Abstract:
:The solution structure of the complex between 4', 6-diamidino-2-phenylindole (DAPI) and DNA oligomer [d(GCGATTCGC)]2, containing a central T.T mismatch, has been characterized by combined use of proton one- and two-dimensional NMR spectroscopy, molecular mechanics and molecular dynamics computations including relaxation matrix refinement. The results show that the DAPI molecule binds in the minor groove of the central region 5'-ATT-3' of the DNA oligomer, which predominantly adopts a duplex structure with a global right-handed B-like conformation. In the final models of the complex, the DAPI molecule is located nearly isohelical with its NH indole proton oriented towards the DNA helix axis and forming a bifurcated hydrogen bond with the carbonyl O2 groups of a mismatched T5 and the T6 residue of the opposite strand. Mismatched thymines adopt a wobble base pair conformation and are found stacked between the flanking base pairs, inducing only minor local conformational changes in global duplex structure. In addition, no other binding mechanisms were observed, showing that minor groove binding of DAPI to the mismatch-containing site is favoured in comparison with any other previously reported interaction with G.C sequences.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Trotta E,Paci Mdoi
10.1093/nar/26.20.4706subject
Has Abstractpub_date
1998-10-15 00:00:00pages
4706-13issue
20eissn
0305-1048issn
1362-4962pii
gkb737journal_volume
26pub_type
杂志文章abstract::The Chemical Effects in Biological Systems database (CEBS) is a comprehensive and unique toxicology resource that compiles individual and summary animal data from the National Toxicology Program (NTP) testing program and other depositors into a single electronic repository. CEBS has undergone significant updates in re...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw1077
更新日期:2017-01-04 00:00:00
abstract::We have developed an improved method for photofootprinting in vivo which utilizes the thermostable DNA polymerase from T. aquaticus (Taq) in a primer extension assay. UV light is used to introduce photoproducts into the genomic DNA of intact yeast cells. The photoproducts are then detected and mapped at the nucleotide...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.1.171
更新日期:1989-01-11 00:00:00
abstract::Intramolecular RNA cross-links were induced within the large ribosomal subunit of E. coli by mild ultraviolet irradiation. Regions of the 23S RNA previously implicated in interactions with ribosomal-bound tRNA were then specifically excised by addressed cleavage using ribonuclease H, in conjunction with synthetic comp...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.15.4325
更新日期:1990-08-11 00:00:00
abstract::The Mediator complex transmits activation signals from DNA bound transcription factors to the core transcription machinery. Genome wide localization studies have demonstrated that Mediator occupancy not only correlates with high levels of transcription, but that the complex also is present at transcriptionally silence...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr551
更新日期:2011-10-01 00:00:00
abstract::The Superimposé webserver performs structural similarity searches with a preference towards 3D structure-based methods. Similarities can be detected between small molecules (e.g. drugs), parts of large structures (e.g. binding sites of proteins) and entire proteins. For this purpose, a number of algorithms were implem...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn285
更新日期:2008-07-01 00:00:00
abstract::Solution structures of DNA duplexes containing oxanine (Oxa, O) opposite a cytosine (O:C duplex) and opposite a thymine (O:T duplex) have been solved by the combined use of (1)H NMR and restrained molecular dynamics calculation. One mismatch pair was introduced into the center of the 11-mer duplex of [d(GTGACO(6)CACTG...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr872
更新日期:2012-02-01 00:00:00
abstract::A minor tRNA-Glu1 constituent of a preparation of E. coli B tRNA-Glu (Oak Ridge) has a guanosine residue at position 66 rather than an adenosine as in the tRNA-Glu2 described by Ohashi et al. (3). Automated sequential degradation was used to sequence this region. ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/2.4.469
更新日期:1975-04-01 00:00:00
abstract::Improving the accuracy of prediction of gene starts is one of a few remaining open problems in computer prediction of prokaryotic genes. Its difficulty is caused by the absence of relatively strong sequence patterns identifying true translation initiation sites. In the current paper we show that the accuracy of gene s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.12.2607
更新日期:2001-06-15 00:00:00
abstract::We report the molecular cloning and characterization of a cDNA derived from a zebrafish gene (ZF-21) related to the mouse homeobox containing gene Hox2.1. Interesting information about the differential conservation of various domains was gained from comparisons between the putative protein sequences from ZF-21 (275 am...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.19.9097
更新日期:1988-10-11 00:00:00
abstract::Using total internal reflection fluorescence microscopy, we directly visualize in real-time, the 1D Brownian motion and transcription elongation of T7 RNA polymerase along aligned DNA molecules bound to substrates by molecular combing. We fluorescently label T7 RNA polymerase with antibodies and use flow to convect th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm332
更新日期:2007-01-01 00:00:00
abstract::Pulsed field gel electrophoresis was used to determine the location of the tumour necrosis factor (TNF) alpha and beta genes. They were shown to be linked to the HLA-B locus; analogous to their location in mouse, between the complement (class III) region and H-2D. However, the distance between the TNF genes and the cl...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.21.8957
更新日期:1987-11-11 00:00:00
abstract::The International Mouse Phenotyping Consortium (IMPC) web portal (http://www.mousephenotype.org) provides the biomedical community with a unified point of access to mutant mice and rich collection of related emerging and existing mouse phenotype data. IMPC mouse clinics worldwide follow rigorous highly structured and ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt977
更新日期:2014-01-01 00:00:00
abstract::Protein structures often show similarities to another which would not be seen at the sequence level. Given the coordinates of a protein chain, the SALAMI server at www.zbh.uni-hamburg.de/salami will search the protein data bank and return a set of similar structures without using sequence information. The results page...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp431
更新日期:2009-07-01 00:00:00
abstract::One challenge in engineering organisms is taking responsibility for their behavior over many generations. Spontaneous mutations arising before or during use can impact heterologous genetic functions, disrupt system integration, or change organism phenotype. Here, we propose restructuring the genetic code itself such t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz745
更新日期:2019-11-04 00:00:00
abstract::In this study, we show that silencing of CITED2 using small-hairpin RNA (shCITED2) induced DNA damage and reduction of ERCC1 gene expression in HEK293, HeLa and H1299 cells, even in the absence of cisplatin. In contrast, ectopic expression of ERCC1 significantly reduced intrinsic and induced DNA damage levels, and res...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv934
更新日期:2015-12-15 00:00:00
abstract::DNase I and MPE.Fe (II) footprinting both employ partial cleavage of ligand-protected DNA restriction fragments and Maxam-Gilbert sequencing gel methods of analysis. One method utilizes the enzyme, DNase I, as the DNA cleaving agent while the other employs the synthetic molecule, methidium-propyl-EDTA (MPE). For actin...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.16.5555
更新日期:1983-08-25 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::Purified 15 S globin mRNA-protein (mRNP) complexes obtained by EDTA dissociation of duck reticulocytes polyribosomes were digested with the calcium dependant Staphylococcus aureus nuclease (EC 3. 1. 4. 7.). 25% of the globin mRNA sequences were resistant to extensive nuclease digestion as determined by TCA precipitati...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/6.8.2787
更新日期:1979-06-25 00:00:00
abstract::A repeated non-coding DNA sequence d(TTAGGG)n is present in the telomeric ends of all human chromosomes. These repeats can adopt multiple inter and intramolecular non-B-DNA conformations that may play an important role in biological processes. Two intramolecular structures of the telomeric oligonucleotide dAGGG(TTAGGG...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh875
更新日期:2004-10-08 00:00:00
abstract::Genotoxic stress induces alternative splicing of the oncogene MDM2 generating MDM2-ALT1, an isoform attributed with tumorigenic properties. However, the mechanisms underlying this event remain unclear. Here we explore MDM2 splicing regulation by utilizing a novel minigene that mimics endogenous MDM2 splicing in respon...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv223
更新日期:2015-04-30 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
pub_type: 杂志文章
doi:10.1093/nar/27.24.4792
更新日期:1999-12-15 00:00:00
abstract::The major immediate early regulatory region of human cytomegalovirus (HCMV) has a complex set of DNA sites through which both cellular and viral factors coordinately regulate immediate early gene expression. In undifferentiated human teratocarcinoma (T2) cells we have previously shown that major immediate early gene e...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.8.1767
更新日期:1991-04-25 00:00:00
abstract::The temperature-sensitive Neurospora nuclear mutant cyt18-1 is deficient in splicing many Group I mitochondrial introns when grown at its non-permissive temperature; however, splicing of intron 1 in the coI gene of the Adiopodoume (formerly called North Africa) strain is unaffected (R.A. Collins and A.M. Lambowitz, J....
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.22.9087
更新日期:1989-11-25 00:00:00
abstract::Genes from yeast to mammals are frequently subject to non-coding transcription of their antisense strand; however the genome-wide role for antisense transcription remains elusive. As transcription influences chromatin structure, we took a genome-wide approach to assess which chromatin features are associated with nasc...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv666
更新日期:2015-09-18 00:00:00
abstract::Engineered derivatives of Autographa californica multiple nucleocapsid nuclear polyhedrosis virus (AcMNPV) possessing a unique restriction site provide a source of viral DNA that can be linearized by digestion with a specific endonuclease. Circular or linearized DNA from two such viruses were compared in terms of thei...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.19.5667
更新日期:1990-10-11 00:00:00
abstract::Simian virus 40 (SV40) nucleoprotein complexes were extracted from nuclei of infected monkey cells and fractionated on neutral sucrose density gradients. Complexes which contained replicating SV40 DNA (95S) separated well from those containing closed circular supercoiled viral DNA (75S). DNA polymerase activity was as...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/5.5.1715
更新日期:1978-05-01 00:00:00
abstract::UV-irradiation (lambda = 254 nm) of liquid aqueous solutions of deoxyguanosine in the presence of oxygen at pH less than 7 causes an intensive degradation of nucleoside. The quantum yield estimated from A254 decrease for the reaction mixture was found to be 1.5X10(-4) at doses to 150 E/mole. The rate of A254 decrease ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/4.4.955
更新日期:1977-04-01 00:00:00
abstract::Onconase, a cytotoxic ribonuclease from Rana pipiens, possesses pyroglutamate (Pyr) at the N-terminus and has a substrate preference for uridine-guanine (UG). To identify residues responsible for onconase's cytotoxicity, we cloned the rpr gene from genomic DNA and expressed it in Escherichia coli BL21(DE3). The recomb...
journal_title:Nucleic acids research
pub_type: 评论,杂志文章
doi:10.1093/nar/gkg746
更新日期:2003-09-15 00:00:00
abstract::In small RNA (smRNA) sequencing studies, highly abundant molecules such as adapter dimer products and tissue-specific microRNAs (miRNAs) inhibit accurate quantification of lowly expressed species. We previously developed a method to selectively deplete highly abundant miRNAs. However, this method does not deplete adap...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz425
更新日期:2019-08-22 00:00:00
abstract::Smarcal1 is a SWI/SNF-family protein with an ATPase domain involved in DNA-annealing activities and a binding site for the RPA single-strand-DNA-binding protein. Although the role played by Smarcal1 in the maintenance of replication forks has been established, it remains unknown whether Smarcal1 contributes to genomic...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv621
更新日期:2015-07-27 00:00:00