Abstract：
:Sequence-specific DNA-binding proteins play a key role in many fundamental biological processes, such as transcription, DNA replication and recombination. Very often, these DNA-binding proteins introduce structural changes to the target DNA-binding sites including DNA bending, twisting or untwisting and wrapping, which in many cases induce a linking number change (Delta Lk) to the DNA-binding site. Due to the lack of a feasible approach, Delta Lk induced by sequence-specific DNA-binding proteins has not been fully explored. In this paper we successfully constructed a series of DNA plasmids that carry many tandem copies of a DNA-binding site for one sequence-specific DNA-binding protein, such as lambda O, LacI, GalR, CRP and AraC. In this case, the protein-induced Delta Lk was greatly amplified and can be measured experimentally. Indeed, not only were we able to simultaneously determine the protein-induced Delta Lk and the DNA-binding constant for lambda O and GalR, but also we demonstrated that the protein-induced Delta Lk is an intrinsic property for these sequence-specific DNA-binding proteins. Our results also showed that protein-mediated DNA looping by AraC and LacI can induce a Delta Lk to the plasmid DNA templates. Furthermore, we demonstrated that the protein-induced Delta Lk does not correlate with the protein-induced DNA bending by the DNA-binding proteins.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Chen B,Xiao Y,Liu C,Li C,Leng Fdoi
10.1093/nar/gkq078subject
Has Abstractpub_date
2010-06-01 00:00:00pages
3643-54issue
11eissn
0305-1048issn
1362-4962pii
gkq078journal_volume
38pub_type
杂志文章abstract：:While it has been long recognized that genes are not randomly positioned along the genome, the degree to which its 3D structure influences the arrangement of genes has remained elusive. In particular, several lines of evidence suggest that actively transcribed genes are spatially co-localized, forming transcription fa...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks1360
更新日期：2013-02-01 00:00:00
abstract：:The third intron from Physarum polycephalum (Pp LSU 3) is one of the closest known relatives to the well-studied Tetrahymena group I intron. Both introns are located at the same position in the 26S rRNA gene, and with the exception of an open reading frame in Pp LSU 3, are highly homologous. While Pp LSU 3 has been sh...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.20.4315
更新日期：1994-10-11 00:00:00
abstract：:Nucleosomes released from oviduct nuclei during brief micrococcal nuclease digestions are enriched in transcribed sequences (bloom K.S. and Anderson, J.N. (1978) Cell, 15, 141-150). Such nucleosomes released into this 1Sf supernatant fraction are enriched in proteins HMG14, 17 and a third lower molecular weight protei...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/9.12.2761
更新日期：1981-06-25 00:00:00
abstract：:Egr-1 is a murine zinc finger encoding cDNA whose expression is modulated by a variety of ligand-receptor interactions and is often coregulated with c-fos (1). This study reports the isolation of a mouse Egr-1 genomic clone, its intron-exon structure, and 935 bp of 5' flanking sequence. The gene spans about 3.8 kb and...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.18.8835
更新日期：1988-09-26 00:00:00
abstract：:A non-enzymic protein factor that increases the in vitro rate of synthesis by HeLa DNA polymerase alpha 15- to 30-fold with denatured DNA as template has been partially purified from the cytoplasmic fraction of HeLa cells. The stimulatory effect is highly specific for HeLa DNA polymerase alpha and for DNA templates th...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/5.1.221
更新日期：1978-01-01 00:00:00
abstract：:Restriction fragments of T7 DNA which selectively bind E. coli RNA polymerase have been identified. These include fragments located close to the beginning of gene 1 where according to Minkley and Pribnow (1973) there is a promoter called C. The smallest fragment from this region which binds RNA polymerase has been seq...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/6.2.525
更新日期：1979-02-01 00:00:00
abstract：:A mathematical model and a computer simulation were used to study PCR specificity. The model describes the occurrences of non-targeted PCR products formed through random primer-template interactions. The PCR simulation scans DNA sequence databases with primers pairs. According to the model prediction, PCR with complex...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/24.18.3538
更新日期：1996-09-15 00:00:00
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 relaxati...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.20.4706
更新日期：1998-10-15 00:00:00
abstract：:We have developed an effective, easy-to-use two-step system for the site-directed insertion of large genetic constructs into arbitrary positions in the Escherichia coli chromosome. The system uses lambda-Red mediated recombineering accompanied by the introduction of double-strand DNA breaks in the chromosome and a don...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp1193
更新日期：2010-04-01 00:00:00
abstract：:The essential elements of the sea urchin L. variegatus U1 snRNA promoter were mapped by microinjection of a U1 maxigene into sea urchin zygotes. Two elements are required for expression: a distal sequence element (DSE) located between -318 and -300 and a proximal sequence element (PSE) centered at -55. Removal or alte...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.14.3743
更新日期：1992-07-25 00:00:00
abstract：:Both Streptomyces lividans and Streptomyces avermitilis encode similar systems of post-replicative DNA modification which act site-specifically on closely opposed guanines on either strand. The modifications can be detected since they react in vitro with an oxidative derivative of Tris, resulting in strand cleavage. P...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.14.3364
更新日期：1998-07-15 00:00:00
abstract：:Wild type p53 assembles into a latent multiprotein complex which can be activated for sequence-specific DNA binding in vitro by proteins targeting the carboxy-terminal domain. Using an optimized system coupling the post-translational modification of wild type p53 to activation of sequence specific DNA binding, we exam...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/21.14.3167
更新日期：1993-07-11 00:00:00
abstract：:The available reagents for the attachment of functional moieties to plasmid DNA are limiting. Most reagents bind plasmid DNA in a non-sequence- specific manner, with undefined stoichiometry, and affect DNA charge and delivery properties or involve chemical modifications that abolish gene expression. The design and abi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg801
更新日期：2003-10-15 00:00:00
abstract：:Cadmium (Cd2+) is a known carcinogen that inactivates the DNA mismatch repair (MMR) pathway. In this study, we have tested the effect of Cd2+ exposure on the enzymatic activity of the mismatch binding complex MSH2-MSH6. Our results indicate that Cd2+ is highly inhibitory to the ATP binding and hydrolysis activities of...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki291
更新日期：2005-03-03 00:00:00
abstract：:Regulation of gene transcription in both prokaryotes and eukaryotes involves formation of various DNA-multiprotein complexes of higher order structure through communication between distant regions of DNA. The communication between distant DNA sites occurs by interaction between proteins bound to the sites by looping o...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/25.4.873
更新日期：1997-02-15 00:00:00
abstract：:The chromatographic profiles of isoaccepting tRNAs were analyzed at five time points during the 96 hr, dimethylsulfoxide induced, erythroid-like differentiation of Friend leukemia cells. Sixty-four isoaccepting species of tRNA for 16 amino acids were resolved by RPC-5 chromatography. The relative amounts of tRNAphe, t...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/8.15.3467
更新日期：1980-08-11 00:00:00
abstract：:To address how eukaryotic replication forks respond to fork stalling caused by strong non-covalent protein-DNA barriers, we engineered the controllable Fob-block system in Saccharomyces cerevisiae. This system allows us to strongly induce and control replication fork barriers (RFB) at their natural location within the...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt051
更新日期：2013-03-01 00:00:00
abstract：:WebProAnalyst is a web-accessible analysis tool (http://wwwmgs.bionet.nsc.ru/mgs/programs/panalyst/) designed for scanning quantitative structure-activity relationships in protein families. The tool allows users to search correlations between protein activity and physicochemical characteristics (i.e. hydrophobicity or...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki421
更新日期：2005-07-01 00:00:00
abstract：:The genome of Kirsten murine sarcoma virus was formed by recombination between Kirsten murine leukaemia virus sequences, and rat sequences derived from a retrovirus-like '30S' (VL30) genetic element encompassing the Kras oncogene. Using cloned DNAs we have determined the nucleotide sequences of the long terminal repea...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.17.6839
更新日期：1984-09-11 00:00:00
abstract：:The Genomes On Line Database (GOLD) is a web resource for comprehensive access to information regarding complete and ongoing genome sequencing projects worldwide. The database currently incorporates information on over 1500 sequencing projects, of which 294 have been completed and the data deposited in the public data...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkj145
更新日期：2006-01-01 00:00:00
abstract：:The glycoprotein C (gC) gene of herpes simplex virus type 1 is a true late gene, in that its expression occurs late in infection with a strict requirement for viral DNA replication. Recently, we reported on gC expression during infection with mutant viruses carrying deletions in the gC gene promoter. Analysis of RNA e...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/15.7.3097
更新日期：1987-04-10 00:00:00
abstract：:In the virion core of retroviruses, the genomic RNA is tightly associated with nucleocapsid (NC) protein molecules, forming the nucleocapsid structure. NC protein, a highly basic protein with two zinc fingers, is indispensable for RNA dimerization, encapsidation and the initiation of reverse transcription in avian, mu...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/21.4.831
更新日期：1993-02-25 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：:DNA from healthy Malaysian newborns was studied on gene maps after digestion with different restriction endonucleases. Of 65 newborns, two were found to be carriers of two different variants of triplicated alpha-globin loci. In variant no. 1, found in an Malay, the three alpha-globin genes are in an elongated DNA frag...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/9.15.3707
更新日期：1981-08-11 00:00:00
abstract：:The lambdagt clones containing fragments of the Drosophila melanogaster genome were prepared and characterized by hybridization of their DNA with (I) lambdagt-cRNA; (2) lambdaC-cRNA; (3) Dm-cRNA; (4) the mRNA of D.melanogaster culture cells and (5) the stable cytoplasmic poly (A) RNA from the same source. The techniqu...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/3.8.2115
更新日期：1976-08-01 00:00:00
abstract：:Significant differences are observed between the CD spectra of eu- and heterochromatin prepared by fractionating mechanically sheared rat liver chromatin on linear sucrose density gradients. Heterochromatin has a broad positive CD at 270--280 nm, a cross-over point at 256 nmn, and a negative shoulder at 248 nm. Euchro...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/6.4.1657
更新日期：1979-04-01 00:00:00
abstract：:N-(guanosin-8-yl) acetylaminofluorene (Guo-AAF) was prepared by the reaction of N-acetoxy-N-2-acetylaminofluorene (AAAF) and guanosine. Antibodies to Guo-AAF were elicited in rabbits by immunization with bovine serum albumin-Guo-AAF conjugate. The antibodies were purified by affinity chromatography on a Sepharose-Guo-...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/6.2.733
更新日期：1979-02-01 00:00:00
abstract：:The crystal structure of d(CATGGGCCCATG)(2) shows unique stacking patterns of a stable B<-->A-DNA intermediate. We evaluated intrinsic base stacking energies in this crystal structure using an ab initio quantum mechanical method. We found that all crystal base pair steps have stacking energies close to their values in...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/28.24.4893
更新日期：2000-12-15 00:00:00
abstract：:Single genes are often subject to alternative splicing, which generates alternative mature mRNAs. This phenomenon is widespread in animals, and observed in over 90% of human genes. Recent data suggest it may also be common in Apicomplexa. These parasites have small genomes, and economy of DNA is evolutionarily favoure...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv311
更新日期：2015-05-19 00:00:00
abstract：:The self-assembly of bis-biotinylated double-stranded DNA and the tetravalent biotin-binding protein streptavidin (STV) have been studied by non-denaturing gel electrophoresis and atomic force microscopy (AFM). The rapid self-assembly reproducibly generated populations of individual oligomeric complexes. Most striking...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/27.23.4553
更新日期：1999-12-01 00:00:00
