Gene mapping and gene enrichment by the avidin-biotin interaction: use of cytochrome-c as a polyamine bridge.

Abstract:

:A modification of previously described methods of electron microscopic gene mapping and of gene enrichment based on the avidin-biotin interaction is presented. The modification consists of coupling cytochrome-c instead of pentane diamine to the oxidized 2', 3' terminus of an RNA by Schiff base formation and BH-4 reduction. The RNA-cytochrome-c conjugate is purified by a simple chromatographic procedure; several biotins are attached to the cytochrome moiety by acylation. The extended arm between biotin and RNA gives efficient electron microscopic gene mapping of DNA:RNA-biotin hybrids with avidin-ferritin and avidin-polymethacylate sphere labels and efficient gene enrichment by buoyant banding of DNA:RNA-biotin:avidin-spheres in CsCl. A 1400 fold enrichment (thus, 25% pure) and a 90% yield of long Drosophila DNA strands with 5S RNA genes is achieved.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Sodja A,Davidson N

doi

10.1093/nar/5.2.385

subject

Has Abstract

pub_date

1978-02-01 00:00:00

pages

385-401

issue

2

eissn

0305-1048

issn

1362-4962

journal_volume

5

pub_type

杂志文章
  • Microbial species delineation using whole genome sequences.

    abstract::Increased sequencing of microbial genomes has revealed that prevailing prokaryotic species assignments can be inconsistent with whole genome information for a significant number of species. The long-standing need for a systematic and scalable species assignment technique can be met by the genome-wide Average Nucleotid...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkv657

    authors: Varghese NJ,Mukherjee S,Ivanova N,Konstantinidis KT,Mavrommatis K,Kyrpides NC,Pati A

    更新日期:2015-08-18 00:00:00

  • RPAN: rice pan-genome browser for ∼3000 rice genomes.

    abstract::A pan-genome is the union of the gene sets of all the individuals of a clade or a species and it provides a new dimension of genome complexity with the presence/absence variations (PAVs) of genes among these genomes. With the progress of sequencing technologies, pan-genome study is becoming affordable for eukaryotes w...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkw958

    authors: Sun C,Hu Z,Zheng T,Lu K,Zhao Y,Wang W,Shi J,Wang C,Lu J,Zhang D,Li Z,Wei C

    更新日期:2017-01-25 00:00:00

  • oriGNAI3: a narrow zone of preferential replication initiation in mammalian cells identified by 2D gel and competitive PCR replicon mapping techniques.

    abstract::The nature of mammalian origins of DNA replication remains controversial and this is primarily because two-dimensional gel replicon mapping techniques have identified broad zones of replication initiation whereas several other techniques, such as quantitative PCR, have disclosed more discrete sites of initiation at th...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/26.10.2313

    authors: Toledo F,Baron B,Fernandez MA,Lachagès AM,Mayau V,Buttin G,Debatisse M

    更新日期:1998-05-15 00:00:00

  • Analysis of the attachment of replicating DNA to a nuclear matrix in mammalian interphase nuclei.

    abstract::The attachment of replicating DNA to a rapidly sedimenting nuclear structure was investigated by digestion with various nucleases. When DNA was gradually removed by DNase I, pulse label incorporated during either 1 min or during 1 hour in the presence of arabinosylcytosine, remained preferentially attached to the nucl...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/6.1.219

    authors: Dijkwel PA,Mullenders LH,Wanka F

    更新日期:1979-01-01 00:00:00

  • DNA regions essential for the function of a bacteriophage fd promoter.

    abstract::The promoter for the major coat protein gene of bacteriophage fd contains a unique sequence. TATAAT, in the non-transcribed region corresponding to the Pribnow box. A R-Hha I cleavage site which destroys functions is located five pairs upstream from the TATAAT sequence (fifteen base pairs upstream from the RNA initiat...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/4.7.2213

    authors: Okamoto T,Sugimoto K,Sugisaki H,Takanami M

    更新日期:1977-07-01 00:00:00

  • Effects of hypoxanthine substitution on bleomycin-mediated DNA strand degradation in DNA-RNA hybrids.

    abstract::We have reported on the differences in site-specific cleavage between DNA and DNA-RNA hybrids by various prototypic DNA cleavers (accompanying paper). In the case of bleomycin (BLM), degradation at 5'-GC-3'sites was suppressed relative to the same sequence in double-stranded DNA, while 5'-GT-3' damage remained constan...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/25.9.1846

    authors: Bansal M,Stubbe J,Kozarich JW

    更新日期:1997-05-01 00:00:00

  • Site-directed transposon integration in human cells.

    abstract::The Sleeping Beauty (SB) transposon is a promising gene transfer vector that integrates nonspecifically into host cell genomes. Herein, we attempt to direct transposon integration into predetermined DNA sites by coupling a site-specific DNA-binding domain (DBD) to the SB transposase. We engineered fusion proteins comp...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkm089

    authors: Yant SR,Huang Y,Akache B,Kay MA

    更新日期:2007-01-01 00:00:00

  • Complex impact of DNA methylation on transcriptional dysregulation across 22 human cancer types.

    abstract::Accumulating evidence has demonstrated that transcriptional regulation is affected by DNA methylation. Understanding the perturbation of DNA methylation-mediated regulation between transcriptional factors (TFs) and targets is crucial for human diseases. However, the global landscape of DNA methylation-mediated transcr...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkaa041

    authors: Wang Z,Yin J,Zhou W,Bai J,Xie Y,Xu K,Zheng X,Xiao J,Zhou L,Qi X,Li Y,Li X,Xu J

    更新日期:2020-03-18 00:00:00

  • Array-based analysis of genomic DNA methylation patterns of the tumour suppressor gene p16INK4A promoter in colon carcinoma cell lines.

    abstract::Aberrant DNA methylation at CpG dinucleotides can result in epigenetic silencing of tumour suppressor genes and represents one of the earliest events in tumourigenesis. To date, however, high-throughput tools that are capable of surveying the methylation status of multiple gene promoters have been restricted to a limi...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gni072

    authors: Mund C,Beier V,Bewerunge P,Dahms M,Lyko F,Hoheisel JD

    更新日期:2005-04-28 00:00:00

  • Analysis of the role of Caenorhabditis elegans GC-AG introns in regulated splicing.

    abstract::GC-AG introns represent 0.7% of total human pre-mRNA introns. To study the function of GC-AG introns in splicing regulation, 196 cDNA-confirmed GC-AG introns were identified in Caenorhabditis elegans. These represent 0.6% of the cDNA- confirmed intron data set for this organism. Eleven of these GC-AG introns are invol...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkf465

    authors: Farrer T,Roller AB,Kent WJ,Zahler AM

    更新日期:2002-08-01 00:00:00

  • miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments.

    abstract::Next-generation sequencing allows now the sequencing of small RNA molecules and the estimation of their expression levels. Consequently, there will be a high demand of bioinformatics tools to cope with the several gigabytes of sequence data generated in each single deep-sequencing experiment. Given this scene, we deve...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkp347

    authors: Hackenberg M,Sturm M,Langenberger D,Falcón-Pérez JM,Aransay AM

    更新日期:2009-07-01 00:00:00

  • Pseudomonas aeruginosa MutL promotes large chromosomal deletions through non-homologous end joining to prevent bacteriophage predation.

    abstract::Pseudomonas aeruginosa is an opportunistic pathogen with a relatively large genome, and has been shown to routinely lose genomic fragments during environmental selection. However, the underlying molecular mechanisms that promote chromosomal deletion are still poorly understood. In a recent study, we showed that by del...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gky160

    authors: Shen M,Zhang H,Shen W,Zou Z,Lu S,Li G,He X,Agnello M,Shi W,Hu F,Le S

    更新日期:2018-05-18 00:00:00

  • Tetracycline-inducible gene regulation in mycobacteria.

    abstract::A system for the tetracycline-inducible regulation of gene expression in mycobacteria has been developed. We have sub-cloned the tetRO region from the Corynebacterium glutamicum TetZ locus into a mycobacterial shuttle plasmid, making expression of genes cloned downstream of tetRO responsive to tetracycline. Using the ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gni023

    authors: Blokpoel MC,Murphy HN,O'Toole R,Wiles S,Runn ES,Stewart GR,Young DB,Robertson BD

    更新日期:2005-02-01 00:00:00

  • Use of a cellular polyadenylation signal by viral transcripts in polyoma virus transformed cells.

    abstract::The DNA sequences at and around the junctions between viral and cellular DNA in the polyoma virus transformed mouse cell line, TS-A-3T3, have been determined. No common sequence specificity or structural features at the joins have been observed. The sequence indicates that the 94K truncated large T antigen found in TS...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/10.15.4515

    authors: Ruley HE,Lania L,Chaudry F,Fried M

    更新日期:1982-08-11 00:00:00

  • Novel cyanine-AMP conjugates for efficient 5' RNA fluorescent labeling by one-step transcription and replacement of [gamma-32P]ATP in RNA structural investigation.

    abstract::Two novel fluorescent cyanine-AMP conjugates, F550/570 and F650/670, have been synthesized to serve as transcription initiators under the T7 phi2.5 promoter. Efficient fluorophore labeling of 5' RNA is achieved in a single transcription step by including F550/570 and F650/670 in the transcription solution. The current...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gni036

    authors: Li N,Yu C,Huang F

    更新日期:2005-02-24 00:00:00

  • Update of the Human MitBASE database.

    abstract::Human MitBASE is a database collecting human mtDNA variants. This database is part of a greater mitochondrial genome database (MitBASE) funded within the EU Biotech Program. The present paper reports the recent improvements in data structure, data quality and data quantity. As far as the database structure is concerne...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/27.1.143

    authors: Attimonelli M,Cooper JM,D'Elia D,de Montalvo A,De Robertis M,Lehväslaiho H,Malladi SB,Memeo F,Stevens K,Schapira AH,Saccone C

    更新日期:1999-01-01 00:00:00

  • The mitoribosome-specific protein mS38 is preferentially required for synthesis of cytochrome c oxidase subunits.

    abstract::Message-specific translational regulation mechanisms shape the biogenesis of multimeric oxidative phosphorylation (OXPHOS) enzyme in mitochondria from the yeast Saccharomyces cerevisiae. These mechanisms, driven mainly by the action of mRNA-specific translational activators, help to coordinate synthesis of OXPHOS cata...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkz266

    authors: Mays JN,Camacho-Villasana Y,Garcia-Villegas R,Perez-Martinez X,Barrientos A,Fontanesi F

    更新日期:2019-06-20 00:00:00

  • Twinkle and POLG defects enhance age-dependent accumulation of mutations in the control region of mtDNA.

    abstract::Autosomal dominant and/or recessive progressive external ophthalmoplegia (ad/arPEO) is associated with mtDNA mutagenesis. It can be caused by mutations in three nuclear genes, encoding the adenine nucleotide translocator 1, the mitochondrial helicase Twinkle or DNA polymerase gamma (POLG). How mutations in these genes...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkh634

    authors: Wanrooij S,Luoma P,van Goethem G,van Broeckhoven C,Suomalainen A,Spelbrink JN

    更新日期:2004-06-04 00:00:00

  • CellBase, a comprehensive collection of RESTful web services for retrieving relevant biological information from heterogeneous sources.

    abstract::During the past years, the advances in high-throughput technologies have produced an unprecedented growth in the number and size of repositories and databases storing relevant biological data. Today, there is more biological information than ever but, unfortunately, the current status of many of these repositories is ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gks575

    authors: Bleda M,Tarraga J,de Maria A,Salavert F,Garcia-Alonso L,Celma M,Martin A,Dopazo J,Medina I

    更新日期:2012-07-01 00:00:00

  • The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities.

    abstract::The PathoSystems Resource Integration Center (PATRIC) is the bacterial Bioinformatics Resource Center funded by the National Institute of Allergy and Infectious Diseases (https://www.patricbrc.org). PATRIC supports bioinformatic analyses of all bacteria with a special emphasis on pathogens, offering a rich comparative...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkz943

    authors: Davis JJ,Wattam AR,Aziz RK,Brettin T,Butler R,Butler RM,Chlenski P,Conrad N,Dickerman A,Dietrich EM,Gabbard JL,Gerdes S,Guard A,Kenyon RW,Machi D,Mao C,Murphy-Olson D,Nguyen M,Nordberg EK,Olsen GJ,Olson RD,Overb

    更新日期:2020-01-08 00:00:00

  • Characterization of the apolipoprotein B mRNA editing enzyme: no similarity to the proposed mechanism of RNA editing in kinetoplastid protozoa.

    abstract::Intestinal apolipoprotein B mRNA is edited at nucleotide 6666 by a C to U transition resulting in a translational stop codon. The enzymatic properties of the editing activity were characterised in vitro using rat enterocyte cytosolic extract. The editing activity has no nucleotide or ion cofactor requirement. It shows...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/19.13.3569

    authors: Greeve J,Navaratnam N,Scott J

    更新日期:1991-07-11 00:00:00

  • In vitro site-directed mutagenesis with synthetic DNA oligonucleotides yields unexpected deletions and insertions at high frequency.

    abstract::We have used in vitro site-directed mutagenesis with synthetic DNA oligonucleotides to introduce single nucleotide mutations in yeast mtDNA. In addition to the expected DNA alterations we also recovered with high frequency mutants with large deletions and insertions which arose through interaction with the synthetic D...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/11.24.8595

    authors: Osinga KA,Van der Bliek AM,Van der Horst G,Groot Koerkamp MJ,Tabak HF,Veeneman GH,Van Boom JH

    更新日期:1983-12-20 00:00:00

  • HOMCOS: a server to predict interacting protein pairs and interacting sites by homology modeling of complex structures.

    abstract::As protein-protein interactions are crucial in most biological processes, it is valuable to understand how and where protein pairs interact. We developed a web server HOMCOS (Homology Modeling of Complex Structure, http://biunit.naist.jp/homcos) to predict interacting protein pairs and interacting sites by homology mo...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkn218

    authors: Fukuhara N,Kawabata T

    更新日期:2008-07-01 00:00:00

  • Cloning regions of the Drosophila genome by microdissection of polytene chromosome DNA and PCR with nonspecific primer.

    abstract::A simple and rapid procedure to isolate clones carrying sequences from a specific region of the polytene chromosome of Drosophila is demonstrated. The procedure involves microdissection of the region of interest, amplification of the DNA by PCR using a primer designed to prime the synthesis nonspecifically, labeling o...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/18.3.599

    authors: Wesley CS,Ben M,Kreitman M,Hagag N,Eanes WF

    更新日期:1990-02-11 00:00:00

  • Unwinding of primer-templates by archaeal family-B DNA polymerases in response to template-strand uracil.

    abstract::Archaeal family-B DNA polymerases bind tightly to deaminated bases and stall replication on encountering uracil in template strands, four bases ahead of the primer-template junction. Should the polymerase progress further towards the uracil, for example, to position uracil only two bases in front of the junction, 3'-5...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gks1364

    authors: Richardson TT,Wu X,Keith BJ,Heslop P,Jones AC,Connolly BA

    更新日期:2013-02-01 00:00:00

  • Long W tracts are over-represented in the Escherichia coli and Haemophilus influenzae genomes.

    abstract::The occurrence of DNA tracts of the three binary base combinations: R.Y, K.M and W;S has been mapped in the complete genomes of Haemophilus influenzae and Escherichia coli. A highly significant over-representation of W tracts is observed in both bacteria. The excess of W tracts is particularly striking in the 10% inte...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/27.22.4491

    authors: Shomer B,Yagil G

    更新日期:1999-11-15 00:00:00

  • Specific ribosomal RNA recognition by a fragment of E. coli ribosomal protein S4 missing the C-terminal 36 amino acid residues.

    abstract::We have previously investigated the role of the N-terminal region of ribosomal protein S4 to participate in 30S ribosome assembly and function (1-3). In this report we extend these studies to the two fragments produced by the chemical cleavage of protein S4 at the tryptophan residue 167. We find that the carboxyl term...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/13.17.6343

    authors: Changchien LM,Craven GR

    更新日期:1985-09-11 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

  • RAG2's non-core domain contributes to the ordered regulation of V(D)J recombination.

    abstract::Variable (diversity) joining [V(D)J] recombination of immune gene loci proceeds in an ordered manner with D to J portions recombining first and then an upstream V joins that recombinant. We present evidence that the non-core domain of recombination activating gene (RAG) protein 2 is involved in the regulation of recom...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkn553

    authors: Curry JD,Schlissel MS

    更新日期:2008-10-01 00:00:00

  • Sequence-specific DNA recognition by the thyroid transcription factor-1 homeodomain.

    abstract::The molecular basis for the DNA binding specificity of the thyroid transcription factor 1 homeodomain (TTF-1HD) has been investigated. Methylation and ethylation interference experiments show that the TTF-1HD alone recapitulates the DNA binding properties of the entire protein. Studies carried out with mutant derivati...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/22.15.3075

    authors: Damante G,Fabbro D,Pellizzari L,Civitareale D,Guazzi S,Polycarpou-Schwartz M,Cauci S,Quadrifoglio F,Formisano S,Di Lauro R

    更新日期:1994-08-11 00:00:00