The conformational landscape of transcription intermediates involved in the regulation of the ZMP-sensing riboswitch from Thermosinus carboxydivorans.

abstract：:MODPROPEP is a web server for knowledge-based modeling of protein-peptide complexes, specifically peptides in complex with major histocompatibility complex (MHC) proteins and kinases. The available crystal structures of protein-peptide complexes in PDB are used as templates for modeling peptides of desired sequence in...

journal_title：Nucleic acids research

authors： Kumar N,Mohanty D

更新日期：2007-07-01 00:00:00

abstract：:Tissue-specific gene expression is critical in understanding biological processes, physiological conditions, and disease. The identification and appropriate use of tissue-specific genes (TissGenes) will provide important insights into disease mechanisms and organ-specific therapeutic targets. To better understand the ...

journal_title：Nucleic acids research

authors： Kim P,Park A,Han G,Sun H,Jia P,Zhao Z

更新日期：2018-01-04 00:00:00

abstract：:A differential effect is found of various bivalent cations (Ba2+, Ca2+, Mg2+, Cd2+, Co2+, Mn2+, Ni2+, Zn2+ and Hg2+) on stability of intermolecular Py-Pu-Pu triplex with different sequence of base triads. Ca2+, Mg2+, Cd2+, Co2+, Mn2+, Ni2+ and Zn2+ do stabilize the d(C)n d(G)n d(G)n triplex whereas Ba2+ and Hg2+ do no...

journal_title：Nucleic acids research

authors： Malkov VA,Voloshin ON,Soyfer VN,Frank-Kamenetskii MD

更新日期：1993-02-11 00:00:00

abstract：:An open reading frame upstream from nifHDK operon of Klebsiella pneumoniae had been described. The orientation of this open reading frame is opposite to that of nifHDK and sequence homology was found between the open reading frame promoter and the promoter of nifHDK operon. A recombinant plasmid carrying the promoter ...

journal_title：Nucleic acids research

authors： Shen SC,Xue ZT,Kong QI,Wu QL

更新日期：1983-06-25 00:00:00

abstract：:The PAH Mutation Analysis Consortium (81 investigators, 26 countries) is engaged in mutation detection at the human PAH locus. Ascertainment of probands occurs largely through newborn screening for hyperphenylalaninemia. A relational database records allelic variation (disease-producing and polymorphic) at the locus. ...

journal_title：Nucleic acids research

authors： Hoang L,Byck S,Prevost L,Scriver CR

更新日期：1996-01-01 00:00:00

abstract：:Nuclear factor I (NFI) is a site-specific DNA binding protein required for the replication of adenovirus type 2 DNA in vitro and in vivo. To study sequence requirements for the interaction of NFI with DNA, we have measured the binding of the protein to a variety of synthetic sites. Binding sites for NFI (FIB sites) we...

journal_title：Nucleic acids research

authors： Gronostajski RM

更新日期：1987-07-24 00:00:00

abstract：:Plant orthologs of the yeast sucrose non-fermenting (Snf1) kinase and mammalian AMP-activated protein kinase (AMPK) represent an emerging class of important regulators of metabolic and stress signalling. The catalytic alpha-subunits of plant Snf1-related kinases (SnRKs) interact in the yeast two-hybrid system with dif...

journal_title：Nucleic acids research

authors： Ferrando A,Koncz-Kálmán Z,Farràs R,Tiburcio A,Schell J,Koncz C

更新日期：2001-09-01 00:00:00

abstract：:We have previously identified a T lymphocyte protein which binds to a site within the LTR of the human immunodeficiency virus type 1 (HIV-1) and exerts an inhibitory effect on virus gene expression. The palindromic site (site B) recognized by this protein is related to the palindromic binding sites of members of the s...

journal_title：Nucleic acids research

authors： Orchard K,Lang G,Collins M,Latchman D

更新日期：1992-10-25 00:00:00

abstract：:The first step in gene expression, transcription, is modulated by the interaction of transcription factors with their corresponding binding sites on the DNA sequence. Pscan is a software tool that scans a set of sequences (e.g. promoters) from co-regulated or co-expressed genes with motifs describing the binding speci...

journal_title：Nucleic acids research

authors： Zambelli F,Pesole G,Pavesi G

更新日期：2009-07-01 00:00:00

abstract：:G-quadruplex (G4) DNA structures can form physical barriers within the genome that must be unwound to ensure cellular genomic integrity. Here, we report unanticipated roles for the Escherichia coli Rep helicase and RecA recombinase in tolerating toxicity induced by G4-stabilizing ligands in vivo. We demonstrate that R...

journal_title：Nucleic acids research

authors： Paul T,Voter AF,Cueny RR,Gavrilov M,Ha T,Keck JL,Myong S

更新日期：2020-07-09 00:00:00

abstract：:Insertion/deletion (indel) is one of the most common methods of protein sequence variation. Recent studies showed that indels could affect their flanking regions and they are important for protein function and evolution. Here, we describe the Indel Flanking Region Database (IndelFR, http://indel.bioinfo.sdu.edu.cn), w...

journal_title：Nucleic acids research

authors： Zhang Z,Xing C,Wang L,Gong B,Liu H

更新日期：2012-01-01 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：:We investigated the effects of the antiviral agent distamycin A and of a distamycin derivative (FCE 24517) which possesses antineoplastic activity on the binding of some regulatory proteins to DNA. Both compounds inhibited the binding to DNA of the ubiquitous octamer binding factor OTF 1 and of the erythroid specific ...

journal_title：Nucleic acids research

authors： Broggini M,Ponti M,Ottolenghi S,D'Incalci M,Mongelli N,Mantovani R

更新日期：1989-02-11 00:00:00

abstract：:The CABS-fold web server provides tools for protein structure prediction from sequence only (de novo modeling) and also using alternative templates (consensus modeling). The web server is based on the CABS modeling procedures ranked in previous Critical Assessment of techniques for protein Structure Prediction competi...

journal_title：Nucleic acids research

authors： Blaszczyk M,Jamroz M,Kmiecik S,Kolinski A

更新日期：2013-07-01 00:00:00

abstract：:Antisense oligodeoxynucleotides (ODNs) have biological activity in treating various forms of cancer. The antisense effects of two types of 20mer ODNs, phosphorothioate-modified ODNs (S-ODNs) and S-ODNs with 12 2'-O-methyl groups (Me-S-ODNs), targeted to sites 109 and 277 of bcl-2 mRNA, were compared. Both types were a...

journal_title：Nucleic acids research

authors： Yoo BH,Bochkareva E,Bochkarev A,Mou TC,Gray DM

更新日期：2004-04-02 00:00:00

abstract：:PrankWeb is an online resource providing an interface to P2Rank, a state-of-the-art method for ligand binding site prediction. P2Rank is a template-free machine learning method based on the prediction of local chemical neighborhood ligandability centered on points placed on a solvent-accessible protein surface. Points...

journal_title：Nucleic acids research

authors： Jendele L,Krivak R,Skoda P,Novotny M,Hoksza D

更新日期：2019-07-02 00:00:00

abstract：:G-quadruplexes (G4s) are nucleic acid structure motifs that are of significance in chemistry and biology. The function of G4s is often governed by their interaction with G4-binding proteins. Few categories of G4-specific tools have been developed to inhibit G4-protein interactions; however, until now there is no aptam...

journal_title：Nucleic acids research

authors： Umar MI,Kwok CK

更新日期：2020-10-09 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：:The gene for human apolipoprotein (apo) A-II has been isolated from a human genomic DNA library. The cloned fragment was approximately 14 kilobase-pair (kb) long, and extended about 9.0 kb upstream as well as 3.5 kb downstream from the apoA-II gene, which was contained within a 3.1 kb HindIII fragment of human DNA. Th...

journal_title：Nucleic acids research

authors： Lackner KJ,Law SW,Brewer HB Jr

更新日期：1985-06-25 00:00:00

abstract：:BsoFI , ItaI and Fsp4HI are isoshizomers of Fnu4HI (5'-GC NGC-3'). Both Fnu4HI and BsoFI have previously been shown to be inhibited by cytosine-specific methylation within the recognition sequence. Fnu4HI is inhibited if either the internal cytosine at position 2 or the external cytosine at position 5 of the restricti...

journal_title：Nucleic acids research

authors： Ramsahoye BH,Burnett AK,Taylor C

更新日期：1997-08-15 00:00:00

abstract：:Bisulfite genomic sequencing is the most widely used technique to analyze the 5-methylation of cytosines, the prevalent covalent DNA modification in mammals. The process is based on the selective transformation of unmethylated cytosines to uridines. Then, the investigated genomic regions are PCR amplified, subcloned a...

journal_title：Nucleic acids research

authors： Tusnády GE,Simon I,Váradi A,Arányi T

更新日期：2005-01-13 00:00:00

abstract：:Melanotransferrin (MTf) is a tumor associated antigen found in abundance on the surface of melanoma cells. It is a transferrin-like protein found in low amount in most adult tissues and whose gene is reminiscent of house-keeping genes. With the goal of understanding the regulatory mechanisms which might explain the en...

journal_title：Nucleic acids research

authors： Duchange N,Ochoa A,Plowman GD,Rozé A,Amdjadi M,Zakin MM

更新日期：1992-06-11 00:00:00

abstract：:Interleukin 2 (IL2) mRNA has a short half-life in the cytoplasm of T lymphocytes, relative to most mRNA. We have discovered a candidate ribonuclease to account for the rapid turnover of IL2 mRNA in the cytosol of the human T lymphocyte cell line Jurkat. In partially purified form, this RNase is about 7 times as active...

journal_title：Nucleic acids research

authors： Hua J,Garner R,Paetkau V

更新日期：1993-01-11 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：:Human Hepatitis B Virus (HBV) RNAs contain a cis -acting sequence, the post-transcriptional regulatory element (HPRE), which facilitates the cytoplasmic localization of intronless transcripts. Our previous studies have shown that the HPRE is composed of at least two independent sub-elements, HPREalpha and HPREbeta, wh...

journal_title：Nucleic acids research

authors： Smith GJ 3rd,Donello JE,Lück R,Steger G,Hope TJ

更新日期：1998-11-01 00:00:00

abstract：:The origin of replication of the c-myc gene in HeLa cells was previously identified at low resolution within 3.5 kb 5' to the P1 promoter, based on replication fork polarity and the location of DNA nascent strands. To define the initiation events in the c-myc origin at higher resolution the template bias of nascent DN...

journal_title：Nucleic acids research

authors： Waltz SE,Trivedi AA,Leffak M

更新日期：1996-05-15 00:00:00

abstract：:Insertion of the four major nucleotides at the 5'-side of the anticodon triplet of E. coli tRNAMetf was performed by joining of the half molecules obtained by limited digestion with RNase A and the chemically synthesized tetranucleotide pN-C-A-U using RNA ligase. Insertion of U-U at the 5'-side or A and A-A at the 3'-...

journal_title：Nucleic acids research

authors： Doi T,Yamane A,Matsugi J,Ohtsuka E,Ikehara M

更新日期：1985-05-24 00:00:00

abstract：:The cartilage matrix is composed of characteristic components including type II collagen, aggrecan and link protein. In this paper, we report two DNA elements that regulate the link protein gene. Using transient transfection assays with link protein gene constructs in chondrocytes, chloramphenicol acetyl transferase (...

journal_title：Nucleic acids research

authors： Rhodes C,Yamada Y

更新日期：1995-06-25 00:00:00

abstract：:Molecular dynamics (MD) simulations and time resolved fluorescence (TRF) spectroscopy were combined to quantitatively describe the conformational landscape of the DNA primary binding sequence (PBS) of the HIV-1 genome, a short hairpin targeted by retroviral nucleocapsid proteins implicated in the viral reverse transcr...

journal_title：Nucleic acids research

authors： Voltz K,Léonard J,Touceda PT,Conyard J,Chaker Z,Dejaegere A,Godet J,Mély Y,Haacke S,Stote RH

更新日期：2016-04-20 00:00:00

abstract：:The distribution patterns of shared short repetitive motifs in the expansion segments of the large subunit rRNA genes of different species show that these segments are coevolving as a set and that in two examined vertebrate species the RNA secondary structures are conserved as a consequence of runs of motifs in one re...

journal_title：Nucleic acids research

authors： Hancock JM,Dover GA

更新日期：1990-10-25 00:00:00