Determination of DNA cooperativity factor.

abstract：:In this article, we introduce the Gypsy Database (GyDB) of mobile genetic elements, an in-progress database devoted to the non-redundant analysis and evolutionary-based classification of mobile genetic elements. In this first version, we contemplate eukaryotic Ty3/Gypsy and Retroviridae long terminal repeats (LTR) ret...

journal_title：Nucleic acids research

authors： Lloréns C,Futami R,Bezemer D,Moya A

更新日期：2008-01-01 00:00:00

abstract：:Alternative splicing is widespread in mammalian gene expression, and variant splice patterns are often specific to different stages of development, particular tissues or a disease state. There is a need to systematically collect data on alternatively spliced exons, introns and splice isoforms, and to annotate this dat...

journal_title：Nucleic acids research

authors： Thanaraj TA,Stamm S,Clark F,Riethoven JJ,Le Texier V,Muilu J

更新日期：2004-01-01 00:00:00

abstract：:The U2 snRNP complex contains two specific proteins, U2B" and U2A'. We have analysed the interaction of U2A' with U2B" and with U2 RNA. U2A' can form an weak but detectable RNA-protein complex with U2 RNA and a stable protein complex with U2B". This protein-protein complex binds efficiently and specifically to U2 RNA....

journal_title：Nucleic acids research

authors： Boelens W,Scherly D,Beijer RP,Jansen EJ,Dathan NA,Mattaj IW,van Venrooij WJ

更新日期：1991-02-11 00:00:00

abstract：:The plastid psbA promoter of tobacco was used with the aim to construct plastid specific marker genes. Upon transfer to the tobacco nuclear genome the plastid promoter fragment appeared to specify a messenger RNA. Placed 5' to the bar or nptII coding sequences the level of expression is sufficient to obtain a selectab...

journal_title：Nucleic acids research

authors： Cornelissen M,Vandewiele M

更新日期：1989-01-11 00:00:00

abstract：:Minimized trans-acting HDV ribozyme systems consisting of three (Rz-3) and two (Rz-2) RNA strands were prepared and their folding conformations were analyzed by NMR spectroscopy. The guanosine residues in one of the enzyme components of Rz-3 were labeled with 13C and 15N. Imino proton signals were assigned by analysis...

journal_title：Nucleic acids research

authors： Tanaka Y,Hori T,Tagaya M,Sakamoto T,Kurihara Y,Katahira M,Uesugi S

更新日期：2002-02-01 00:00:00

abstract：:Optimization of primer sequences for polymerase chain reaction (PCR) and quantitative PCR (qPCR) and reaction conditions remains an experimental challenge. We have developed a resource, PrimerBank, which contains primers that can be used for PCR and qPCR under stringent and allele-invariant amplification conditions. A...

journal_title：Nucleic acids research

authors： Wang X,Spandidos A,Wang H,Seed B

更新日期：2012-01-01 00:00:00

abstract：:The HAMSTeRS WWW site was set up in 1996 in order to facilitate easy access to, and aid understanding of, the causes of haemophilia A at the molecular level; previously, the first and second text editions of the database have been published in Nucleic Acids Research. This report describes the facilities originally ava...

journal_title：Nucleic acids research

authors： Kemball-Cook G,Tuddenham EG

更新日期：1997-01-01 00:00:00

abstract：:Many lists containing biological identifiers, such as gene lists, have been generated in various genomics projects. Identifying the overlap among gene lists can enable us to understand the similarities and differences between the data sets. Here, we present an interactome network-based web application platform named N...

journal_title：Nucleic acids research

authors： Wang Y,Thilmony R,Gu YQ

更新日期：2014-07-01 00:00:00

abstract：:The polymerase encoded by human hepatitis B virus, which has reverse transcriptase and RNase H activity, binds to its pregenomic RNA template in a two-step process involving a terminal redundancy. Both first strand and second strand DNA synthesis involve primer translocation and second strand synthesis involves a temp...

journal_title：Nucleic acids research

authors： Kidd AH,Kidd-Ljunggren K

更新日期：1996-09-01 00:00:00

abstract：:Riboswitch RNAs fold into complex tertiary structures upon binding to their cognate ligand. Ligand recognition is accomplished by key residues in the binding pocket. In addition, it often crucially depends on the stability of peripheral structural elements. The ligand-bound complex of the guanine-sensing riboswitch fr...

journal_title：Nucleic acids research

authors： Buck J,Wacker A,Warkentin E,Wöhnert J,Wirmer-Bartoschek J,Schwalbe H

更新日期：2011-12-01 00:00:00

abstract：:Human telomerase is a ribonucleoprotein which uses its internal RNA moiety as a template for telomeric DNA synthesis. This enzyme is up-regulated in most malignant tumors and is therefore considered as a possible cancer target. Here we examined the effects of differently modified oligomers on telomeraseactivity from H...

journal_title：Nucleic acids research

authors： Matthes E,Lehmann C

更新日期：1999-02-15 00:00:00

abstract：:Telomere G-quadruplex is emerging as a promising anti-cancer target due to its inhibition to telomerase, an enzyme expressed in more than 85% tumors. Telomerase-mediated telomere extension and some other reactions require a free 3' telomere end in single-stranded form. G-quadruplex formation near the 3' end of telomer...

journal_title：Nucleic acids research

authors： Wang Q,Liu JQ,Chen Z,Zheng KW,Chen CY,Hao YH,Tan Z

更新日期：2011-08-01 00:00:00

abstract：:A key issue when designing and using DNA-targeting nucleases is specificity. Ideally, an optimal DNA-targeting tool has only one recognition site within a genomic sequence. In practice, however, almost all designer nucleases available today can accommodate one to several mutations within their target site. The ability...

journal_title：Nucleic acids research

authors： Juillerat A,Dubois G,Valton J,Thomas S,Stella S,Maréchal A,Langevin S,Benomari N,Bertonati C,Silva GH,Daboussi F,Epinat JC,Montoya G,Duclert A,Duchateau P

更新日期：2014-04-01 00:00:00

abstract：:MiRNAs post-transcriptionally regulate gene expression by recruiting the miRNA-induced silencing complex (miRISC) to target mRNAs. However, the mechanisms by which miRISC components are maintained at appropriate levels for proper function are largely unknown. Here, we demonstrate that Caenorhabditis elegans TEG-1 regu...

journal_title：Nucleic acids research

authors： Wang C,Gupta P,Fressigne L,Bossé GD,Wang X,Simard MJ,Hansen D

更新日期：2017-02-17 00:00:00

abstract：:One of the major issues in expression profiling analysis still is to outline proper thresholds to determine differential expression, while avoiding false positives. The problem being that the variance is inversely proportional to the log of signal intensities. Aiming to solve this issue, we describe a model, expressio...

journal_title：Nucleic acids research

authors： Chuchana P,Marchand D,Nugoli M,Rodriguez C,Molinari N,Garcia-Sanz JA

更新日期：2007-01-01 00:00:00

abstract：:In continuation with work regarding the evaluation of the energy of association of various RNA bases with various base pairs, the results of the computations of the electrostatic interaction energy of A-U base pair with four RNA bases viz. Adenine, Uracil, Guanine and Cytosine have been reported. Non bonded induced po...

journal_title：Nucleic acids research

authors： Sanyal NK,Kumar U,Roychoudhury M

更新日期：1980-09-11 00:00:00

abstract：:A positive cis-acting DNA element in the near 5'-upstream region of the CYP2B1/B2 genes in rat liver was found to play an important role in the transcription of these genes. An oligonucleotide covering -69 to -98 nt mimicked the gel mobility shift pattern given by the fragment -179 to +29 nt, which was earlier found a...

journal_title：Nucleic acids research

authors： Upadhya P,Rao MV,Venkateswar V,Rangarajan PN,Padmanaban G

更新日期：1992-02-11 00:00:00

abstract：:Herpes simplex virus-1 US11 is a RNA-binding protein with a novel RNA-binding domain. US11 has been reported to exhibit sequence- and conformation-specific RNA-binding, but the sequences and conformations important for binding are not known. US11 has also been described as a double-stranded RNA (dsRNA)-binding protein...

journal_title：Nucleic acids research

authors： Bryant KF,Cox JC,Wang H,Hogle JM,Ellington AD,Coen DM

更新日期：2005-10-24 00:00:00

abstract：:To achieve drug resistance Leishmania parasite alters gene copy number by using its repeated sequences widely distributed through the genome. Even though homologous recombination (HR) is ascribed to maintain genome stability, this eukaryote exploits this potent mechanism driven by the Rad51 recombinase to form benefic...

journal_title：Nucleic acids research

authors： Genois MM,Plourde M,Éthier C,Roy G,Poirier GG,Ouellette M,Masson JY

更新日期：2015-03-11 00:00:00

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：:Analysis of processing, assembly, and function of higher eukaryotic ribosomal RNA (rRNA) has been hindered by the lack of an expression system that enables rRNA to be modified and then examined functionally. Given the potential usefulness of such a system, we have developed one for mammalian 18S rRNA. We inserted a se...

journal_title：Nucleic acids research

authors： Burman LG,Mauro VP

更新日期：2012-09-01 00:00:00

abstract：:The MspI restriction-modification system, which recognizes the sequence 5'-CCGG-3', has been previously cloned and sequenced (1). We subcloned the methyltransferase gene (M.MspI) downstream of the ptac promoter in the multicopy vector pUC119 and overexpressed it in E. coli. Upon induction with IPTG, M.MspI constitutes...

journal_title：Nucleic acids research

authors： Dubey AK,Mollet B,Roberts RJ

更新日期：1992-04-11 00:00:00

abstract：:Preparation of large amount of single-stranded circular DNA in high selectivity is crucial for further developments of nanotechnology and other DNA sciences. Herein, a simple but practically useful methodology to prepare DNA rings has been presented. One of the essential factors is to use highly diluted T4 ligase buff...

journal_title：Nucleic acids research

authors： An R,Li Q,Fan Y,Li J,Pan X,Komiyama M,Liang X

更新日期：2017-09-06 00:00:00

abstract：:Post-transcriptional gene regulation is mediated through complex networks of protein-RNA interactions. The targets of only a few RNA binding proteins (RBPs) are known, even in the well-characterized budding yeast. In silico prediction of protein-RNA interactions is therefore useful to guide experiments and to provide ...

journal_title：Nucleic acids research

authors： Pancaldi V,Bähler J

更新日期：2011-08-01 00:00:00

abstract：:The strand displacement activity of DNA polymerase δ is strongly stimulated by its interaction with proliferating cell nuclear antigen (PCNA). However, inactivation of the 3'-5' exonuclease activity is sufficient to allow the polymerase to carry out strand displacement even in the absence of PCNA. We have examined in ...

journal_title：Nucleic acids research

authors： Koc KN,Stodola JL,Burgers PM,Galletto R

更新日期：2015-04-30 00:00:00

abstract：:PARP1 and PARP2 are implicated in the synthesis of poly(ADP-ribose) (PAR) after detection of DNA damage. The specificity of PARP1 and PARP2 interaction with long DNA fragments containing single- and/or double-strand breaks (SSBs and DSBs) have been studied using atomic force microscopy (AFM) imaging in combination wit...

journal_title：Nucleic acids research

authors： Sukhanova MV,Abrakhi S,Joshi V,Pastre D,Kutuzov MM,Anarbaev RO,Curmi PA,Hamon L,Lavrik OI

更新日期：2016-04-07 00:00:00

abstract：:We have isolated the 5'-end of the gene for the rat and human link protein by screening genomic libraries with oligonucleotides corresponding to the 5'-cDNA sequence. Several overlapping clones were isolated for the human link protein gene, while only one clone was obtained for the rat. All the clones contained a sing...

journal_title：Nucleic acids research

authors： Rhodes C,Savagner P,Line S,Sasaki M,Chirigos M,Doege K,Yamada Y

更新日期：1991-04-25 00:00:00

abstract：:Non-coding genetic variants/mutations can play functional roles in the cell by disrupting regulatory interactions between transcription factors (TFs) and their genomic target sites. For most human TFs, a myriad of DNA-binding models are available and could be used to predict the effects of DNA mutations on TF binding....

journal_title：Nucleic acids research

authors： Martin V,Zhao J,Afek A,Mielko Z,Gordân R

更新日期：2019-07-02 00:00:00

abstract：:The effect of mutations in the highly conserved Y-GG/A motif of B-type DNA polymerases was studied in the DNA polymerase from the hyperthermophilic euryarchaeon Thermococcus aggregans. This motif plays a critical role in the balance between the synthesis and degradation of the DNA chain. Five different mutations of th...

journal_title：Nucleic acids research

authors： Böhlke K,Pisani FM,Vorgias CE,Frey B,Sobek H,Rossi M,Antranikian G

更新日期：2000-10-15 00:00:00

abstract：:The thermodynamics of 13 hybridization reactions between 10 base DNA sequences of design 5'-ATGCXYATGC-3' with X, Y = A, C, G, T and their complementary PNA and DNA sequences were determined from isothermal titration calorimetry (ITC) measurements at ambient temperature. For the PNA/DNA hybridization reactions, the bi...

journal_title：Nucleic acids research

authors： Schwarz FP,Robinson S,Butler JM

更新日期：1999-12-15 00:00:00