Solid phase technology improves coupled gel shift/footprinting analysis.

abstract：:The transactivator responsive region (TAR) present in the 5'-NTR of the HIV-1 genome represents a potential target for antiretroviral intervention and a model system for the development of specific inhibitors of RNA-protein interaction. Earlier, we have shown that an anti-TAR polyamide nucleotide analog (PNA(TAR)) con...

journal_title：Nucleic acids research

authors： Tripathi S,Chaubey B,Ganguly S,Harris D,Casale RA,Pandey VN

更新日期：2005-08-02 00:00:00

abstract：:Rad54 protein is a key member of the RAD52 epistasis group required for homologous recombination in eukaryotes. Rad54 is a duplex DNA translocase that remodels both DNA and protein-DNA complexes, and functions at multiple steps in the recombination process. Here we use biochemical criteria to demonstrate the existence...

journal_title：Nucleic acids research

authors： Haseltine CA,Kowalczykowski SC

更新日期：2009-05-01 00:00:00

abstract：:Nuclear factors NF90 and NF45 form a complex involved in a variety of cellular processes and are thought to affect gene expression both at the transcriptional and translational level. In addition, this complex affects the replication of several viruses through direct interactions with viral RNA. NF90 and NF45 dimerize...

journal_title：Nucleic acids research

authors： Wolkowicz UM,Cook AG

更新日期：2012-10-01 00:00:00

abstract：:Elastic network models (ENMs) are valuable and efficient tools for characterizing the collective internal dynamics of proteins based on the knowledge of their native structures. The increasing evidence that the biological functionality of RNAs is often linked to their innate internal motions poses the question of whet...

journal_title：Nucleic acids research

authors： Pinamonti G,Bottaro S,Micheletti C,Bussi G

更新日期：2015-09-03 00:00:00

abstract：:Human single-strand (ss) DNA binding proteins 1 (hSSB1) has been shown to participate in DNA damage response and maintenance of genome stability by regulating the initiation of ATM-dependent signaling. ATM phosphorylates hSSB1 and prevents hSSB1 from ubiquitin-proteasome-mediated degradation. However, the E3 ligase th...

journal_title：Nucleic acids research

authors： Chen ZW,Liu B,Tang NW,Xu YH,Ye XY,Li ZM,Niu XM,Shen SP,Lu S,Xu L

更新日期：2014-10-01 00:00:00

abstract：:The Galaxy HiCExplorer provides a web service at https://hicexplorer.usegalaxy.eu. It enables the integrative analysis of chromosome conformation by providing tools and computational resources to pre-process, analyse and visualize Hi-C, Capture Hi-C (cHi-C) and single-cell Hi-C (scHi-C) data. Since the last publicatio...

journal_title：Nucleic acids research

authors： Wolff J,Rabbani L,Gilsbach R,Richard G,Manke T,Backofen R,Grüning BA

更新日期：2020-07-02 00:00:00

abstract：:Two triple helix structures (15-mers containing only T.A-T triplets or containing mixed T.A-T and C.G-C triplets) have been studied by uranyl mediated DNA photocleavage to probe the accessibility of the phosphates of the DNA backbone. Whereas the phosphates of the pyrimidine strand are at least as accessible as in dou...

journal_title：Nucleic acids research

authors： Nielsen PE

更新日期：1992-06-11 00:00:00

abstract：:Enzymes involved in nucleic acid transactions often have a helicase-like ATPase coordinating and driving their functional activities, but our understanding of the mechanistic details of their coordination is limited. For example, DNA cleavage by the antiphage defense system Type ISP restriction-modification enzyme req...

journal_title：Nucleic acids research

authors： Chand MK,Carle V,Anuvind KG,Saikrishnan K

更新日期：2020-03-18 00:00:00

abstract：:Because of their high nucleotide sequence homology, the specific detection of mRNA transcripts of individual members of a gene family presents certain problems. Here we apply and defend the single nucleotide primer extension (SNuPE) as a simple, specific, and highly quantitative assay for this purpose. The method dist...

journal_title：Nucleic acids research

authors： Lombardo AJ,Brown GB

更新日期：1996-12-01 00:00:00

abstract：:Initiation of Adenovirus (Ad) DNA replication occurs by a protein-priming mechanism in which the viral precursor terminal protein (pTP) and DNA polymerase (pol) as well as two nuclear DNA-binding proteins from uninfected HeLa cells are required. Biochemical studies on the pTP and DNA polymerase proteins separately hav...

journal_title：Nucleic acids research

authors： Stunnenberg HG,Lange H,Philipson L,van Miltenburg RT,van der Vliet PC

更新日期：1988-03-25 00:00:00

abstract：:Translation regulation plays an important role in eukaryotic gene expression. Upstream open reading frames (uORFs) are potent regulatory elements located in 5' mRNA transcript leaders. Translation of uORFs usually inhibit the translation of downstream main open reading frames, but some enhance expression. While a mino...

journal_title：Nucleic acids research

authors： Lin Y,May GE,Kready H,Nazzaro L,Mao M,Spealman P,Creeger Y,McManus CJ

更新日期：2019-09-26 00:00:00

abstract：:IS200 is found throughout Enterobacteriaceae and transposes at a notoriously low frequency. In addition to the transposase protein (TnpA), IS200 encodes an uncharacterized Hfq-binding sRNA that is encoded opposite to the tnpA 5'UTR. In the current work we asked if this sRNA represses tnpA expression. We show here that...

journal_title：Nucleic acids research

authors： Ellis MJ,Trussler RS,Haniford DB

更新日期：2015-07-27 00:00:00

abstract：:One surprisingly common element of RNA secondary structure consists of a hairpin capped by a four-base loop (or the tetraloop). Recently the 3-D structures of two RNA-tetraloops have been determined by NMR-studies. Both structures have a similar architecture: the first and the last bases of the loop form a hydrogen bo...

journal_title：Nucleic acids research

authors： Kajava A,Rüterjans H

更新日期：1993-09-25 00:00:00

abstract：:Despite much information as to the structure and function of the general transcription factors, little is known about the regulation of their expression. Transcription of the Saccharomyces cerevisiae SUA7 (TFIIB) gene results in the formation of two discrete transcripts. It was originally reported that the two transcr...

journal_title：Nucleic acids research

authors： Hoopes BC,Bowers GD,DiVisconte MJ

更新日期：2000-11-15 00:00:00

abstract：:Eukaryotic gene expression is regulated by enhancer-promoter interactions but the molecular mechanisms that govern specificity have remained elusive. Genome-wide studies utilizing STARR-seq identified two enhancer classes in Drosophila that interact with different core promoters: housekeeping enhancers (hkCP) and deve...

journal_title：Nucleic acids research

authors： Cubeñas-Potts C,Rowley MJ,Lyu X,Li G,Lei EP,Corces VG

更新日期：2017-02-28 00:00:00

abstract：:This paper describes a computer program designed to look for similarities between pairs of nucleic or amino acid sequences. The program looks both for segments of perfect identity or for regions where, using a scoring matrix, a minimum value is exceeded. The results of comparisons are presented as a matrix which is di...

journal_title：Nucleic acids research

authors： Staden R

更新日期：1982-05-11 00:00:00

abstract：:From a sarkosyl-insoluble outer membrane fraction prepared from the Helicobacter pylori strain ATCC 43504, 19 proteins could be sequenced N-terminally by Edman degradation. Oligonucleotides were deduced and used for screening of a genomic library. From the isolated genes, five code for different members of a H.pylori ...

journal_title：Nucleic acids research

authors： Peck B,Ortkamp M,Diehl KD,Hundt E,Knapp B

更新日期：1999-08-15 00:00:00

abstract：:Human Silent Information Regulator Type 1 (SIRT1) is an NAD(+)-dependent deacetylase protein which is an intermediary of cellular metabolism in gene silencing and aging. SIRT1 has been extensively investigated and shown to delay senescence; however, less is known about the regulation of SIRT1 during aging. In this stu...

journal_title：Nucleic acids research

authors： Han L,Zhou R,Niu J,McNutt MA,Wang P,Tong T

更新日期：2010-11-01 00:00:00

abstract：:The nucleoside analogs 1-(2'-deoxy-beta-D-ribofuranosyl)- 3-nitropyrrole (9), 1-(2'-deoxy-beta-D-ribofuranosyl)-4-nitropyrazole (10), 1-(2'-deoxy-beta-D-ribofuranosyl)-4-nitroimidazole (11) and 1-(2'-deoxy-beta-D-ribofuranosyl)-5-nitroindole (21) were incorporated into the oligonucleotide 5'-d(CGCXAATTYGCG)-3'in the f...

journal_title：Nucleic acids research

authors： Bergstrom DE,Zhang P,Johnson WT

更新日期：1997-05-15 00:00:00

abstract：:The reaction of the tetranucleotide, pA-A(2)-A, with 2'(3')-0-(alpha-methoxyethyl)uridine 5'-diphosphate, Mg(2+) ions, and M. luteus polynucleotide phosphorylase followed by mild acid treatment to remove the blocking groups results in a 49% yield of the desired single addition product, pA-A(3)-U, together with smaller...

journal_title：Nucleic acids research

authors： Sninsky JJ,Bennett GN,Gilham PT

更新日期：1974-12-01 00:00:00

abstract：:The tumor suppressor p53 is a sequence-specific transcription factor, which regulates the expression of target genes involved in different stress responses. To understand p53's essential transcriptional functions, unbiased analysis of its DNA-binding repertoire is pivotal. In a genome-wide tiling ChIP-on-chip approach...

journal_title：Nucleic acids research

authors： Smeenk L,van Heeringen SJ,Koeppel M,van Driel MA,Bartels SJ,Akkers RC,Denissov S,Stunnenberg HG,Lohrum M

更新日期：2008-06-01 00:00:00

abstract：:To prevent progressive telomere shortening as a result of conventional DNA replication, new telomeric DNA must be added onto the chromosome end. The de novo DNA synthesis involves elongation of the G-rich strand of the telomere by telomerase. In human cells, the CST complex (CTC1-STN1-TEN1) also functions in telomere ...

journal_title：Nucleic acids research

authors： Feng X,Hsu SJ,Kasbek C,Chaiken M,Price CM

更新日期：2017-05-05 00:00:00

abstract：:The HIV-1 nucleocapsid (NC) protein is a small, basic protein containing two retroviral zinc fingers. It is a highly active nucleic acid chaperone; because of this activity, it plays a crucial role in virus replication as a cofactor during reverse transcription, and is probably important in other steps of the replicat...

journal_title：Nucleic acids research

authors： Fisher RJ,Fivash MJ,Stephen AG,Hagan NA,Shenoy SR,Medaglia MV,Smith LR,Worthy KM,Simpson JT,Shoemaker R,McNitt KL,Johnson DG,Hixson CV,Gorelick RJ,Fabris D,Henderson LE,Rein A

更新日期：2006-01-24 00:00:00

abstract：:Intestinal apolipoprotein B mRNA is edited at nucleotide 6666 by a C to U transition resulting in a translational stop codon. The enzymatic properties of the editing activity were characterised in vitro using rat enterocyte cytosolic extract. The editing activity has no nucleotide or ion cofactor requirement. It shows...

journal_title：Nucleic acids research

authors： Greeve J,Navaratnam N,Scott J

更新日期：1991-07-11 00:00:00

abstract：:The sequential arrangement of histones along DNA in nucleosome core particles was determined between 0.5 and 600 mM salt and from 0 to 8 M urea. These concentrations of salt and urea up to 6 M had no significant effect on the linear order of histones along DNA but 8 M urea caused the rearrangement of histones. Conform...

journal_title：Nucleic acids research

authors： Zayetz VW,Bavykin SG,Karpov VL,Mirzabekov AD

更新日期：1981-03-11 00:00:00

abstract：:A stable conformer of Escherichia coli tRNA(Glu), obtained in the absence of Mg(2+), is inactive in the aminoacylation reaction. Probing it with diethylpyrocarbonate, dimethyl sulfate and ribonuclease V1 revealed that it has a hairpin structure with two internal loops; the helical segments at both extremities have the...

journal_title：Nucleic acids research

authors： Madore E,Florentz C,Giegé R,Lapointe J

更新日期：1999-09-01 00:00:00

abstract：:The mutations of 76 haemophilia B patients representing the whole population registered with the Malmö haemophilia centre (42) and referrals from the UK, were characterised. RFLP haplotype analysis of the defective genes indicated that 51 single base pair substitutions were definitely of independent origin and 27 of t...

journal_title：Nucleic acids research

authors： Green PM,Montandon AJ,Bentley DR,Ljung R,Nilsson IM,Giannelli F

更新日期：1990-06-11 00:00:00

abstract：:Specific binding of HIV-1 viral protein NCp7 to a unique 35-base RNA stem-loop SL1 is critical for formation and packaging of the genomic RNA dimer found within HIV-1 virions. NCp7 binding stimulates refolding of SL1 from a metastable kissing dimer (KD) into thermodynamically stable linear dimer (LD). Using UV melting...

journal_title：Nucleic acids research

authors： Mujeeb A,Ulyanov NB,Georgantis S,Smirnov I,Chung J,Parslow TG,James TL

更新日期：2007-01-01 00:00:00

abstract：:Multiple regulatory modules contribute to the complex expression programs realized by many loci. Although long thought of as isolated components, recent studies demonstrate that such regulatory sequences can physically associate with promoters and with each other and may localize to specific sub-nuclear transcription ...

journal_title：Nucleic acids research

authors： Dib S,Denarier E,Dionne N,Beaudoin M,Friedman HH,Peterson AC

更新日期：2011-04-01 00:00:00

abstract：:The EcoCyc database (http://EcoCyc.org/) is a comprehensive source of information on the biology of the prototypical model organism Escherichia coli K12. The mission for EcoCyc is to contain both computable descriptions of, and detailed comments describing, all genes, proteins, pathways and molecular interactions in E...

journal_title：Nucleic acids research

authors： Keseler IM,Collado-Vides J,Gama-Castro S,Ingraham J,Paley S,Paulsen IT,Peralta-Gil M,Karp PD

更新日期：2005-01-01 00:00:00