当前位置： SCI文献检索 > NUCLEIC ACIDS RESEARCH期刊下所有文献 > Determination of the molecular weight of DNA-bound protein(s) responsible for gel electrophoretic mobility shift of linear DNA fragments examplified with purified viral myb protein.

Determination of the molecular weight of DNA-bound protein(s) responsible for gel electrophoretic mobility shift of linear DNA fragments examplified with purified viral myb protein.

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 a function of the molecular weight (MW) of the bound protein(s). Based on the evaluation of the lac repressor induced mobility shift of a 203 bp DNA fragment containing the lac operator in a 5% non-denaturating polyacrylamide gel a direct proportionality could be shown between (m/m'-1) and MW with the proportionality factor K = 215 kDa. The factor K depends on the acrylamide concentration in the gel, getting lower values with increasing acrylamide concentrations. A calculation is given to determine the molecular weight of DNA-binding factors responsible for the decreased electrophoretic mobility of a linear DNA fragment. As an example this calculation was used in order to analyse DNA-binding of the isolated viral myb protein. It could be demonstrated that the viral myb protein binds to DNA as a monomer and as a dimer.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Bading H

doi

10.1093/nar/16.12.5241

subject

Has Abstract

pub_date

1988-06-24 00:00:00

pages

5241-8

issue

12

eissn

0305-1048

issn

1362-4962

journal_volume

16

pub_type

杂志文章

相关文献

NUCLEIC ACIDS RESEARCH文献大全
  • The DNA binding affinity of HhaI methylase is increased by a single amino acid substitution in the catalytic center.

    abstract：:The HhaI methyltransferase recognizes the sequence GCGC and transfers a methyl group to C5 of the first cytosine residue. All m5C-methyltransferases contain a highly conserved sequence motif called the P-C motif. The cysteine residue of this motif is involved in catalysis by forming a covalent bond with the 6-position...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/21.10.2459

    authors： Mi S,Roberts RJ

    更新日期：1993-05-25 00:00:00

  • Isolation and characterization of the DNA fraction of rat liver chromatin which binds polylysine.

    abstract：:The structure of eukaryotic chromatin has been investigated by isolating and analyzing the "accessible" DNA fraction of rat liver chromatin. This DNA fraction has been isolated by titrating the chromatin with the protese-resistant D isomer of polylysine to bind the "accessible" DNA sites. After removal of chromosomal ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/2.5.667

    authors： Arnold EA,Wahn U,Young KE

    更新日期：1975-05-01 00:00:00

  • Investigation of Mg2+- and temperature-dependent folding of the hairpin ribozyme by photo-crosslinking: effects of photo-crosslinker tether length and chemistry.

    abstract：:We have used photo-crosslinking to investigate the structure and dynamics of four-way junction hairpin ribozyme constructs. Four phenylazide photo-crosslinkers were coupled to 2'-NH2-modified U+2 in the substrate and irradiated at different Mg2+ concentrations and temperatures. Consistent with the role of divalent met...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gki237

    authors： Borda EJ,Sigurdsson ST

    更新日期：2005-02-18 00:00:00

  • Degradation of initiator tRNAMet by Xrn1/2 via its accumulation in the nucleus of heat-treated HeLa cells.

    abstract：:Stress response mechanisms that modulate the dynamics of tRNA degradation and accumulation from the cytoplasm to the nucleus have been studied in yeast, the rat hepatoma and human cells. In the current study, we investigated tRNA degradation and accumulation in HeLa cells under various forms of stress. We found that i...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkt153

    authors： Watanabe K,Miyagawa R,Tomikawa C,Mizuno R,Takahashi A,Hori H,Ijiri K

    更新日期：2013-04-01 00:00:00

  • 2'-O-methyl, 2'-O-ethyl oligoribonucleotides and phosphorothioate oligodeoxyribonucleotides as inhibitors of the in vitro U7 snRNP-dependent mRNA processing event.

    abstract：:We describe the synthesis of 2'-O-methyl, 2'-O-ethyl oligoribonucleotides and phosphorothioate oligodeoxyribonucleotides and demonstrate their utility as inhibitors of the in vitro U7 snRNP-dependent mRNA processing event. These 2'-O-modified compounds were designed to possess the binding affinity of an RNA molecule t...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/19.10.2629

    authors： Cotten M,Oberhauser B,Brunar H,Holzner A,Issakides G,Noe CR,Schaffner G,Wagner E,Birnstiel ML

    更新日期：1991-05-25 00:00:00

  • Hierarchy of nonhomologous end-joining, single-strand annealing and gene conversion at site-directed DNA double-strand breaks.

    abstract：:In mammalian cells, DNA double-strand breaks (DSBs) are repaired by three pathways, nonhomologous end-joining (NHEJ), gene conversion (GC) and single-strand annealing (SSA). These pathways are distinct with regard to repair efficiency and mutagenic potential and must be tightly controlled to preserve viability and gen...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkn347

    authors： Mansour WY,Schumacher S,Rosskopf R,Rhein T,Schmidt-Petersen F,Gatzemeier F,Haag F,Borgmann K,Willers H,Dahm-Daphi J

    更新日期：2008-07-01 00:00:00

  • ΔNp63 activates the Fanconi anemia DNA repair pathway and limits the efficacy of cisplatin treatment in squamous cell carcinoma.

    abstract：:TP63, a member of the p53 gene family gene, encodes the ΔNp63 protein and is one of the most frequently amplified genes in squamous cell carcinomas (SCC) of the head and neck (HNSCC) and lungs (LUSC). Using an epiallelic series of siRNAs with intrinsically different knockdown abilities, we show that the complete loss ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkw036

    authors： Bretz AC,Gittler MP,Charles JP,Gremke N,Eckhardt I,Mernberger M,Mandic R,Thomale J,Nist A,Wanzel M,Stiewe T

    更新日期：2016-04-20 00:00:00

  • Highly specific and sensitive method for measuring nucleotide excision repair kinetics of ultraviolet photoproducts in human cells.

    abstract：:The nucleotide excision repair pathway removes ultraviolet (UV) photoproducts from the human genome in the form of short oligonucleotides ∼ 30 nt in length. Because there are limitations to many of the currently available methods for investigating UV photoproduct repair in vivo, we developed a convenient non-radioisot...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkt1179

    authors： Choi JH,Gaddameedhi S,Kim SY,Hu J,Kemp MG,Sancar A

    更新日期：2014-02-01 00:00:00

  • Spectral clustering of protein sequences.

    abstract：:An important problem in genomics is automatically clustering homologous proteins when only sequence information is available. Most methods for clustering proteins are local, and are based on simply thresholding a measure related to sequence distance. We first show how locality limits the performance of such methods by...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkj515

    authors： Paccanaro A,Casbon JA,Saqi MA

    更新日期：2006-03-17 00:00:00

  • Consensus inverted terminal repeat sequence of Paramecium IESs: resemblance to termini of Tc1-related and Euplotes Tec transposons.

    abstract：:During the formation of a transcriptionally active macronucleus, ciliated protozoa excise large numbers of interstitial segments of DNA (internal eliminated sequences; IESs) from their chromosomes. In this study we analyze the published sequences of 20 IESs that interrupt surface protein genes of Paramecium and identi...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/23.11.2006

    authors： Klobutcher LA,Herrick G

    更新日期：1995-06-11 00:00:00

  • The FSSP database: fold classification based on structure-structure alignment of proteins.

    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

    authors： Holm L,Sander C

    更新日期：1996-01-01 00:00:00

  • Characterization of hybridization between synthetic oligodeoxynucleotides and RNA in living cells.

    abstract：:Cells internalized synthetic oligonucleotides (oligos) in culture. The hybridization of these molecules to target RNA in the living cell was subsequently detected and characterized after fixation of the cells, with or without previous detergent extraction. Hybridized oligo was distinguished from free oligo in the cell...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/23.24.4946

    authors： Politz JC,Taneja KL,Singer RH

    更新日期：1995-12-25 00:00:00

  • Human CTF18-RFC clamp-loader complexed with non-synthesising DNA polymerase ε efficiently loads the PCNA sliding clamp.

    abstract：:The alternative proliferating-cell nuclear antigen (PCNA)-loader CTF18-RFC forms a stable complex with DNA polymerase ε (Polε). We observed that, under near-physiological conditions, CTF18-RFC alone loaded PCNA inefficiently, but loaded it efficiently when complexed with Polε. During efficient PCNA loading, CTF18-RFC ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkx096

    authors： Fujisawa R,Ohashi E,Hirota K,Tsurimoto T

    更新日期：2017-05-05 00:00:00

  • Efficient detection of RNA-protein interactions using tethered RNAs.

    abstract：:The diverse localization of transcripts in cells suggests that there are many specific RNA-protein interactions that have yet to be identified. Progress has been limited, however, by the lack of a robust method to detect and isolate the RNA-binding proteins. Here we describe the use of an RNA aptamer, scaffolded to a ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkq1316

    authors： Iioka H,Loiselle D,Haystead TA,Macara IG

    更新日期：2011-04-01 00:00:00

  • SIGNOR 2.0, the SIGnaling Network Open Resource 2.0: 2019 update.

    abstract：:The SIGnaling Network Open Resource 2.0 (SIGNOR 2.0) is a public repository that stores signaling information as binary causal relationships between biological entities. The captured information is represented graphically as a signed directed graph. Each signaling relationship is associated to an effect (up/down-regul...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkz949

    authors： Licata L,Lo Surdo P,Iannuccelli M,Palma A,Micarelli E,Perfetto L,Peluso D,Calderone A,Castagnoli L,Cesareni G

    更新日期：2020-01-08 00:00:00

  • A genome-wide analysis of Cas9 binding specificity using ChIP-seq and targeted sequence capture.

    abstract：:Clustered regularly interspaced short palindromic repeat (CRISPR) RNA-guided nucleases have gathered considerable excitement as a tool for genome engineering. However, questions remain about the specificity of target site recognition. Cleavage specificity is typically evaluated by low throughput assays (T7 endonucleas...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkv137

    authors： O'Geen H,Henry IM,Bhakta MS,Meckler JF,Segal DJ

    更新日期：2015-03-31 00:00:00

  • Metal sensing and regulation of adaptive responses to manganese limitation by MtsR is critical for group A streptococcus virulence.

    abstract：:Pathogenic bacteria encounter host-imposed manganese (Mn) limitation during infection. Herein we report that in the human pathogen Streptococcus pyogenes, the adaptive response to Mn limitation is controlled by a DtxR family metalloregulator, MtsR. Genes upregulated by MtsR during Mn limitation include Mn (mtsABC) and...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkz524

    authors： Do H,Makthal N,Chandrangsu P,Olsen RJ,Helmann JD,Musser JM,Kumaraswami M

    更新日期：2019-08-22 00:00:00

  • Analysis of recombination in mammalian cells using SV40 genome segments having homologous overlapping termini.

    abstract：:Segments of SV40 DNA having homologous overlapping termini recombine to produce viable genomes in monkey cells. Frequencies of recombination on either side of a deletion marker are non-random; replication and palindromes do not appear to be essential. Since recombination involves host enzymes, a suitable system has be...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/8.12.2725

    authors： Upcroft P,Carter B,Kidson C

    更新日期：1980-06-25 00:00:00

  • Release of promoter-proximal paused Pol II in response to histone deacetylase inhibition.

    abstract：:A correlation between histone acetylation and transcription has been noted for a long time, but little is known about what step(s) in the transcription cycle is influenced by acetylation. We have examined the immediate transcriptional response to histone deacetylase (HDAC) inhibition, and find that release of promoter...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkaa234

    authors： Vaid R,Wen J,Mannervik M

    更新日期：2020-05-21 00:00:00

  • DNA replication initiates non-randomly at multiple sites near the c-myc gene in HeLa cells.

    abstract：:The origin of replication of the c-myc gene in HeLa cells was previously identified at low resolution within 3.5 kb 5' to the P1 promoter, based on replication fork polarity and the location of DNA nascent strands. To define the initiation events in the c-myc origin at higher resolution the template bias of nascent DN...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/24.10.1887

    authors： Waltz SE,Trivedi AA,Leffak M

    更新日期：1996-05-15 00:00:00

  • Annealing helicase HARP closes RPA-stabilized DNA bubbles non-processively.

    abstract：:We investigate the mechanistic nature of the Snf2 family protein HARP, mutations of which are responsible for Schimke immuno-osseous dysplasia. Using a single-molecule magnetic tweezers assay, we construct RPA-stabilized DNA bubbles within torsionally constrained DNA to investigate the annealing action of HARP on a ph...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkx147

    authors： Burnham DR,Nijholt B,De Vlaminck I,Quan J,Yusufzai T,Dekker C

    更新日期：2017-05-05 00:00:00

  • PubChem in 2021: new data content and improved web interfaces.

    abstract：:PubChem (https://pubchem.ncbi.nlm.nih.gov) is a popular chemical information resource that serves the scientific community as well as the general public, with millions of unique users per month. In the past two years, PubChem made substantial improvements. Data from more than 100 new data sources were added to PubChem...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkaa971

    authors： Kim S,Chen J,Cheng T,Gindulyte A,He J,He S,Li Q,Shoemaker BA,Thiessen PA,Yu B,Zaslavsky L,Zhang J,Bolton EE

    更新日期：2021-01-08 00:00:00

  • Effects of temperature on excluded volume-promoted cyclization and concatemerization of cohesive-ended DNA longer than 0.04 Mb.

    abstract：:The 0.048502 megabase (Mb), primarily double-stranded DNA of bacteriophage lambda has single-stranded, complementary termini (cohesive ends) that undergo either spontaneous intramolecular joining to form open circular DNA or spontaneous intermolecular joining to form linear, end-to-end oligomeric DNAs (concatemers); c...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/19.11.3047

    authors： Louie D,Serwer P

    更新日期：1991-06-11 00:00:00

  • Combining structure probing data on RNA mutants with evolutionary information reveals RNA-binding interfaces.

    abstract：:Systematic structure probing experiments (e.g. SHAPE) of RNA mutants such as the mutate-and-map (MaM) protocol give us a direct access into the genetic robustness of ncRNA structures. Comparative studies of homologous sequences provide a distinct, yet complementary, approach to analyze structural and functional proper...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkw217

    authors： Reinharz V,Ponty Y,Waldispühl J

    更新日期：2016-06-20 00:00:00

  • Complex cis-elements determine an RNA editing site in pea mitochondria.

    abstract：:The cis-requirements for the first editing site in the atp9 mRNA from pea mitochondria were investigated in an in vitro RNA editing system. Template RNAs deleted 5' of -20 are edited correctly, but with decreased efficiency. Deletions between -20 and the edited nucleotide abolish editing activity. Substitution of the ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkh763

    authors： Takenaka M,Neuwirt J,Brennicke A

    更新日期：2004-08-04 00:00:00

  • The Mouse Gene Expression Database (GXD).

    abstract：:The Gene Expression Database (GXD) is a community resource of gene expression information for the laboratory mouse. By combining the different types of expression data, GXD aims to provide increasingly complete information about the expression profiles of genes in different mouse strains and mutants, thus enabling val...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/29.1.98

    authors： Ringwald M,Eppig JT,Begley DA,Corradi JP,McCright IJ,Hayamizu TF,Hill DP,Kadin JA,Richardson JE

    更新日期：2001-01-01 00:00:00

  • The nucleotide sequence of chloroplast 4.5S rRNA from a fern, Dryopteris acuminata.

    abstract：:The 4.5S rRNA was isolated from the chloroplast ribosomes from Dryopteris acuminata. The complete nucleotide sequence was determined to be: OHUAAGGUCACGGCAAGACGAGCCGUUUAUCACCACGAUAGGUGCUAAGUGGAGGUGCAGUAAUGUAUGCAGCUGAGGC AUCCUAAUAGACCGAGAGGUUUGAACOH. The 4.5S rRNA is composed of 103 nucleotides and shows strong homolog...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/10.7.2257

    authors： Takaiwa F,Kusuda M,Sugiura M

    更新日期：1982-04-10 00:00:00

  • Discover 1: a new program to search for unusually represented DNA motifs.

    abstract：:DISCOVER1 (DIStribution COunter VERsion 1) is a new program that can identify DNA motifs occurring with a high deviation from the expected frequency. The program generates families of patterns, each family having a common set of defined bases. Undefined bases are inserted amongst the defined bases in different ways, t...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/21.22.5152

    authors： Valle G

    更新日期：1993-11-11 00:00:00

  • Specific hydrolysis of methionyl-tRNA Met f catalyzed by a purified peptide.

    abstract：:A peptide initiation factor purified from rat liver and promoting the binding of initiator tRNA and model initiators to 40S and 80S ribosome at an acid pH liberates methionine and N-acetylmethionine from Trna Met f at neutral reaction. Phenylalanyl-tRNA, N-acetylphenylalanyl-tRNA and methionyl-tRNA Met m are not hydro...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/2.11.2119

    authors： Hradec J

    更新日期：1975-11-01 00:00:00

  • The nucleotide sequences of two tRNAAsn genes from tobacco chloroplasts.

    abstract：:Recombinant plasmids which contain EcoRI fragments of tobacco chloroplast DNA carrying tRNA genes were constructed. Plasmids pTC211 and pTC293 contain the base sequences for tRNAAsn in their 1.4 and 1.1 Md EcoRI fragments, respectively. These two tRNA sequences are identical and are; 5'-TCCTCAGTAGCTCAGTGGTAGAGCGGTCGGC...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/9.21.5601

    authors： Kato A,Shimada H,Kusuda M,Sugiura M

    更新日期：1981-11-11 00:00:00