当前位置： SCI文献检索 > NUCLEIC ACIDS RESEARCH期刊下所有文献 > Methidiumpropyl-EDTA.Fe(II) and DNase I footprinting report different small molecule binding site sizes on DNA.

Methidiumpropyl-EDTA.Fe(II) and DNase I footprinting report different small molecule binding site sizes on DNA.

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 actinomycin D, chromomycin A3 and distamycin A, DNase I footprinting reports larger binding site sizes than MPE.Fe (II). DNase I footprinting appears more sensitive for weakly bound sites. MPE.Fe (II) footprinting appears more accurate in determining the actual size and location of the binding sites for small molecules on DNA, especially in cases where several small molecules are closely spaced on the DNA. MPE.Fe (II) and DNase I report the same sequence and binding site size for lac repressor protein on operator DNA.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Van Dyke MW,Dervan PB

doi

10.1093/nar/11.16.5555

subject

Has Abstract

pub_date

1983-08-25 00:00:00

pages

5555-67

issue

16

eissn

0305-1048

issn

1362-4962

journal_volume

11

pub_type

杂志文章

相关文献

NUCLEIC ACIDS RESEARCH文献大全
  • The Radiation Hybrid Database.

    abstract：:Since July 1995, the European Bioinformatics Institute (EBI) has maintained RHdb (http://www.ebi.ac.uk/RHdb/RHdb.html ), a public database for radiation hybrid data. Radiation hybrid mapping is an important technique for determining high resolution maps. Recently, CORBA access has been added to Rhdb. The EBI is an Out...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/26.1.102

    authors： Lijnzaad P,Helgesen C,Rodriguez-Tomé P

    更新日期：1998-01-01 00:00:00

  • Interaction of trans and cis regulatory elements in the INO1 promoter of Saccharomyces cerevisiae.

    abstract：:Electrophoretic mobility shift assays (EMSA) were used to define the regions of the INO1 promoter that interact with factors present in extracts prepared from the yeast, Saccharomyces cerevisae. These experiments identified three different types of protein:DNA complexes that assemble with the INO1 promoter. Formation ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/19.14.3987

    authors： Lopes JM,Henry SA

    更新日期：1991-07-25 00:00:00

  • Dlx2 homeobox gene transcriptional regulation of Trkb neurotrophin receptor expression during mouse retinal development.

    abstract：:Dlx homeobox genes are first expressed in embryonic retina at E11.5. The Dlx1/Dlx2 null retina has a reduced ganglion cell layer (GCL), with loss of late-born differentiated retinal ganglion cells (RGCs) due to increased apoptosis. TrkB signaling is proposed to regulate the dynamics of RGC apoptosis throughout develop...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkm1099

    authors： de Melo J,Zhou QP,Zhang Q,Zhang S,Fonseca M,Wigle JT,Eisenstat DD

    更新日期：2008-02-01 00:00:00

  • The EcoCyc and MetaCyc databases.

    abstract：:EcoCyc is an organism-specific Pathway/Genome Database that describes the metabolic and signal-transduction pathways of Escherichia coli, its enzymes, and-a new addition-its transport proteins. MetaCyc is a new metabolic-pathway database that describes pathways and enzymes of many different organisms, with a microbial...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/28.1.56

    authors： Karp PD,Riley M,Saier M,Paulsen IT,Paley SM,Pellegrini-Toole A

    更新日期：2000-01-01 00:00:00

  • On the cooperative and noncooperative binding of ethidium to DNA.

    abstract：:The equilibrium binding of ethidium bromide to native DNAs and to poly(dG-dC) X poly(dG-dC) has been studied by both phase partition and direct spectrophotometric techniques. The binding isotherms obtained from both experimental techniques show that ethidium binds in a cooperative manner to E. coli DNA. On the other h...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/10.24.8211

    authors： Winkle SA,Rosenberg LS,Krugh TR

    更新日期：1982-12-20 00:00:00

  • Quality assessment and data analysis for microRNA expression arrays.

    abstract：:MicroRNAs are small (approximately 22 nt) RNAs that regulate gene expression and play important roles in both normal and disease physiology. The use of microarrays for global characterization of microRNA expression is becoming increasingly popular and has the potential to be a widely used and valuable research tool. H...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkn932

    authors： Sarkar D,Parkin R,Wyman S,Bendoraite A,Sather C,Delrow J,Godwin AK,Drescher C,Huber W,Gentleman R,Tewari M

    更新日期：2009-02-01 00:00:00

  • Characterization of a human cDNA encoding a widely expressed and highly conserved cysteine-rich protein with an unusual zinc-finger motif.

    abstract：:A human term placental cDNA library was screened at low stringency with a human prolactin cDNA probe. One of the cDNAs isolated hybridizes to a 1.8 kb mRNA present in all four tissues of the placenta as well as to every nucleated tissue and cell line tested. The sequence of the full-length cDNA was determined. An exte...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/18.13.3871

    authors： Liebhaber SA,Emery JG,Urbanek M,Wang XK,Cooke NE

    更新日期：1990-07-11 00:00:00

  • Extension of helix II of an HIV-1-directed hammerhead ribozyme with long antisense flanks does not alter kinetic parameters in vitro but causes loss of the inhibitory potential in living cells.

    abstract：:When designed to cleave a target RNA in trans, the hammerhead ribozyme contains two antisense flanks which form helix I and helix III by pairing with the complementary target RNA. The sequences forming helix II are contained on the ribozyme strand and represent a major structural component of the hammerhead structure....

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/22.19.3951

    authors： Homann M,Tabler M,Tzortzakaki S,Sczakiel G

    更新日期：1994-09-25 00:00:00

  • A novel technique for the identification of CpG islands exhibiting altered methylation patterns (ICEAMP).

    abstract：:Aberrant CpG methylation changes occurring during tumour progression include the loss (hypomethylation) and gain (hypermethylation) of methyl groups. Techniques currently available for examining such changes either require selection of a region, then examination of methylation changes, or utilise methylation-sensitive...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/29.24.e123

    authors： Brock GJ,Huang TH,Chen CM,Johnson KJ

    更新日期：2001-12-15 00:00:00

  • The impact of trans-regulation on the evolutionary rates of metazoan proteins.

    abstract：:Transcription factor (TF) and microRNA (miRNA) are two crucial trans-regulatory factors that coordinately control gene expression. Understanding the impacts of these two factors on the rate of protein sequence evolution is of great importance in evolutionary biology. While many biological factors associated with evolu...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkt349

    authors： Chen YC,Cheng JH,Tsai ZT,Tsai HK,Chuang TJ

    更新日期：2013-07-01 00:00:00

  • End-bridging is required for pol mu to efficiently promote repair of noncomplementary ends by nonhomologous end joining.

    abstract：:DNA polymerase mu is a member of the mammalian pol X family and reduces deletion during chromosome break repair by nonhomologous end joining (NHEJ). This biological role is linked to pol mu's ability to promote NHEJ of ends with noncomplementary 3' overhangs, but questions remain regarding how it performs this role. W...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkn164

    authors： Davis BJ,Havener JM,Ramsden DA

    更新日期：2008-05-01 00:00:00

  • Degeneration of a homing endonuclease and its target sequence in a wild yeast strain.

    abstract：:Mobile introns and inteins self-propagate by 'homing', a gene conversion process initiated by site-specific homing endonucleases. The VMA intein, which encodes the PI-SceI endonuclease in Saccharomyces cerevisiae, is present in several different yeast strains. Surprisingly, a wild wine yeast (DH1-1A) contains not only...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/29.20.4215

    authors： Gimble FS

    更新日期：2001-10-15 00:00:00

  • Next-generation RNA-based fluorescent biosensors enable anaerobic detection of cyclic di-GMP.

    abstract：:Bacteria occupy a diverse set of environmental niches with differing oxygen availability. Anaerobic environments such as mammalian digestive tracts and industrial reactors harbor an abundance of both obligate and facultative anaerobes, many of which play significant roles in human health and biomanufacturing. Studying...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkw580

    authors： Wang XC,Wilson SC,Hammond MC

    更新日期：2016-09-30 00:00:00

  • H-DNA and Z-DNA in the mouse c-Ki-ras promoter.

    abstract：:The mouse c-Ki-ras protooncogene promoter contains a homopurine-homopyrimidine domain that exhibits S1 nuclease sensitivity in vitro. We have studied the structure of this DNA region in a supercoiled state using a number of chemical probes for non-B DNA conformations including diethyl pyrocarbonate, osmium tetroxide, ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/19.23.6527

    authors： Pestov DG,Dayn A,Siyanova EYu,George DL,Mirkin SM

    更新日期：1991-12-11 00:00:00

  • Alternatively spliced p53 RNA in transformed and normal cells of different tissue types.

    abstract：:The alternatively spliced RNA species of tumor suppressor gene p53, containing an additional 96 bases derived from intron 10, is present at approximately 25 to 30% the level of regularly spliced p53 RNA in both normal epidermal and carcinoma cells. The presence of this alternatively spliced RNA in 10T1/2 fibroblast ce...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/20.8.1979

    authors： Han KA,Kulesz-Martin MF

    更新日期：1992-04-25 00:00:00

  • The MH1 domain of Smad3 interacts with Pax6 and represses autoregulation of the Pax6 P1 promoter.

    abstract：:Pax6 transcription is under the control of two main promoters (P0 and P1), and these are autoregulated by Pax6. Additionally, Pax6 expression is under the control of the TGFbeta superfamily, although the precise mechanisms of such regulation are not understood. The effect of TGFbeta on Pax6 expression was studied in t...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkl1105

    authors： Grocott T,Frost V,Maillard M,Johansen T,Wheeler GN,Dawes LJ,Wormstone IM,Chantry A

    更新日期：2007-01-01 00:00:00

  • Impact of probe annotation on the integration of miRNA-mRNA expression profiles for miRNA target detection.

    abstract：:MicroRNAs (miRNAs) are small non-coding RNAs that mediate gene expression at the post-transcriptional and translational levels by an imperfect binding to target mRNA 3'UTR regions. While the ab-initio computational prediction of miRNA-mRNA interactions still poses significant challenges, it is possible to overcome som...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkp1239

    authors： Sales G,Coppe A,Bicciato S,Bortoluzzi S,Romualdi C

    更新日期：2010-04-01 00:00:00

  • Force and twist dependence of RepC nicking activity on torsionally-constrained DNA molecules.

    abstract：:Many bacterial plasmids replicate by an asymmetric rolling-circle mechanism that requires sequence-specific recognition for initiation, nicking of one of the template DNA strands and unwinding of the duplex prior to subsequent leading strand DNA synthesis. Nicking is performed by a replication-initiation protein (Rep)...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkw689

    authors： Pastrana CL,Carrasco C,Akhtar P,Leuba SH,Khan SA,Moreno-Herrero F

    更新日期：2016-10-14 00:00:00

  • Human epidermal growth factor precursor: cDNA sequence, expression in vitro and gene organization.

    abstract：:Complementary DNA clones encoding the human kidney epidermal growth factor (EGF) precursor have been isolated and sequenced. They predict the sequence of a 1,207 amino acid protein which contains EGF flanked by polypeptide segments of 970 and 184 residues at its NH2- and COOH-termini, respectively. The structural orga...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/14.21.8427

    authors： Bell GI,Fong NM,Stempien MM,Wormsted MA,Caput D,Ku LL,Urdea MS,Rall LB,Sanchez-Pescador R

    更新日期：1986-11-11 00:00:00

  • The bacteriophage lambda O and P protein initiators promote the replication of single-stranded DNA.

    abstract：:A soluble enzyme system that specifically initiates lambda dv plasmid DNA replication at a bacteriophage lambda replication origin [Wold et al. (1982) Proc. Natl. Acad. Sci. USA 79, 6176-6180] is also capable of replicating the single-stranded circular chromosomes of phages M13 and phi X174 to a duplex form. This chai...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/12.7.3069

    authors： LeBowitz JH,McMacken R

    更新日期：1984-04-11 00:00:00

  • Anisotropic overall and internal motions of short DNA fragments.

    abstract：:Anisotropic motions of DNA fragments in the size range 6-118 base pairs are studied by the steady-state fluorescence polarization of different excitation transitions in the intercalated ethidium cation. Calculated effective tumbling and twisting times are found to be shorter than predicted for overall motions of rigid...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/14.9.3945

    authors： Härd T,Kearns DR

    更新日期：1986-05-12 00:00:00

  • Highly recurring sequence elements identified in eukaryotic DNAs by computer analysis are often homologous to regulatory sequences or protein binding sites.

    abstract：:We have used computer assisted dot matrix and oligonucleotide frequency analyses to identify highly recurring sequence elements of 7-11 base pairs in eukaryotic genes and viral DNAs. Such elements are found much more frequently than expected, often with an average spacing of a few hundred base pairs. Furthermore, the ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/15.4.1835

    authors： Bodnar JW,Ward DC

    更新日期：1987-02-25 00:00:00

  • The effects of a unique D-loop structure of a minor tRNA(UUALeu) from Streptomyces on its structural stability and amino acid accepting activity.

    abstract：:Streptomyces bldA gene, which encodes a tRNA corresponding to a very minor leucine codon, UUA, regulates pleiotropic gene expression which is involved in sporulation and secondary metabolism. The unique structural feature of this tRNA is the lack of GG sequence in dihydrouridine loop (D-loop) that generally is conserv...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/20.15.3911

    authors： Ueda Y,Kumagai I,Miura K

    更新日期：1992-08-11 00:00:00

  • Dissecting cancer heterogeneity with a probabilistic genotype-phenotype model.

    abstract：:One of the obstacles hindering a better understanding of cancer is its heterogeneity. However, computational approaches to model cancer heterogeneity have lagged behind. To bridge this gap, we have developed a new probabilistic approach that models individual cancer cases as mixtures of subtypes. Our approach can be s...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkt577

    authors： Cho DY,Przytycka TM

    更新日期：2013-09-01 00:00:00

  • Structural and functional properties of ribosomal protein L7 from humans and rodents.

    abstract：:By subtractive screening of a library made from mRNA of lipopolysaccharide (LPS)-stimulated mouse B lymphocytes we isolated cDNA-clones encoding the ribosomal protein L7. Human L7 mRNA was cloned from activated T-lymphocytes. Although no specific function of L7 in the translation apparatus is known as yet, it should b...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/21.2.223

    authors： Hemmerich P,von Mikecz A,Neumann F,Sözeri O,Wolff-Vorbeck G,Zoebelein R,Krawinkel U

    更新日期：1993-01-25 00:00:00

  • A group II intron in the Neurospora mitochondrial coI gene: nucleotide sequence and implications for splicing and molecular evolution.

    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

    authors： Field DJ,Sommerfield A,Saville BJ,Collins RA

    更新日期：1989-11-25 00:00:00

  • Identification and classification of bacterial Type III toxin-antitoxin systems encoded in chromosomal and plasmid genomes.

    abstract：:Toxin-antitoxin systems are widespread in bacteria and archaea. They perform diverse functional roles, including the generation of persistence, maintenance of genetic loci and resistance to bacteriophages through abortive infection. Toxin-antitoxin systems have been divided into three types, depending on the nature of...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gks231

    authors： Blower TR,Short FL,Rao F,Mizuguchi K,Pei XY,Fineran PC,Luisi BF,Salmond GP

    更新日期：2012-07-01 00:00:00

  • Sequence analysis of T1 ribonuclease fragments of 18S ribosomal RNA by 5'-terminal labeling, partial digestion, and homochromatography fingerprinting.

    abstract：:The method employed to determine the sequence of a T1 RNase fragment, A-A-A-A-A-U-A-A-C-A-A-U-A-C-A-Gp, from Novikoff rat hepatoma 18S ribosomal RNA is described. This method is applicable to any oligoribonucleotide produced by specific endonucleases that leave the newly cleaved 5'-end free for labeling with polynucle...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/4.2.339

    authors： Fuke M,Busch H

    更新日期：1977-02-01 00:00:00

  • M.HhaI binds tightly to substrates containing mismatches at the target base.

    abstract：:The (cytosine-5) DNA methyltransferase M.HhaI causes its target cytosine base to be flipped completely out of the DNA helix upon binding. We have investigated the effects of replacing the target cytosine by other, mismatched bases, including adenine, guanine, thymine and uracil. We find that M.HhaI binds more tightly ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/23.8.1388

    authors： Klimasauskas S,Roberts RJ

    更新日期：1995-04-25 00:00:00

  • ExPASy: SIB bioinformatics resource portal.

    abstract：:ExPASy (http://www.expasy.org) has worldwide reputation as one of the main bioinformatics resources for proteomics. It has now evolved, becoming an extensible and integrative portal accessing many scientific resources, databases and software tools in different areas of life sciences. Scientists can henceforth access s...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gks400

    authors： Artimo P,Jonnalagedda M,Arnold K,Baratin D,Csardi G,de Castro E,Duvaud S,Flegel V,Fortier A,Gasteiger E,Grosdidier A,Hernandez C,Ioannidis V,Kuznetsov D,Liechti R,Moretti S,Mostaguir K,Redaschi N,Rossier G,Xenarios

    更新日期：2012-07-01 00:00:00