Abstract：
:The interaction of Hoechst 33258 with the minor groove of the adenine-tract DNA duplex d(CTTTTGCAAAAG)2 has been studied in both D2O and H2O solutions by 1D and 2D 1H NMR spectroscopy. Thirty-one nuclear Overhauser effects between drug and nucleotide protons within the minor groove of the duplex, together with ring-current induced perturbations to the chemical shifts of basepair and deoxyribose protons, define the position and orientation of the bound dye molecules. Two drug molecules bind cooperatively and in symmetry related orientations at the centre of the 5'-TTTT and 5'-AAAA sequences with the binding interactions spanning only the four A-T basepairs. The positively charged N-methylpiperazine moieties point towards the centre of the duplex while the phenol groups are disposed towards the 3'-ends of the sequence. Resonance averaging is apparent for both the D2/D6 and D3/D5 phenol protons and D2"'/D6"' and D3"'/D5"' of the N-methylpiperazine ring and is consistent with these groups being involved in rapid rotation or ring-flipping motions in the bound state. Interstrand NOEs between adenine H2s and deoxyribose H1' are consistent with a high degree of propeller twisting of the A-T basepairs at the binding site of the aromatic benzimidazole and phenol rings of Hoechst. The data imply that the minor groove is particularly narrow with many contacts between the complementary curved surfaces of the drug and DNA indicating that strong van der Waals interactions, involving the floor and the walls of the minor groove, stabilize the complex. In our model the NH groups of the benzimidazole rings are positioned to make a pair of bifurcated hydrogen bonds with the adenine N3 and thymine O2 on the floor of the minor groove.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Searle MS,Embrey KJdoi
10.1093/nar/18.13.3753subject
Has Abstractpub_date
1990-07-11 00:00:00pages
3753-62issue
13eissn
0305-1048issn
1362-4962journal_volume
18pub_type
杂志文章abstract：:A new class of synthetic DNA duplexes containing repeating oligonucleotide sequences, double-helical concatemers, is characterized. The UV-absorption and circular dichroism of a concatemer formed in self-association of d(T-G-C-A-C-A-T-G) have been studied. The thermodynamical parameters of complex formation are the fo...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/8.11.2413
更新日期：1980-06-11 00:00:00
abstract：:Single-stranded mRNA molecules form secondary structures through complementary self-interactions. Several hypotheses have been proposed on the relationship between the nucleotide sequence, encoded amino acid sequence and mRNA secondary structure. We performed the first transcriptome-wide in silico analysis of the huma...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl287
更新日期：2006-05-08 00:00:00
abstract：:To understand how potential for G-quadruplex formation might influence regulation of gene expression, we examined the 2 kb spanning the transcription start sites (TSS) of the 18 217 human RefSeq genes, distinguishing contributions of template and nontemplate strands. Regions both upstream and downstream of the TSS are...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm1138
更新日期：2008-03-01 00:00:00
abstract：:Initiation of σ(54)-dependent transcription requires assistance to melt DNA at the promoter site but is impeded by numerous protein-protein and nucleo-protein interactions. To alleviate these inhibitory interactions, hexameric bacterial enhancer binding proteins (bEBP), a subset of the ATPases associated with various ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks661
更新日期：2012-10-01 00:00:00
abstract：:At the DNA/RNA level, biological signals are defined by a combination of spatial structures and sequence motifs. Until now, few attempts had been made in writing general purpose search programs that take into account both sequence and structure criteria. Indeed, the most successful structure scanning programs are usua...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/24.8.1395
更新日期：1996-04-15 00:00:00
abstract：:Recent studies indicate that controlling the nuclear decondensation and intra-nuclear localization of plasmid DNA (pDNA) would result in an increased transfection efficiency. In the present study, we established a technology for imaging the nuclear condensation/decondensation status of pDNA in nuclear subdomains using...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq1327
更新日期：2011-04-01 00:00:00
abstract：:The genetic organization of the multiple ribosomal transcription units (RTUs) on the genome of the yeast Saccharomyces carlsbergensis was studied by electron microscopy of purified ribosomal DNA hybridized to 26S rRNA using the R-loop technique (Thomas, M., White, R.L. and Davis, R.W. (1973) Proc. Natl. Acad. Sci. U.S...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/5.8.2801
更新日期：1978-08-01 00:00:00
abstract：:T1DBase (http://www.t1dbase.org) is web platform, which supports the type 1 diabetes (T1D) community. It integrates genetic, genomic and expression data relevant to T1D research across mouse, rat and human and presents this to the user as a set of web pages and tools. This update describes the incorporation of new dat...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq912
更新日期：2011-01-01 00:00:00
abstract：:A type II restriction endonuclease, named CviJI, was isolated from a eukaryotic Chlorella-like green alga infected with the dsDNA containing virus IL-3A. CviJI is the first restriction endonuclease to recognize the sequence PuGCPy; CviJI cleaves DNA between the G and C. Methylation of the cytosine in PuGCPy sequences ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/15.15.6075
更新日期：1987-08-11 00:00:00
abstract：:VapD-like virulence-associated proteins have been found in many organisms, but little is known about this protein family including the 3D structure of these proteins. Recently, a relationship between the Cas2 family of ribonucleases associated with the CRISPR system of microbial immunity and VapD was suggested. Here, ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr1305
更新日期：2012-05-01 00:00:00
abstract：:The emergence of massively parallel sequencing technology has revolutionized microbial profiling, allowing the unprecedented comparison of microbial diversity across time and space in a wide range of host-associated and environmental ecosystems. Although the high-throughput nature of such methods enables the detection...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt1070
更新日期：2013-12-01 00:00:00
abstract：:This paper describes a simple program that uses a digitizing device to enter DNA sequences directly from autoradiographs into a computer. ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.1part2.499
更新日期：1984-01-11 00:00:00
abstract：:NRPS-PKS is web-based software for analysing large multi-enzymatic, multi-domain megasynthases that are involved in the biosynthesis of pharmaceutically important natural products such as cyclosporin, rifamycin and erythromycin. NRPS-PKS has been developed based on a comprehensive analysis of the sequence and structur...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh359
更新日期：2004-07-01 00:00:00
abstract：:Cryptic splice sites are used only when use of a natural splice site is disrupted by mutation. To determine the features that distinguish authentic from cryptic 5' splice sites (5'ss), we systematically analyzed a set of 76 cryptic 5'ss derived from 46 human genes. These cryptic 5'ss have a similar frequency distribut...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg830
更新日期：2003-11-01 00:00:00
abstract：:Owing to their great potentials in genetic code extension and the development of nucleic acid-based functional nanodevices, DNA duplexes containing HgII-mediated base pairs have been extensively studied during the past 60 years. However, structural basis underlying these base pairs remains poorly understood. Herein, w...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw1296
更新日期：2017-03-17 00:00:00
abstract：:Restriction endonucleases HindII and TaqI, but not SalI, were found to efficiently cleave synthetic hexadecanucleotide duplexes which contained either an A/C or a G/T mismatch within their respective restriction sites. Double-stranded M13 DNAs with identical mismatches were also cleaved under the assay conditions. The...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/14.5.1943
更新日期：1986-03-11 00:00:00
abstract：:We have developed a simple but powerful method and web server to quickly locate charged and hydrophobic clusters in proteins (http://www.netasa.org/qgrid/index.html). For the charged clusters, each atom in the protein is first assigned a charge according to a standard force field. Then a box is created with dimensions...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh363
更新日期：2004-07-01 00:00:00
abstract：:The Diatom Expressed Sequence Tag (EST) Database was constructed to provide integral access to ESTs from these ecologically and evolutionarily interesting microalgae. It has now been updated with 130,000 Phaeodactylum tricornutum ESTs from 16 cDNA libraries and 77,000 Thalassiosira pseudonana ESTs from seven libraries...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkn905
更新日期：2009-01-01 00:00:00
abstract：:Treatment of responsive cells by interferons (IFNs) induces within a few hours a rise in the concentration of several proteins and mRNAs. In order to characterize these IFN-induced mRNA species, we have cloned in E. coli the cDNA made from a 17-18S poly(A)+ RNA of human fibroblastoid cells (SV80) treated with IFN-beta...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/11.5.1213
更新日期：1983-03-11 00:00:00
abstract：:Sensory photoreceptors have enabled non-invasive and spatiotemporal control of numerous biological processes. Photoreceptor engineering has expanded the repertoire beyond natural receptors, but to date no generally applicable strategy exists towards constructing light-regulated protein actuators of arbitrary function....
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw930
更新日期：2016-11-16 00:00:00
abstract：:The ability of the tumor suppressor protein, p53, to recognize certain types of DNA lesions may represent one of the mechanisms by which this protein modulates cellular response to DNA damage. p53 DNA binding properties are regulated by several factors, such as post-translational modifications including phosphorylatio...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/30.11.2427
更新日期：2002-06-01 00:00:00
abstract：:DNA intercalators are found to recognize a DNA lesion as a high affinity receptor site. This lesion-specific binding is observed when one strand of a DNA double helix contains an extra, unpaired nucleotide. Our assay for binding controls for the effects of sequence with a series of oligodeoxynucleotide duplexes which ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.24.11607
更新日期：1988-12-23 00:00:00
abstract：:Altering zinc bioavailability to bacterial pathogens is a key component of host innate immunity. Thus, the ability to sense and adapt to the alterations in zinc concentrations is critical for bacterial survival and pathogenesis. To understand the adaptive responses of group A Streptococcus (GAS) to zinc limitation and...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku1304
更新日期：2015-01-01 00:00:00
abstract：:The complete nucleotide sequence of the mitochondrial DNA of the amphioxus Branchiostoma lanceolatum has been determined. This mitochondrial genome is small (15 076 bp) because of the short size of the two rRNA genes and the tRNA genes. In addition, this genome contains a very short non-coding region (57 bp) with no s...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.13.3279
更新日期：1998-07-01 00:00:00
abstract：:An efficient procedure for the synthesis of unnatural alpha-anomeric oligodeoxyribonucleotides is described. This solid-phase procedure is based on the use of alpha-nucleoside phosphoramidites and alpha-nucleoside derivatized solid supports corresponding to the four natural bases and allow rapid synthesis of oligonucl...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.3.833
更新日期：1988-02-11 00:00:00
abstract：:The chicken erythroid proteins binding to the histone H5 5' promoter and 3' erythroid-specific enhancer regions were identified. In DNase I footprinting and gel mobility shift experiments with immature adult erythrocyte nuclear extracts, we have demonstrated the binding of proteins to the GC-box, a high affinity Sp1 b...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.23.6385
更新日期：1992-12-11 00:00:00
abstract：:The synthesis of stable RNA in Mycoplasma capricolum was studied by [32P] labeling of cellular RNA of cells grown in a partially-defined medium in the presence or absence of an amino acid mixture supplement. The results indicate that M. capricolum employs the same stringent control mechanism used by E. coli cells, as ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/9.15.3641
更新日期：1981-08-11 00:00:00
abstract：:EpoDB is a database of genes expressed in vertebrate red blood cells. It is also a prototype for the creation of cell and tissue-specific databases from multiple external sources. The information in EpoDB obtained from GenBank, SWISS-PROT, Transfac, TRRD and GERD is curated to provide high quality data for sequence an...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/27.1.200
更新日期：1999-01-01 00:00:00
abstract：:The RNA bacteriophages of E. coli specifically encapsidate a single copy of the viral genome in a protein shell composed mainly of 180 molecules of coat protein. Coat protein is also a translational repressor and shuts off viral replicase synthesis by interaction with a RNA stem-loop containing the replicase initiatio...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/21.19.4621
更新日期：1993-09-25 00:00:00
abstract：:An improved contact hybridization technique for the analysis of labelled RNA species is presented. The method combines high sensitivity of detection with the high resolution of polyacrylamide gel electrophoresis and should be especially useful for the characterization of transient RNA precursor molecules. Its applicat...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/6.9.2963
更新日期：1979-07-11 00:00:00
