An obligate intermediate along the slow folding pathway of a group II intron ribozyme.

abstract：:Chewie Nomenclature Server (chewie-NS, https://chewbbaca.online/) allows users to share genome-based gene-by-gene typing schemas and to maintain a common nomenclature, simplifying the comparison of results. The combination between local analyses and a public repository of allelic data strikes a balance between potenti...

journal_title：Nucleic acids research

authors： Mamede R,Vila-Cerqueira P,Silva M,Carriço JA,Ramirez M

更新日期：2021-01-08 00:00:00

abstract：:In neural stem cells (NSCs), the balance between stem cell maintenance and neuronal differentiation depends on cell-fate determinants such as TRIM32. Previously, we have shown that TRIM32 associates with the RNA-induced silencing complex and increases the activity of microRNAs such as Let-7a. However, the exact mechan...

journal_title：Nucleic acids research

authors： Nicklas S,Okawa S,Hillje AL,González-Cano L,Del Sol A,Schwamborn JC

更新日期：2015-03-11 00:00:00

abstract：:We describe LincSNP 2.0 (http://bioinfo.hrbmu.edu.cn/LincSNP), an updated database that is used specifically to store and annotate disease-associated single nucleotide polymorphisms (SNPs) in human long non-coding RNAs (lncRNAs) and their transcription factor binding sites (TFBSs). In LincSNP 2.0, we have updated the ...

journal_title：Nucleic acids research

authors： Ning S,Yue M,Wang P,Liu Y,Zhi H,Zhang Y,Zhang J,Gao Y,Guo M,Zhou D,Li X,Li X

更新日期：2017-01-04 00:00:00

abstract：:Several derivatives of N2,N2-7-trimethylguanosine (m3(2,2,7G)-cap, which was found at the 5' ends of small nuclear RNAs, were synthesized by use of S-phenyl N2,N2,7-trimethylguanosine 5'-phosphorothioate (PhSpm3(2,2,7)G) as a key intermediate. This compound was activated by iodine in the presence of phosphoric acid an...

journal_title：Nucleic acids research

authors： Iwase R,Sekine M,Tokumoto Y,Ohshima Y,Hata T

更新日期：1989-11-25 00:00:00

abstract：:The 3'-untranslated region (UTR) of tobacco mosaic virus (TMV), which terminates in a tRNA-like structure, functionally substitutes for a poly(A) tail in both plant and animal cells. The addition of the TMV 3'-UTR to chimeric mRNA constructs increases their expression up to 100-fold, increasing both translational effi...

journal_title：Nucleic acids research

authors： Gallie DR,Feder JN,Schimke RT,Walbot V

更新日期：1991-09-25 00:00:00

abstract：:The noncoding RNA database (ncRNAdb) was created as a source of information on RNA molecules, which do not possess protein-coding capacity. It is now widely accepted that, in addition to constitutively expressed, housekeeping or infrastructural RNAs, there is a wide variety of RNAs participating in mechanisms involved...

journal_title：Nucleic acids research

authors： Szymanski M,Erdmann VA,Barciszewski J

更新日期：2007-01-01 00:00:00

abstract：:Fully modified 4'-thioDNA, an oligonucleotide only comprising 2'-deoxy-4'-thionucleosides, exhibited resistance to an endonuclease, in addition to preferable hybridization with RNA. Therefore, 4'-thioDNA is promising for application as a functional oligonucleotide. Fully modified 4'-thioDNA was found to behave like an...

journal_title：Nucleic acids research

authors： Matsugami A,Ohyama T,Inada M,Inoue N,Minakawa N,Matsuda A,Katahira M

更新日期：2008-04-01 00:00:00

abstract：:The variation of the proton chemical shifts due to the formation intermolecular hydrogen bonds is computed for a number of complexes which can be formed between the bases of the nucleic acids. The shifts expected for the isolated base pairs, in particular for the G-N1 H, T(or U)-N3H protons and the protons of the amin...

journal_title：Nucleic acids research

authors： Giessner-Prettre C,Pullman B,Caillet J

更新日期：1977-01-01 00:00:00

abstract：:We identify a new subgroup of Type I Restriction-Modification enzymes that modify cytosine in one DNA strand and adenine in the opposite strand for host protection. Recognition specificity has been determined for ten systems using SMRT sequencing and each recognizes a novel DNA sequence motif. Previously characterized...

journal_title：Nucleic acids research

authors： Morgan RD,Luyten YA,Johnson SA,Clough EM,Clark TA,Roberts RJ

更新日期：2016-11-02 00:00:00

abstract：:A DNA methylase has been purified 270-fold from HeLa cell nuclei by chromatography on DEAE-cellulose, phosphocellulose, and hydroxyapatite. The enzyme transfers methyl groups from S-adenosyl-L-methionine to cytosine residues in DNA. The sole product of the reaction has been identified as 5-methylcytosine. The enzyme i...

journal_title：Nucleic acids research

authors： Roy PH,Weissbach A

更新日期：1975-10-01 00:00:00

abstract：:Previous studies have established a critical role of both TFIIB and RNA polymerase II (RNAPII) in start site selection in the yeast Saccharomyces cerevisiae. However, it remains unclear how the TFIIB-RNAPII interaction impacts on this process since such an interaction can potentially influence both preinitiation compl...

journal_title：Nucleic acids research

authors： Zhang DY,Carson DJ,Ma J

更新日期：2002-07-15 00:00:00

abstract：:The Biodegradative Strain Database (BSD) is a freely-accessible, web-based database providing detailed information on degradative bacteria and the hazardous substances that they degrade, including corresponding literature citations, relevant patents and links to additional web-based biological and chemical data. The B...

journal_title：Nucleic acids research

authors： Urbance JW,Cole J,Saxman P,Tiedje JM

更新日期：2003-01-01 00:00:00

abstract：:We have shown previously that DNA demethylation by chick embryo 5-methylcytosine (5-MeC)-DNA glycosylase needs both protein and RNA. Amino acid sequences of nine peptides derived from a highly purified 5-MeC-DNA glycosylase complex were identified by Nanoelectrospray ionisation mass spectrometry to be identical to the...

journal_title：Nucleic acids research

authors： Jost JP,Schwarz S,Hess D,Angliker H,Fuller-Pace FV,Stahl H,Thiry S,Siegmann M

更新日期：1999-08-15 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：:A hallmark of defense mechanisms based on clustered regularly interspaced short palindromic repeats (CRISPR) and associated sequences (Cas) are the crRNAs that guide these complexes in the destruction of invading DNA or RNA. Three separate CRISPR-Cas systems exist in the cyanobacterium Synechocystis sp. PCC 6803. Base...

journal_title：Nucleic acids research

authors： Reimann V,Alkhnbashi OS,Saunders SJ,Scholz I,Hein S,Backofen R,Hess WR

更新日期：2017-01-25 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：:The human RAD54B protein is a paralog of the RAD54 protein, which plays important roles in homologous recombination. RAD54B contains an N-terminal region outside the SWI2/SNF2 domain that shares less conservation with the corresponding region in RAD54. The biochemical roles of this region of RAD54B are not known, alth...

journal_title：Nucleic acids research

authors： Sarai N,Kagawa W,Fujikawa N,Saito K,Hikiba J,Tanaka K,Miyagawa K,Kurumizaka H,Yokoyama S

更新日期：2008-10-01 00:00:00

abstract：:Mature tRNAPhe from Escherichia coli and the transcript of its gene lacking modified nucleotides were compared by a variety of physical techniques. Melting experiments revealed that at a low Mg2+level the transcript was partially denatured, while the mature tRNA possessed intact tertiary interactions. Mg2+binding to b...

journal_title：Nucleic acids research

authors： Serebrov V,Vassilenko K,Kholod N,Gross HJ,Kisselev L

更新日期：1998-06-01 00:00:00

abstract：:We have previously investigated the role of the N-terminal region of ribosomal protein S4 to participate in 30S ribosome assembly and function (1-3). In this report we extend these studies to the two fragments produced by the chemical cleavage of protein S4 at the tryptophan residue 167. We find that the carboxyl term...

journal_title：Nucleic acids research

authors： Changchien LM,Craven GR

更新日期：1985-09-11 00:00:00

abstract：:The Human Genome Project has facilitated the sequencing of many species, yet the current Sanger method is too expensive, labor intensive and time consuming to accomplish medical resequencing of human genomes en masse. Of the 'next-generation' technologies, cyclic reversible termination (CRT) is a promising method with...

journal_title：Nucleic acids research

authors： Wu W,Stupi BP,Litosh VA,Mansouri D,Farley D,Morris S,Metzker S,Metzker ML

更新日期：2007-01-01 00:00:00

abstract：:Increasing evidence indicates that active DNA demethylation is involved in several processes in mammals, resulting in developmental stage-specificity and cell lineage-specificity. The recently discovered Ten-Eleven Translocation (TET) dioxygenases are accepted to be involved in DNA demethylation by initiating 5-mC oxi...

journal_title：Nucleic acids research

authors： Chen H,Kazemier HG,de Groote ML,Ruiters MH,Xu GL,Rots MG

更新日期：2014-02-01 00:00:00

abstract：:Alternative splicing generates multiple transcript and protein isoforms from a single gene and controls transcript intracellular localization and stability by coupling to mRNA export and nonsense-mediated mRNA decay (NMD). RNA interference (RNAi) is a potent mechanism to modulate gene expression. However, its interact...

journal_title：Nucleic acids research

authors： Fuchs A,Riegler S,Ayatollahi Z,Cavallari N,Giono LE,Nimeth BA,Mutanwad KV,Schweighofer A,Lucyshyn D,Barta A,Petrillo E,Kalyna M

更新日期：2021-01-25 00:00:00

abstract：:In eukaryotes, the transcription of tRNA genes is initiated by the concerted action of transcription factors IIIC (TFIIIC) and IIIB (TFIIIB) which direct the recruitment of polymerase III. While TFIIIC recognizes highly conserved, intragenic promoter elements, TFIIIB binds to the non-coding 5'-upstream regions of the ...

journal_title：Nucleic acids research

authors： Zhang G,Lukoszek R,Mueller-Roeber B,Ignatova Z

更新日期：2011-04-01 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：:Protein-based methods of siRNA delivery are capable of uniquely specific targeting, but are limited by technical challenges such as low potency or poor biophysical properties. Here, we engineered a series of ultra-high affinity siRNA binders based on the viral protein p19 and developed them into siRNA carriers targete...

journal_title：Nucleic acids research

authors： Yang NJ,Kauke MJ,Sun F,Yang LF,Maass KF,Traxlmayr MW,Yu Y,Xu Y,Langer RS,Anderson DG,Wittrup KD

更新日期：2017-07-27 00:00:00

abstract：:The genes encoding the RNA subunit of ribonuclease P from the unicellular cyanobacterium Synechocystis sp. PCC 6803, and from the heterocyst-forming strains Anabaena sp. PCC 7120 and Calothrix sp. PCC 7601 were cloned using the homologous gene from Anacystis nidulans (Synechococcus sp. PCC 6301) as a probe. The genes ...

journal_title：Nucleic acids research

authors： Vioque A

更新日期：1992-12-11 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：:The alternative proliferating-cell nuclear antigen (PCNA)-loader CTF18-RFC forms a stable complex with DNA polymerase ε (Polε). We observed that, under near-physiological conditions, CTF18-RFC alone loaded PCNA inefficiently, but loaded it efficiently when complexed with Polε. During efficient PCNA loading, CTF18-RFC ...

journal_title：Nucleic acids research

authors： Fujisawa R,Ohashi E,Hirota K,Tsurimoto T

更新日期：2017-05-05 00:00:00

abstract：:The J-binding protein 1 (JBP1) is essential for biosynthesis and maintenance of DNA base-J (β-d-glucosyl-hydroxymethyluracil). Base-J and JBP1 are confined to some pathogenic protozoa and are absent from higher eukaryotes, prokaryotes and viruses. We show that JBP1 recognizes J-containing DNA (J-DNA) through a 160-res...

journal_title：Nucleic acids research

authors： Heidebrecht T,Christodoulou E,Chalmers MJ,Jan S,Ter Riet B,Grover RK,Joosten RP,Littler D,van Luenen H,Griffin PR,Wentworth P Jr,Borst P,Perrakis A

更新日期：2011-07-01 00:00:00

abstract：:The advances of next-generation sequencing technology have facilitated metagenomics research that attempts to determine directly the whole collection of genetic material within an environmental sample (i.e. the metagenome). Identification of genes directly from short reads has become an important yet challenging probl...

journal_title：Nucleic acids research

authors： Rho M,Tang H,Ye Y

更新日期：2010-11-01 00:00:00