Abstract：
:Various strategies employed in genomic DNA cloning by subtractive hybridization have been examined by computer simulations, with the comparison between the predictions and the published results. The result shows that the efficiency of target sequence enrichment and the sensitivity to experimental conditions depend strongly on the enrichment strategy employed. The strategy selecting only tester/tester after hybridization can be very efficient to enrich targets. For successful target enrichment, however, the strategy requires a highly efficient subtraction method and proper hybridization conditions. The strategy also requires that the selected DNA be amplified by polymerase chain reaction (PCR) after each or each alternate subtraction. By contrast, the strategy selecting tester/tester plus single-stranded tester is less sensitive to various experimental factors, compared with the strategy selecting only tester/tester. However, it is not as efficient. With this strategy, the tester DNA selected may or may not be amplified by PCR before the next round. In the case of the strategy selecting single-stranded tester, the target DNA can be successfully enriched only when the selected DNA is directly used without PCR amplification in the next round. The strong features of existing methods can be combined to develop a protocol that is more efficient and more reliable.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Cho TJ,Park SSdoi
10.1093/nar/26.6.1440subject
Has Abstractpub_date
1998-03-15 00:00:00pages
1440-8issue
6eissn
0305-1048issn
1362-4962pii
gkb212journal_volume
26pub_type
杂志文章abstract：:A precursor of modified nucleoside Q isolated from E. coli methyl-deficient tRNA was determined to be 7-(aminomethyl)-7-deazaguanosine. The structure was deduced by means of its chromatographic and electrophoretic mobilities, and UV and mass spectra, in addition to comparison with the synthesized authentic compound. T...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/5.7.2289
更新日期：1978-07-01 00:00:00
abstract：:One of the major issues in expression profiling analysis still is to outline proper thresholds to determine differential expression, while avoiding false positives. The problem being that the variance is inversely proportional to the log of signal intensities. Aiming to solve this issue, we describe a model, expressio...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm093
更新日期：2007-01-01 00:00:00
abstract：:In some preparations of DNA dependent RNA polymerase a new enzymatic activity has been found which catalyzes the condensation of two pyrophosphate molecules, liberated in the process of RNA synthesis, to one molecule of orthophosphate and one molecule of Mg (or Mn) - chelate complex with trimetaphosphate. This activit...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/6.4.1521
更新日期：1979-04-01 00:00:00
abstract：:Gene promoters are enriched in guanine clusters that potentially fold into quadruplex structures. Such quadruplexes were implicated in the regulation of gene expression, plausibly by interacting with transcription factors. We showed previously that homodimers of the myogenic transcription factor MyoD bound in vitro mo...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp1208
更新日期：2010-04-01 00:00:00
abstract：:OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genomes. Initiated in 2004, the project is at its 11th release. It now includes 1000 genomes, making it one of the largest resources of its kind. Here, we describe recent developments in terms of species covered; the al...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq1238
更新日期：2011-01-01 00:00:00
abstract：:The pattern of preferential DNA repair of UV-induced pyrimidine dimers was studied in repair-deficient Chinese hamster ovary (CHO) cells transfected with the human excision repair gene, ERCC-1. Repair efficiency was measured in the active dihydrofolate reductase (DHFR) gene and in its flanking, non-transcribed sequenc...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.15.7397
更新日期：1988-08-11 00:00:00
abstract：:Kaposi's sarcoma-associated herpesvirus encodes four viral homologues to cellular interferon regulatory factors (IRFs), where the most studied is vIRF-1. Even though vIRF-1 shows sequence homology to the N-terminal DNA-binding domain (DBD) of human IRFs, a specific role for this domain in vIRF-1's function has remaine...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt082
更新日期：2013-04-01 00:00:00
abstract：:S/MARt DB, the S/MAR transaction database, is a relational database covering scaffold/matrix attached regions (S/MARs) and nuclear matrix proteins that are involved in the chromosomal attachment to the nuclear scaffold. The data are mainly extracted from original publications, but a World Wide Web interface for direct...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/30.1.372
更新日期：2002-01-01 00:00:00
abstract：:Rapidly evolving pathogens cause a diverse array of diseases and epidemics that threaten crop yield, food security as well as human, animal and ecosystem health. To combat infection greater comparative knowledge is required on the pathogenic process in multiple species. The Pathogen-Host Interactions database (PHI-bas...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku1165
更新日期：2015-01-01 00:00:00
abstract：:Random amplified polymorphic DNA (RAPD) markers are used widely to develop high resolution genetic maps and for genome fingerprinting. Typically, single oligomers of approximately 10 nucleotides are used to PCR amplify characteristic RAPD marker fragments. We describe an efficient method for the direct end-sequencing ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/27.19.e28
更新日期：1999-10-01 00:00:00
abstract：:FIMM database (http://sdmc.krdl.org.sg:8080/fimm) contains data relevant to functional molecular immunology, focusing on cellular immunology. It contains fully referenced data on protein antigens, major histocompatibility complex (MHC) molecules, MHC-associated peptides and relevant disease associations. FIMM has a se...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/30.1.226
更新日期：2002-01-01 00:00:00
abstract：:The k-junction is a structural motif in RNA comprising a three-way helical junction based upon kink turn (k-turn) architecture. A computer program written to examine relative helical orientation identified the three-way junction of the Arabidopsis TPP riboswitch as an elaborated k-turn. The Escherichia coli TPP ribosw...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku144
更新日期：2014-04-01 00:00:00
abstract：:PomBase (http://www.pombase.org) is the model organism database for the fission yeast Schizosaccharomyces pombe. PomBase provides a central hub for the fission yeast community, supporting both exploratory and hypothesis-driven research. It provides users easy access to data ranging from the sequence level, to molecula...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku1040
更新日期：2015-01-01 00:00:00
abstract：:A novel class of RNA-binding proteins, Puf, regulates translation and RNA stability by binding to specific sequences in the 3'-untranslated region of target mRNAs. Members of this protein family share a conserved Puf domain consisting of eight 36 amino acid imperfect repeats. Here we report two Puf family member genes...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkf600
更新日期：2002-11-01 00:00:00
abstract：:The Deciphering the Mechanisms of Developmental Disorders (DMDD) consortium is a research programme set up to identify genes in the mouse, which if mutated (or knocked-out) result in embryonic lethality when homozygous, and initiate the study of why disruption of their function has such profound effects on embryo deve...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv1138
更新日期：2016-01-04 00:00:00
abstract：:A cDNA library was constructed from the mRNA of the ZR-75 oestrogen responsive human breast cancer cell line and screened for oestrogen regulated mRNA sequences. Of the recombinants isolated, 30 contained cDNA that corresponded to a single mRNA species of 2.1 kb that was induced between 10 and 15 fold by oestradiol tr...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/15.9.3773
更新日期：1987-05-11 00:00:00
abstract：:Homologous recombination provides a means for the in vivo construction of recombinant DNA molecules that may be problematic to assemble in vitro. We have investigated the efficiency of recombination within the Caenorhabditis elegans germ line as a function of the length of homology between recombining molecules. Our f...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm857
更新日期：2007-01-01 00:00:00
abstract：:Nucleosomes are the most abundant protein-DNA complexes in eukaryotes that provide compaction of genomic DNA and are implicated in regulation of transcription, DNA replication and repair. The details of DNA positioning on the nucleosome and the DNA conformation can provide key regulatory signals. Hydroxyl-radical foot...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx616
更新日期：2017-09-19 00:00:00
abstract：:Microbial enzymes have many known applications as biocatalysts in biotechnology, agriculture, medical and other industries. However, only a few enzymes are currently employed for such commercial applications. In this scenario, the current onslaught of metagenomic data provides a new unexplored treasure trove of genomi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp1001
更新日期：2010-01-01 00:00:00
abstract：:Posttranslational modifications (PTMs) of histones represent a crucial regulatory mechanism of nucleosome and chromatin dynamics in various of DNA-based cellular processes, such as replication, transcription and DNA damage repair. Lysine succinylation (Ksucc) is a newly identified histone PTM, but its regulation and f...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa663
更新日期：2020-09-25 00:00:00
abstract：:Bacterial small RNAs (sRNAs) are a heterogeneous group of post-transcriptional regulators that often act at the heart of large networks. Hundreds of sRNAs have been discovered by genome-wide screens and most of these sRNAs exert their functions by base-pairing with target mRNAs. However, studies addressing the molecul...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky765
更新日期：2018-11-16 00:00:00
abstract：:We describe the characterisation of four thermo-stable NAD(+)-dependent DNA ligases, from Thermus thermophilus (Tth), Thermus scotoductus (Ts), Rhodothermus marinus (Rm) and Thermus aquaticus (Taq), by an assay which measures ligation rate and mismatch discrimination. Complete libraries of octa-, nona- and decanucleot...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/28.3.e10
更新日期：2000-02-01 00:00:00
abstract：:The template requirements for efficient adenovirus DNA replication were studied in vitro in a reconstituted system with cloned DNA fragments, containing the Ad2 origin region, as templates. Replication is enhanced by nuclear factor I, a cellular protein that binds specifically to the Ad2 origin. This stimulation is sh...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/13.13.4935
更新日期：1985-07-11 00:00:00
abstract：:ANISEED (www.aniseed.cnrs.fr) is the main model organism database for tunicates, the sister-group of vertebrates. This release gives access to annotated genomes, gene expression patterns, and anatomical descriptions for nine ascidian species. It provides increased integration with external molecular and taxonomy datab...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx1108
更新日期：2018-01-04 00:00:00
abstract：:The Mouse Genome Database (MGD) (http://www.informatics.jax.org) one component of a community database resource for the laboratory mouse, a key model organism for interpreting the human genome and for understanding human biology. MGD strives to provide an extensively integrated information resource with experimental d...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg047
更新日期：2003-01-01 00:00:00
abstract：:RaftProt (http://lipid-raft-database.di.uq.edu.au/) is a database of mammalian lipid raft-associated proteins as reported in high-throughput mass spectrometry studies. Lipid rafts are specialized membrane microdomains enriched in cholesterol and sphingolipids thought to act as dynamic signalling and sorting platforms....
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku1131
更新日期：2015-01-01 00:00:00
abstract：:TIGRFAMs is a collection of protein family definitions built to aid in high-throughput annotation of specific protein functions. Each family is based on a hidden Markov model (HMM), where both cutoff scores and membership in the seed alignment are chosen so that the HMMs can classify numerous proteins according to the...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl1043
更新日期：2007-01-01 00:00:00
abstract：:Pluripotency, the ability of embryonic stem cells to differentiate into specialized cell types, is determined by ESC-specific gene regulators such as transcription factors and chromatin modification factors. It is not well understood how ESCs are poised for differentiation, however, and methods are needed for prognosi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx752
更新日期：2017-10-13 00:00:00
abstract：:Prokaryotic genomic DNA is generally negatively supercoiled in vivo. Many regulatory processes, including the initiation of transcription, are known to depend on the superhelical state of the DNA substrate. The stresses induced within DNA by negative superhelicity can destabilize the DNA duplex at specific sites. Vari...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkj007
更新日期：2006-01-01 00:00:00
abstract：:DIAL (dihedral alignment) is a web server that provides public access to a new dynamic programming algorithm for pairwise 3D structural alignment of RNA. DIAL achieves quadratic time by performing an alignment that accounts for (i) pseudo-dihedral and/or dihedral angle similarity, (ii) nucleotide sequence similarity a...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm334
更新日期：2007-07-01 00:00:00
