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 comprised of a hyperactive SB transposase (HSB5) joined via a variable-length linker to either end of the polydactyl zinc-finger protein E2C, which binds a unique sequence on human chromosome 17. Although DBD linkage to the C-terminus of SB abolished activity in a human cell transposition assay, the N-terminal addition of the E2C or Gal4 DBD did not. Molecular analyses indicated that these DBD-SB fusion proteins retained DNA-binding specificity for their respective substrate molecules and were capable of mediating bona fide transposition reactions. We also characterized transposon integrations in the presence of the E2C-SB fusion protein to determine its potential to target predefined DNA sites. Our results indicate that fusion protein-mediated tethering can effectively redirect transposon insertion site selection in human cells, but suggest that stable docking of integration complexes may also partially interfere with the cut-and-paste mechanism. These findings illustrate the feasibility of directed transposon integration and highlight potential means for future development.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Yant SR,Huang Y,Akache B,Kay MAdoi
10.1093/nar/gkm089subject
Has Abstractpub_date
2007-01-01 00:00:00pages
e50issue
7eissn
0305-1048issn
1362-4962pii
gkm089journal_volume
35pub_type
杂志文章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
更新日期:1984-04-11 00:00:00
abstract::The gene encoding the DNA methyltransferase M.CviRI from Chlorella virus XZ-6E was cloned and expressed in Escherichia coli. M.CviRI methylates adenine in TGCA sequences. DNA containing the M.CviRI gene was sequenced and a single open reading frame of 1137 bp was identified which could code for a polypeptide of 379 am...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.2.307
更新日期:1991-01-25 00:00:00
abstract::The isolation and characterization of deletion mutants of the bacteriocinogenic plasmid Clo DF13 is described. To construct these deletion mutants, DNA of Clo DF13::Tn901 and Clo DF13-rep3::Tn901 plasmids was digested with restriction endonucleases, ligated with T4 ligase and introduced by transformation into Escheric...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/5.6.1801
更新日期:1978-06-01 00:00:00
abstract::A small cloned DNA segment previously shown to contain all genetic information for the expression of the tRNA1met gene of Xenopus laevis was cleaved into an anterior and posterior portion by Hae III restriction. Both restriction fragments were cloned in pCR1 using EcoRI linkers. Starting from these tDNA subclones, a s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/7.7.1749
更新日期:1979-12-11 00:00:00
abstract::Chewie Nomenclature Server (chewie-NS, https://chewbbaca.online/) allows users to share genome-based gene-by-gene typing schemas and to maintain a common nomenclature, simplifying the comparison of results. The combination between local analyses and a public repository of allelic data strikes a balance between potenti...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa889
更新日期:2021-01-08 00:00:00
abstract::Protein-RNA interactions play essential roles in a number of regulatory mechanisms for gene expression such as RNA splicing, transport, translation and post-transcriptional control. As the number of available protein-RNA complex 3D structures has increased, it is now possible to statistically examine protein-RNA inter...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl819
更新日期:2006-01-01 00:00:00
abstract::Cpf1 nucleases were recently reported to be highly specific and programmable nucleases with efficiencies comparable to those of SpCas9. AsCpf1 and LbCpf1 require a single crRNA and recognize a 5'-TTTN-3' protospacer adjacent motif (PAM) at the 5' end of the protospacer for genome editing. For widespread application in...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx783
更新日期:2017-11-02 00:00:00
abstract::We have determined the three-dimensional structure of a non-selfcomplementary nonanucleotide duplex which contains an abasic (apyrimidinic) site in the centre, i.e. a deoxyribose residue opposite an adenosine. The majority of the base and sugar proton resonances were assigned by NOESY, COSY and 2DQF spectra in D2O and...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.19.8003
更新日期:1987-10-12 00:00:00
abstract::Many complex viruses package their genomes into empty protein shells and bacteriophages of the Cystoviridae family provide some of the simplest models for this. The cystoviral hexameric NTPase, P4, uses chemical energy to translocate single-stranded RNA genomic precursors into the procapsid. We previously dissected th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt713
更新日期:2013-11-01 00:00:00
abstract::A nucleic acid affinity matrix containing a short oligodeoxynucleotide ligand has been prepared as an example of a material which can be used for the rapid and effective isolation of sequence specific DNA binding proteins. Two complementary oligodeoxynucleotides have been employed, one of which contains a small 5'-spa...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.21.10283
更新日期:1988-11-11 00:00:00
abstract::We describe a method for anchoring bacteriophage lambda DNA by one end to gold by Au-biotin-streptavidin-biotin-DNA bonds. DNA anchored to a microfabricated Au line could be aligned and stretched in flow and electric fields. The anchor was shown to resist a force of at least 11 pN, a linkage strong enough to allow DNA...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.3.492
更新日期:1994-02-11 00:00:00
abstract::The role of uracil in genomic DNA has been recently re-evaluated. It is now widely accepted to be a physiologically important DNA element in diverse systems from specific phages to antibody maturation and Drosophila development. Further relevant investigations would largely benefit from a novel reliable and fast metho...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv977
更新日期:2016-02-18 00:00:00
abstract::Adenosine to inosine editing of mRNA from the human 5-HT2C receptor gene (HTR2C) occurs at five exonic positions (A-E) in a stable stem-loop that includes the normal 5' splice site of intron 5 and is flanked by two alternative splice sites. Using in vitro editing, we identified a novel editing site (F) located in the ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh536
更新日期:2004-04-15 00:00:00
abstract::IGF2 mRNA-binding protein 1 (IMP1) is a key regulator of messenger RNA (mRNA) metabolism and transport in organismal development and, in cancer, its mis-regulation is an important component of tumour metastasis. IMP1 function relies on the recognition of a diverse set of mRNA targets that is mediated by the combinator...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz136
更新日期:2019-05-07 00:00:00
abstract::The RNA 3D Structure-to-Multiple Sequence Alignment Server (R3D-2-MSA) is a new web service that seamlessly links RNA three-dimensional (3D) structures to high-quality RNA multiple sequence alignments (MSAs) from diverse biological sources. In this first release, R3D-2-MSA provides manual and programmatic access to cu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv543
更新日期:2015-07-01 00:00:00
abstract::The KEGG RPAIR database is a collection of biochemical structure transformation patterns, called RDM patterns, and chemical structure alignments of substrate-product pairs (reactant pairs) in all known enzyme-catalyzed reactions taken from the Enzyme Nomenclature and the KEGG PATHWAY database. Here, we present PathPre...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq318
更新日期:2010-07-01 00:00:00
abstract::The early DNa products of reverse transcription have been analyzed from reconstructed reactions containing avian myeloblastosis virus 35S RNA . tRNAtrp complex and highly purified reverse transcriptase. We describe conditions for the synthesis of genome-length complementary DNA and two discrete species of plus strand ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.3.1009
更新日期:1982-02-11 00:00:00
abstract::Correlation of motif occurrences with gene expression intensity is an effective strategy for elucidating transcriptional cis-regulatory logic. Here we demonstrate that this approach can also identify cis-regulatory elements for alternative pre-mRNA splicing. Using data from a human exon microarray, we identified 56 ca...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm485
更新日期:2007-01-01 00:00:00
abstract::The three dimensional structures for representatives of nearly half of all protein families are now available in public databases. Thus, no matter which protein one investigates, it is increasingly likely that the 3D structure of a homolog will be known and may reveal unsuspected structure-function relationships. The ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.1.240
更新日期:1999-01-01 00:00:00
abstract::Despite the development of new high-throughput sequencing techniques, microarrays are still attractive tools to study small genome organisms, thanks to sample multiplexing and high-feature densities. However, the oligonucleotide design remains a delicate step for most users. A vast array of software is available to de...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq110
更新日期:2010-06-01 00:00:00
abstract::In the field of RNA, the technologies for studying the transcriptome have created a tremendous potential for deciphering the puzzles of the RNA biology. Along with the excitement, the unprecedented volume of RNA related omics data is creating great challenges in bioinformatics analyses. Here, we present the RNA Centri...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx120
更新日期:2017-06-02 00:00:00
abstract::Nitrated polycyclic aromatic hydrocarbons are common environmental pollutants, of which many are mutagenic and carcinogenic. 1-Nitropyrene is the most abundant nitrated polycyclic aromatic hydrocarbon, which causes DNA damage and is carcinogenic in experimental animals. Error-prone translesion synthesis of 1-nitropyre...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks1296
更新日期:2013-02-01 00:00:00
abstract::Accumulation of replicative intermediates of the bacteriophage phi X174 was observed in E. coli C infected cells when phage DNA methylation has been inhibited by nicotinamide or when cells were infected with a temperature-sensitive mutant in gene A. Analysis of the accumulating replicative intermediates by electron mi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/4.10.3483
更新日期:1977-10-01 00:00:00
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
更新日期:1981-11-11 00:00:00
abstract::The protein property prediction and testing database (PPT-DB) is a database housing nearly 30 carefully curated databases, each of which contains commonly predicted protein property information. These properties include both structural (i.e. secondary structure, contact order, disulfide pairing) and dynamic (i.e. orde...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm800
更新日期:2008-01-01 00:00:00
abstract::Bacteriophage DNA packaging motors translocate their genomic DNA into viral heads, compacting it to near-crystalline density. The Bacillus subtilis phage 29 has a unique ring of RNA (pRNA) that is an essential component of its motor, serving as a scaffold for the packaging ATPase. Previously, deletion of a three-base ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks724
更新日期:2012-10-01 00:00:00
abstract::The shape of the chromosomal DNA of the sulfur-dependent archaebacterium Sulfolobus acidocaldarius was analyzed by the pulsed-field gel electrophoresis(PFGE). S.acidocaldarius DNA digested with Notl showed two DNA bands at around 1.0 Mbp and 2.1 Mbp. Notl-linking clones were isolated from the library of S.acidocaldari...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.5.1133
更新日期:1990-03-11 00:00:00
abstract::Thousands of eukaryotic protein-coding genes generate circular RNAs that have covalently linked ends and are resistant to degradation by exonucleases. To prove their circularity as well as biochemically enrich these transcripts, it has become standard in the field to use the 3'-5' exonuclease RNase R. Here, we demonst...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz576
更新日期:2019-09-19 00:00:00
abstract::With the high number of sequences and structures streaming in from genomic projects, there is a need for more powerful and sophisticated annotation tools. Most problematic of the annotation efforts is predicting gene and protein function. Over the past few years there has been considerable progress in automated protei...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl045
更新日期:2006-07-01 00:00:00
abstract::High density oligonucleotide array technology is widely used in many areas of biomedical research for quantitative and highly parallel measurements of gene expression. Affymetrix GeneChip arrays are the most popular. In this technology each gene is typically represented by a set of 11-20 pairs of probes. In order to o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gng015
更新日期:2003-02-15 00:00:00