Abstract:
:We have used DNase I footprinting to examine the association kinetics of GA-, GT- and CT-containing oligonucleotides with the target sequence (GGA)5GG. (CCT)5CC. These reactions are slow yielding bimolecular association rate constants between 50 and 2000 M-1s-1. We find that GT-containing oligonucleotides bind much faster than GA- or CT-containing third strands. In each case the observed rate constants are faster at the centre than at the edges of the target site. Although several explanations can be offered for this observation, it is consistent with a model in which triplex formation at this repetitive site is achieved via intermediate complexes in which the third strand is not properly aligned with its target and which subsequently migrate to the correct position.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Paes HM,Fox KRdoi
10.1093/nar/25.16.3269subject
Has Abstractpub_date
1997-08-15 00:00:00pages
3269-74issue
16eissn
0305-1048issn
1362-4962pii
gka544journal_volume
25pub_type
杂志文章abstract::The sequence of a DNA fragment about 1 Kbp long located at the 3' boundary of the chicken alpha globin gene domain, including the 3'-side matrix attachment point and the site of transcription termination, was determined. It contains a repetitive DNA element and the AT-rich (easily denaturable) DNA segment conserved at...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.3.401
更新日期:1990-02-11 00:00:00
abstract::The 5' portions and flanking sequences of genes encoding types 1, 12, 24, and 6 M proteins were compared. Although the DNA sequences encoding the amino-termini of the mature M proteins had no obvious similarity, upstream sequences, and those encoding the signal peptides (leader sequences) of the four M protein genes h...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.10.4667
更新日期:1988-05-25 00:00:00
abstract::The Neurospora VS ribozyme is a catalytic RNA that has the unique ability to specifically recognize and cleave a stem-loop substrate through formation of a highly stable kissing-loop interaction (KLI). In order to explore the engineering potential of the VS ribozyme to cleave alternate substrates, we substituted the w...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw401
更新日期:2016-08-19 00:00:00
abstract::Proper cytokine gene expression is essential in development, homeostasis and immune responses. Studies on the transcriptional control of cytokine genes have mostly focused on highly researched transcription factors (TFs) and cytokines, resulting in an incomplete portrait of cytokine gene regulation. Here, we used enha...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa1055
更新日期:2020-12-02 00:00:00
abstract::Murine embryonic stem (ES) cells are commonly cultured on feeder layers of primary murine embryonic fibroblasts (MEFs). Because gene targeting experiments often involve sequential selection for multiple-drug resistance in single ES cell lines, we have developed a new mouse strain which represents an economical donor f...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.18.3745
更新日期:1997-09-15 00:00:00
abstract::Argonaute (Ago) proteins function in RNA silencing as components of the RNA-induced silencing complex (RISC). In lower organisms, the small interfering RNA and miRNA pathways diverge due in part to sorting mechanisms that direct distinct small RNA (sRNA) duplexes onto specific Ago-RISCs. However, such sorting mechanis...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku137
更新日期:2014-04-01 00:00:00
abstract::The chloroplast ribosomal protein CS1 is an essential component of the plastids translational machinery involved in translation initiation. Southern analysis suggests that the corresponding nuclear gene is present in one copy in the spinach genome. We have isolated and sequenced the gene (rps1) to study its expression...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.16.4153
更新日期:1992-08-25 00:00:00
abstract::Restriction fragments containing established curved regions, such as the pBR322 tn3 region, the phage lambda attP region and the SV40 T-antigen and terminus of replication regions, exhibit systematically retarded elution upon anion exchange based HPLC. Using this method, we were able to detect readily other SV40 curve...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.15.4181
更新日期:1991-08-11 00:00:00
abstract::RNA helicases of the DEAD-box protein family form the largest group of helicases. The human DEAD-box protein 1 (DDX1) plays an important role in tRNA and mRNA processing, is involved in tumor progression and is also hijacked by several virus families such as HIV-1 for replication and nuclear export. Although important...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv106
更新日期:2015-03-11 00:00:00
abstract::The deoxyoligonucleotide 5' AATCGGGCATGGATT (15-mer) was synthesized containing 12 phosphoramidate linkages derived from 2 primary and 2 secondary amines. The oligonucleotides were purified by reverse phase HPLC and characterized by PAGE. The thermal stability of the duplexes derived from these compounds, when hybridi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.11.4831
更新日期:1988-06-10 00:00:00
abstract::Liquid-liquid phase separation plays an important role in a variety of cellular processes, including the formation of membrane-less organelles, the cytoskeleton, signalling complexes, and many other biological supramolecular assemblies. Studies on the molecular basis of phase separation in cells have focused on protei...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz978
更新日期:2019-12-16 00:00:00
abstract::A method is described which allows selection of sequences which can substitute for the normal AATAAA hexanucleotide involved in polyadenylation of SV40 late mRNAs. Plaques were generated from viral DNA lacking the motif, forcing acquisition of substitute sequences. Four variants were characterized. All displayed wild-...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.22.8053
更新日期:1985-11-25 00:00:00
abstract::A cDNA encoding the 60 kDa subunit of mammalian splicing factor SF3a has been isolated. The deduced protein sequence reveals a 30% identity to the PRP9 splicing protein of the yeast S.cerevisiae. The highest homology is present in a zinc finger-like region in the C-terminal domain of both proteins. The PRP9 zinc finge...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.24.5223
更新日期:1994-12-11 00:00:00
abstract::A protein-DNA complex has less gel electrophoretic mobility than the free DNA fragment. One parameter for the degree of retardation of a linear DNA fragment in a protein-DNA complex is the molecular weight of the bound protein(s). The quotient of the migration distances of free DNA (m) and protein-DNA complex (m') is ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.12.5241
更新日期:1988-06-24 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
pub_type: 杂志文章
doi:10.1093/nar/26.3.703
更新日期:1998-02-01 00:00:00
abstract::We report the first investigation of oligoribonucleotides containing a few 1-(2-deoxy-2-alpha-C-hydroxymethyl-beta-D-ribofuranosyl)thymine units (or 2'-hm-dT, abbreviated in this work as 'H'). Both the 2'-CH2O-phosphoramidite and 3'-O-phosphoramidite derivatives of H were synthesized and incorporated into both 2',5'-R...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki1003
更新日期:2005-12-23 00:00:00
abstract::In two-colour microarrays, the ratio of signal intensities of two co-hybridized samples is used as a relative measure of gene expression. Ratio-based analysis becomes complicated and inefficient in multi-class comparisons. We therefore investigated the validity of an intensity-based analysis procedure. To this end, tw...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gnh038
更新日期:2004-02-24 00:00:00
abstract::Based on the secondary structural model of MS2 RNA, it is shown that, in base-pairing regions of the RNA, there is a bias in the use of synonymous codons which favours C and/or G over U and/or A in the third codon positions, and that in non-pairing regions, there is an opposite bias which favours U and/or A over C and...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/7.7.2073
更新日期:1979-12-11 00:00:00
abstract::We have studied the regulation of DNA ligase I gene expression in UV-C irradiated human primary fibroblasts. An increase of approximately 6-fold both in DNA ligase I messenger and activity levels was observed 24 h after UV treatment, when nucleotide excision repair (NER) is no longer operating. DNA ligase I induction ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.6.962
更新日期:1995-03-25 00:00:00
abstract::This work presents the Apo-Holo DataBase (AH-DB, http://ahdb.ee.ncku.edu.tw/ and http://ahdb.csbb.ntu.edu.tw/), which provides corresponding pairs of protein structures before and after binding. Conformational transitions are commonly observed in various protein interactions that are involved in important biological f...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr940
更新日期:2012-01-01 00:00:00
abstract::The NCBI Assembly database (www.ncbi.nlm.nih.gov/assembly/) provides stable accessioning and data tracking for genome assembly data. The model underlying the database can accommodate a range of assembly structures, including sets of unordered contig or scaffold sequences, bacterial genomes consisting of a single compl...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv1226
更新日期:2016-01-04 00:00:00
abstract::The rolling circle DNA replication structures generated by the in vitro phage T4 replication system were analyzed using two-dimensional agarose gels. Replication structures were generated in the presence or absence of T4 primase (gp61), permitting the analysis of replication forks with either duplex or single-stranded...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.11.2166
更新日期:1996-06-01 00:00:00
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::We define phosphovariants as genetic variations that change phosphorylation sites or their interacting kinases. Considering the essential role of phosphorylation in protein functions, it is highly likely that phosphovariants change protein functions. Therefore, a comparison of phosphovariants between individuals or be...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn1008
更新日期:2009-03-01 00:00:00
abstract::Motor proteins that translocate on nucleic acids are key players in gene expression and maintenance. While the function of these proteins is diverse, they are driven by highly conserved core motor domains. In transcription-coupled DNA repair, motor activity serves to remove RNA polymerase stalled on damaged DNA, makin...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp680
更新日期:2009-10-01 00:00:00
abstract::We have constructed and tested several new vectors for P element-mediated gene transfer. These vectors contain restriction sites for cloning a wide variety of DNA fragments within a small, non-autonomous P element and can be used to efficiently transduce microinjected DNA sequences into the germ line chromosomes of D....
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.18.6341
更新日期:1983-09-24 00:00:00
abstract::The FSSP database presents a continuously updated classification of 3-D protein folds based on an all-against-all comparison of structures currently in the Protein Data Bank (PDB) [Bernstein et al. (1977) J. Mol. Biol., 112, 535- 542]. The database currently contains an extended structural family for each of 600 repre...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.1.206
更新日期:1996-01-01 00:00:00
abstract::The p53 transcription factor confers its potent tumor suppressor functions primarily through the regulation of a large network of target genes. The recent explosion of next generation sequencing protocols has enabled the study of the p53 gene regulatory network (GRN) and underlying mechanisms at an unprecedented depth...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa666
更新日期:2020-09-18 00:00:00
abstract::Many RNP proteins contain one or more copies of the RNA recognition motif (RRM) and are thought to be involved in cellular RNA metabolism. We have previously characterized in Xenopus a nervous system specific gene, nrp1, that is more similar to the hnRNP A/B proteins than to other known proteins (K. Richter, P. J. Goo...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.4.999
更新日期:1993-02-25 00:00:00
abstract::Leishmania species are protozoan parasites whose remarkably plastic genome limits the establishment of effective genetic manipulation and leishmaniasis treatment. The strategies used by Leishmania to maintain its genome while allowing variability are not fully understood. Here, we used DiCre-mediated conditional gene ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky1017
更新日期:2018-12-14 00:00:00