorophor-labeled oligonucleotide substrates have been examined using fluorescence resonance energy transfer (FRET). A series of duplex substrates were synthesized with an internal CTCGAG PaeR7 recognition site and donor (fluorescein) and acceptor (rh...

journal_title：Nucleic acids research

authors： Ghosh SS,Eis PS,Blumeyer K,Fearon K,Millar DP

更新日期：1994-08-11 00:00:00

abstract：:An improved method was developed for microdissection and cloning of metaphase as well as pachytene chromosomes. The protocol incorporates efficient ligation of chromosomal DNA with linker adaptors, abolishment of microcloning steps and the reduction of micromanipulation. The threshold for amplifying genomic DNA templa...

journal_title：Nucleic acids research

authors： Ponelies N,Stein N,Weber G

更新日期：1997-09-01 00:00:00

abstract：:Histone proteins are synthesized in large amounts during S-phase to package the newly replicated DNA, and are among the most stable proteins in the cell. The replication-dependent (RD)-histone mRNAs expressed during S-phase end in a conserved stem-loop rather than a polyA tail. In addition, there are replication-indep...

journal_title：Nucleic acids research

authors： Lyons SM,Cunningham CH,Welch JD,Groh B,Guo AY,Wei B,Whitfield ML,Xiong Y,Marzluff WF

更新日期：2016-11-02 00:00:00

abstract：:The R-Coffee web server produces highly accurate multiple alignments of noncoding RNA (ncRNA) sequences, taking into account predicted secondary structures. R-Coffee uses a novel algorithm recently incorporated in the T-Coffee package. R-Coffee works along the same lines as T-Coffee: it uses pairwise or multiple seque...

journal_title：Nucleic acids research

authors： Moretti S,Wilm A,Higgins DG,Xenarios I,Notredame C

更新日期：2008-07-01 00:00:00

abstract：:Chemically modified antisense oligonucleotides (ASOs) with phosphorothioate (PS) linkages have been extensively studied as research and therapeutic agents. PS-ASOs can enter the cell and trigger cleavage of complementary RNA by RNase H1 even in the absence of transfection reagent. A number of cell surface proteins hav...

journal_title：Nucleic acids research

authors： Wang S,Allen N,Vickers TA,Revenko AS,Sun H,Liang XH,Crooke ST

更新日期：2018-04-20 00:00:00

abstract：:N7-Methyl-2'-deoxyguanosine (m7dG) is the predominant lesion formed by methylating agents. A systematic investigation on the effect of m7dG on DNA replication has been difficult due to the chemical instability of m7dG. To gain insights into the m7dG effect, we employed a 2'-fluorine-mediated transition-state destabilz...

journal_title：Nucleic acids research

authors： Koag MC,Kou Y,Ouzon-Shubeita H,Lee S

更新日期：2014-07-01 00:00:00

abstract：:A computer program package has been made available which contains five compound programs written in FORTRAN 10 (for DECsystem-10). Program DATBAS is for storing and improving DNA sequence data, especially those obtained by the sequencing method using M13 phages. Programs NUCDAT and PROTEN are for analyzing DNA/RNA and...

journal_title：Nucleic acids research

authors： Isono K

更新日期：1984-01-11 00:00:00

abstract：:Anti-silencing function 1 (Asf1) and Chromatin Assembly Factor 1 (CAF-1) chaperone histones H3/H4 during the assembly of nucleosomes on newly replicated DNA. To understand the mechanism of histone H3/H4 transfer among Asf1, CAF-1 and DNA from a thermodynamic perspective, we developed and employed biophysical approache...

journal_title：Nucleic acids research

authors： Liu WH,Roemer SC,Port AM,Churchill ME

更新日期：2012-12-01 00:00:00

abstract：:Exon arrays are regularly used to analyze differential splicing events. GeneChip Gene 1.0 ST Arrays (gene arrays) manufactured by Affymetrix, Inc. are primarily used to determine expression levels of transcripts, although their basic design is rather similar to GeneChip Exon 1.0 ST Arrays (exon arrays). Here, we show ...

journal_title：Nucleic acids research

authors： Gellert P,Teranishi M,Jenniches K,De Gaspari P,John D,Kreymborg Kg,Braun T,Uchida S

更新日期：2012-03-01 00:00:00

abstract：:The U1 snRNP-specific 70K protein is one of the few snRNP proteins from higher eukaryotic cells that is phosphorylated in vivo (1,2). Immunoaffinity purified spliceosomal snRNPs (U1, U2, U5, and U4/U6) were tested for their ability to phosphorylate in vitro the U1-specific 70K protein. An snRNP-associated kinase activ...

journal_title：Nucleic acids research

authors： Woppmann A,Will CL,Kornstädt U,Zuo P,Manley JL,Lührmann R

更新日期：1993-06-25 00:00:00

abstract：:Cpf1 nucleases were recently reported to be highly specific and programmable nucleases with efficiencies comparable to those of SpCas9. AsCpf1 and LbCpf1 require a single crRNA and recognize a 5'-TTTN-3' protospacer adjacent motif (PAM) at the 5' end of the protospacer for genome editing. For widespread application in...

journal_title：Nucleic acids research

authors： Tu M,Lin L,Cheng Y,He X,Sun H,Xie H,Fu J,Liu C,Li J,Chen D,Xi H,Xue D,Liu Q,Zhao J,Gao C,Song Z,Qu J,Gu F

更新日期：2017-11-02 00:00:00

abstract：:Interferons (IFNs) are a family of multifunctional proteins involved in immune activation, regulation of cell growth and antiviral response. They exert their functions by induction of several IFN-stimulated genes, including IFN regulatory factors (IRFs), a family of transcriptional regulators. One of these factors, IR...

journal_title：Nucleic acids research

authors： Koenig Merediz SA,Schmidt M,Hoppe GJ,Alfken J,Meraro D,Levi BZ,Neubauer A,Wittig B

更新日期：2000-11-01 00:00:00

abstract：:Lambda exonuclease processively degrades one strand of double-stranded DNA (dsDNA) in the 5"-3" direction. To understand the mechanism through which this enzyme generates high processivity we are analyzing the first step in the reaction, namely the interaction of lambda exonuclease with the ends of substrate DNA. Endo...

journal_title：Nucleic acids research

authors： Mitsis PG,Kwagh JG

更新日期：1999-08-01 00:00:00