Abstract：
:The U1A protein is a sequence-specific RNA binding protein found in the U1 snRNP particle where it binds to stem/loop II of U1 snRNA. U1A contains two 'RNP' or 'RRM' (RNA Recognition Motif) domains, which are common to many RNA-binding proteins. The N-terminal RRM has been shown to bind specifically to the U1 RNA stem/loop, while the RNA target of the C-terminal domain is unknown. Here, we describe experiments using a 102 amino acid N-terminal RRM of U1A (102A) and a 25-nucleotide RNA stem/loop to measure the binding constants and thermodynamic parameters of this RNA:protein complex. Using nitrocellulose filter binding, we measure a dissociation constant KD = 2 x 10(-11) M in 250 mM NaCl, 2 mM MgC2, and 10 mM sodium cacodylate, pH 6 at room temperature, and a half-life for the complex of 5 minutes. The free energy of association (delta G degrees) of this complex is about -14 kcal/mol in these conditions. Determination of the salt dependence of the binding suggests that at least 8 ion-pairs are formed upon complex formation. A mutation in the RNA loop sequence reduces the affinity 10 x, or about 10% of the total free energy.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Hall KB,Stump WTdoi
10.1093/nar/20.16.4283keywords:
subject
Has Abstractpub_date
1992-08-25 00:00:00pages
4283-90issue
16eissn
0305-1048issn
1362-4962journal_volume
20pub_type
杂志文章abstract：:The CRISPR system has become a powerful biological tool with a wide range of applications. However, improving targeting specificity and accurately predicting potential off-targets remains a significant goal. Here, we introduce a web-based CR: ISPR/Cas9 O: ff-target P: rediction and I: dentification T: ool (CROP-IT) th...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv575
更新日期：2015-10-15 00:00:00
abstract：:Ribosome synthesis involves the concomitance of pre-rRNA processing and ribosomal protein assembly. In eukaryotes, this is a complex process that requires the participation of specific sequences and structures within the pre-rRNAs, at least 200 trans-acting factors and the ribosomal proteins. There is little informati...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq260
更新日期：2010-08-01 00:00:00
abstract：:The genes for mitoribosomal protein S12 (Mrps12) and mitochondrial seryl-tRNA ligase (Sarsm and Sars2) are oppositely transcribed from a conserved promoter region of <200 bp in both human and mouse. Using a dual reporter vector we identified an array of 4 CCAAT box elements required for efficient transcription of the ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl1037
更新日期：2007-01-01 00:00:00
abstract：:MAGIA(2) (http://gencomp.bio.unipd.it/magia2) is an update, extension and evolution of the MAGIA web tool. It is dedicated to the integrated analysis of in silico target prediction, microRNA (miRNA) and gene expression data for the reconstruction of post-transcriptional regulatory networks. miRNAs are fundamental post...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks460
更新日期：2012-07-01 00:00:00
abstract：:Bacterial retrons consist of a reverse transcriptase (RT) and a contiguous non-coding RNA (ncRNA) gene. One third of annotated retrons carry additional open reading frames (ORFs), the contribution and significance of which in retron biology remains to be determined. In this study we developed a computational pipeline ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa1149
更新日期：2020-12-16 00:00:00
abstract：:Many nucleic acid-binding proteins and the AAA+ family form hexameric rings, but the mechanism of hexamer assembly is unclear. It is generally believed that the specificity in protein/RNA interaction relies on molecular contact through a surface charge or 3D structure matching via conformational capture or induced fit...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkn669
更新日期：2008-11-01 00:00:00
abstract：:Integration of foreign genes into plant genomes by the Agrobacterium T-DNA transfer system has been considered to occur at random. It has been speculated that the chromosomal structure of the integration site might affect the expression pattern of the introduced genes. To gain insight into the molecular structure of T...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.14.2744
更新日期：1994-07-25 00:00:00
abstract：:The family of ten-eleven translocation (Tet) dioxygenases is widely distributed across the eukaryotic tree of life, from mammals to the amoeboflagellate Naegleria gruberi. Like mammalian Tet proteins, the Naegleria Tet-like protein, NgTet1, acts on 5-methylcytosine (5mC) and generates 5-hydroxymethylcytosine (5hmC), 5...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv870
更新日期：2015-12-15 00:00:00
abstract：:Calf thymus nucleosomes exhibit two different and independent hydrodynamic responses to diminishing salt concentration. One change is gradual over the range 40 to 0.2 mM Na+ and is accompanied by decreases in contact-site cross-linking efficiency. The other change is abrupt, being centered between 1 and 2 mM Na+. We f...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/8.21.4969
更新日期：1980-11-11 00:00:00
abstract：:Use of the polymerase chain reaction (PCR) to amplify variable numbers of tandem repeat (VNTR) loci has become widely used in genetic typing. Unfortunately, preferential amplification of small allelic products relative to large allelic products may result in incorrect or ambiguous typing in a heterozygous sample. The ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/23.15.3050
更新日期：1995-08-11 00:00:00
abstract：:We have previously characterized an extracellular nuclease from Pseudomonas BAL 31 which, in addition to other activities, displays a double-strand exonuclease activity which progressively shortens both strands of linear duplex DNA molecules from both termini. This degradation is accomplished without the introduction ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/5.5.1445
更新日期：1978-05-01 00:00:00
abstract：:New transcripts generated by RNA polymerase II (RNAPII) are generally processed in order to form mature mRNAs. Two key processing steps include a precise cleavage within the 3' end of the pre-mRNA, and the subsequent polymerization of adenosines to produce the poly(A) tail. In yeast, these two functions are performed ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx674
更新日期：2017-09-29 00:00:00
abstract：:Over 50 introns have been reported in archaeal rRNA genes (rDNAs), a subset of which nests putative homing endonuclease (HEase) genes. Here, we report the identification and characterization of a novel archaeal LAGLIDADG-type HEase, I-ApeKI [corrected], encoded by the ApeK1.S908 intron within the 16S rDNA of Aeropyrum...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gni118
更新日期：2005-07-26 00:00:00
abstract：:DNA primase has been partially purified from wheat germ. This enzyme, like DNA primases characterized from many procaryotic and eucaryotic sources, catalyses the synthesis of primers involved in DNA replication. However, the wheat enzyme differs from animal DNA primase in that it is found partially associated with a D...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.16.4867
更新日期：1990-08-25 00:00:00
abstract：:Knowledge of the various interactions between molecules in the cell is crucial for understanding cellular processes in health and disease. Currently available interaction databases, being largely complementary to each other, must be integrated to obtain a comprehensive global map of the different types of interactions...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks1055
更新日期：2013-01-01 00:00:00
abstract：:Adaptation to the host cell environment to efficiently take-over the host cell's machinery is crucial in particular for small RNA viruses like picornaviruses that come with only small RNA genomes and replicate exclusively in the cytosol. Their Internal Ribosome Entry Site (IRES) elements are specific RNA structures th...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks182
更新日期：2012-07-01 00:00:00
abstract：:Triple helix-forming oligonucleotides covalently linked to topoisomerase I inhibitors, in particular the antitumor agent camptothecin, trigger topoisomerase I-mediated DNA cleavage selectively in the proximity of the binding site of the oligonucleotide vector. In the present study, we have performed a systematic analy...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg457
更新日期：2003-07-15 00:00:00
abstract：:Several authors, including ourselves, have reported the existence of chromatosomes with DNA size larger than 166 bp in bird erythrocyte chromatin. It was tempting to correlate this increased DNA size with the presence of histone H5. In order to substantiate this hypothesis, we performed a micrococcal nuclease digestio...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/9.15.3671
更新日期：1981-08-11 00:00:00
abstract：:In Eukaryotes, DNA is wound around the histone octamer forming the basic chromatin unit, the nucleosome. Atomic structures have been obtained from crystallography and single particle cryo-electron microscopy (cryoEM) of identical engineered particles. But native nucleosomes are dynamical entities with diverse DNA sequ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky670
更新日期：2018-09-28 00:00:00
abstract：:IslandViewer (http://pathogenomics.sfu.ca/islandviewer) is a web-accessible application for the computational prediction and analysis of genomic islands (GIs) in bacterial and archaeal genomes. GIs are clusters of genes of probable horizontal origin and are of high interest because they disproportionately encode virul...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt394
更新日期：2013-07-01 00:00:00
abstract：:Hg-UMP-containing transcripts made from chick erythroid chromatins with E. coli RNA polymerase hybridize to chick globin cDNA. Contamination with endogenous globin RNA has been largely removed by purification on SH-agarose columns at 55 degrees C. Some endogenous globin mRNA sequences remain, probably as hybrids with ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/5.4.1237
更新日期：1978-04-01 00:00:00
abstract：:The detailed conformational features and dynamics of the naturally occurring deoxyribotrinucleoside diphosphates d-TpTpT and d-TpTpC have been investigated at 20 degrees C and 80 degrees C in aqueous solution by nuclear magnetic resonance spectroscopy. The observed NMR parameters indicate that the conformational prope...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/5.11.4399
更新日期：1978-11-01 00:00:00
abstract：:The use of bacterial artificial chromosomes (BACs) provides a consistent and high targeting efficiency of homologous recombination in embryonic stem (ES) cells, facilitated by long stretches of sequence homology. Here, we introduce a BAC targeting method which employs restriction fragment length polymorphisms (RFLPs) ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr550
更新日期：2011-10-01 00:00:00
abstract：:The human beta-globin LCR plays a key role in the transcriptional regulation of the beta-globin locus and comprises four erythroid specific DNase I hypersensitive sites, designated 5'HS1-4. We have now isolated genomic clones containing 5'HS3 and 5'HS4 of the mouse beta-globin LCR. 5'HS3 and 5'HS4 are located 15 kb an...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.21.5797
更新日期：1992-11-11 00:00:00
abstract：:Polyketide synthases (PKSs) catalyze biosynthesis of a diverse family of pharmaceutically important secondary metabolites. Bioinformatics analysis of sequence and structural features of PKS proteins plays a crucial role in discovery of new natural products by genome mining, as well as in design of novel secondary meta...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq340
更新日期：2010-07-01 00:00:00
abstract：:An oligonucleotide hybrid is described which possesses two triple helix forming oligonucleotides which have been connected by a flexible polymeric linker chain. As a prototype, binding of this class of oligonucleotide to duplex DNA has been studied using a segment of the HSV-1 D-glycoprotein promoter, which possesses ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/21.20.4810
更新日期：1993-10-11 00:00:00
abstract：:Stabilization of stalled replication forks prevents excessive fork reversal or degradation, which can undermine genome integrity. The WRN protein is unique among the other human RecQ family members to possess exonuclease activity. However, the biological role of the WRN exonuclease is poorly defined. Recently, the WRN...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz431
更新日期：2019-07-26 00:00:00
abstract：:The DNA sequence of the spacer (plus flanking) regions separating the 16S rRNA and 23S rRNA genes of two presumptive rDNA operons of the archaebacterium Methanococcus vannielii was determined. The spacers are 156 and 242 base pairs in size and they share a sequence homology of 49 base pairs following the 3' terminus o...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/11.21.7537
更新日期：1983-11-11 00:00:00
abstract：:Alternative splicing of pre-mRNA generates protein diversity. Dysfunction of splicing machinery and expression of specific transcripts has been linked to cancer progression and drug response. Exon microarray technology enables genome-wide quantification of expression levels of the majority of exons and facilitates the...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr513
更新日期：2011-10-01 00:00:00
abstract：:A type II restriction endonuclease, DraI, isolated from Deinococcus radiophilus ATCC 27603 recognises the palindromic hexanucleotide sequence (formula; see text) and cleaves it, as indicated by the arrows, to produce blunt-ended fragments. The yield of enzyme is 100 to 1000 times that of the only other known type II r...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/11.16.5467
更新日期：1983-08-25 00:00:00
