Abstract:
:Partial restriction digestion is used to map restriction sites and the location of genes within yeast artificial chromosomes (YACs). Locus-specific probes are hybridised to the partially digested YAC DNA and the fragments to which they hybridise are compared with the pattern of partial digestion products that include each map region. A least squares criterion is presented which allows for error in fragment length determination. This rapidly defines the most likely location of a marker within the restriction map and permits the combination of results from digestions with different restriction enzymes. Approximate confidence intervals may be assigned to gene locations, and tests of goodness-of-fit of the data may be performed. Since the number of erroneously matched fragments increases in proportion to the square of the number of sites, denser maps are not necessarily more informative. Simulations indicate that the optimal number of internal restriction sites given typical experimental error (1% of YAC length) is about five sites; the associated broad support interval (on average one third of YAC length) may be reduced by combining results from different enzyme digestions. Application of a computer implementation of this model to experimental data showed that the model fitted well, and estimates of location were found to be consistent with other evidence.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Shields DC,Butler A,Mosurski KR,Walsh MT,Whitehead ASdoi
10.1093/nar/24.22.4495subject
Has Abstractpub_date
1996-11-15 00:00:00pages
4495-500issue
22eissn
0305-1048issn
1362-4962pii
6s0384journal_volume
24pub_type
杂志文章abstract::The results of differential expression analyses provide scientists with hundreds to thousands of differentially expressed genes that need to be interpreted in light of the biology of the specific system under study. This requires mapping the genes to functional classifications that can be, for example, the KEGG pathwa...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt516
更新日期:2013-07-01 00:00:00
abstract::The transcriptional promoter of satellite 2 from the eastern newt, Notophthalmus viridescens, was analyzed by assaying the activity of deleted or mutated satellite 2 clones in Xenopus laevis oocytes. Two elements in the promoter were found to be important for transcription. These elements have sequences that are simil...
journal_title:Nucleic acids research
pub_type: 杂志文章
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更新日期:1994-11-11 00:00:00
abstract::HbVar (http://globin.bx.psu.edu/hbvar) is one of the oldest and most appreciated locus-specific databases launched in 2001 by a multi-center academic effort to provide timely information on the genomic alterations leading to hemoglobin variants and all types of thalassemia and hemoglobinopathies. Database records incl...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt911
更新日期:2014-01-01 00:00:00
abstract::We have previously shown that hedamycin, a GC-rich DNA-binding antitumor agent, downregulates survivin transcription (Wu et al. (2005) Molecular mechanism of inhibition of survivin transcription by the GC-rich sequence selective DNA-binding antitumor agent, hedamycin: evidence of survivin downregulation associated wit...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm149
更新日期:2007-01-01 00:00:00
abstract::Evidence will be presented to show that the allyl group is suitable for the protection of a 3'-terminal phosphodiester function. The latter will be demonstrated by the synthesis, via a phosphotriester approach, of two cyclic tetraribonucleotides [r(AAAA) and r(UAMe2UAMe2)], two cyclic hexadeoxyribonucleotides [d(CGCGC...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.10.4607
更新日期:1988-05-25 00:00:00
abstract::Nuclear extracts prepared from growth hormone-secreting (GC) and prolactin-secreting (235-1) rat anterior pituitary cell lines were compared for their ability to bind to the DNA sequences conferring tissue-specificity to the expression of the rat growth hormone (rGH) gene promoter. Cell-specific differences in the int...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.17.5235
更新日期:1990-09-11 00:00:00
abstract::(19)F NMR spectroscopy has proved to be a valuable tool to monitor functionally important conformational transitions of nucleic acids. Here, we present a systematic investigation on the application of 5-fluoro pyrimidines to probe DNA and RNA secondary structures. Oligonucleotides with the propensity to adapt secondar...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp862
更新日期:2009-12-01 00:00:00
abstract::Fourteen P-element insertion mutants at the yellow (y) gene of D. melanogaster have been analysed by restriction mapping and DNA sequencing. The distribution of the insertion sites is nonrandom, with a preferred target site in the 5'-transcribed but non-translated leader of the gene. Transcription analysis indicates t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.7.3039
更新日期:1988-04-11 00:00:00
abstract::We describe here a novel method for integrating gene and miRNA expression profiles in cancer using feed-forward loops (FFLs) consisting of transcription factors (TFs), miRNAs and their common target genes. The dChip-GemiNI (Gene and miRNA Network-based Integration) method statistically ranks computationally predicted ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks395
更新日期:2012-09-01 00:00:00
abstract::Cre recombinase catalyzes the cleavage and religation of DNA at loxP sites. The enzyme is a homotetramer in its functional state, and the symmetry of the protein complex enforces a pseudo-palindromic symmetry upon the loxP sequence. The Cre-lox system is a powerful tool for many researchers. However, broader applicati...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv901
更新日期:2015-10-15 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg215
更新日期:2003-02-15 00:00:00
abstract::High affinity antisense oligonucleotides (ASOs) containing bicylic modifications (BNA) such as locked nucleic acid (LNA) designed to induce target RNA cleavage have been shown to have enhanced potency along with a higher propensity to cause hepatotoxicity. In order to understand the mechanism of this hepatotoxicity, t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv1210
更新日期:2016-03-18 00:00:00
abstract::The web software CHOP was developed to visualize the 'wobbling' in the third codon position of aligned DNA sequences. The simple features of this tool allow users to easily find regions suspected of containing coding sequences (CDSs). The program also allows visualization of the nucleotide diversity between two genomi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh448
更新日期:2004-07-01 00:00:00
abstract::Identification of MHC-binding peptides is a prerequisite in rational design of T-cell based peptide vaccines. During the past decade a number of computational approaches have been introduced for the prediction of MHC-binding peptides, efficiently reducing the number of candidate binders that need to be experimentally ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl284
更新日期:2006-07-01 00:00:00
abstract::CAG repeats occur predominantly in the coding regions of human genes, which suggests their functional importance. In some genes, these sequences can undergo pathogenic expansions leading to neurodegenerative polyglutamine (poly-Q) diseases. The mutant transcripts containing expanded CAG repeats possibly contribute to ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq700
更新日期:2010-12-01 00:00:00
abstract::The intrinsic stiffness of DNA limits its ability to be bent and twisted over short lengths, but such deformations are required for gene regulation. One classic paradigm is DNA looping in the regulation of the Escherichia coli lac operon. Lac repressor protein binds simultaneously to two operator sequences flanking th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm419
更新日期:2007-01-01 00:00:00
abstract::We report here the different ways in which four subunits of the basal transcription/repair factor TFIIH (XPB, XPD, p62 and p44) and the damage recognition XPC repair protein can enter the nucleus. We examined their nuclear localization by transiently expressing the gene products tagged with the enhanced green fluoresc...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.7.1574
更新日期:2001-04-01 00:00:00
abstract::ETS-domain transcription factors play important roles in controlling gene expression in a variety of different contexts; however, these proteins bind to very similar sites and it is unclear how in vivo specificity is achieved. In silico analysis is unlikely to reveal specific targets for individual family members and ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp804
更新日期:2009-12-01 00:00:00
abstract::Diastereomeric dithymidine methanephosphonamidates (TnpmT) were synthesized by reaction of 3'-amino-3'-deoxythymidine with 3'- O -acetylthymidin-5-yl-methanephosphonochloridate. Separated dinucleotide TnpmT(fast) and TnpmT(slow) diastereomers were used as building blocks to prepare chimeric dodecathy-midylates, posses...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.11.2650
更新日期:1998-06-01 00:00:00
abstract::Two group I introns (CpSSU.1 and CpSSU.2) that each potentially encode a protein with two copies of the LAGLI-DADG motif were identified in the Chlamydomonas pallidostigmatica chloroplast small subunit rRNA gene. They both belong to subgroup IA3 and represent novel insertion positions in this gene (sites 508 and 793 i...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.13.2519
更新日期:1995-07-11 00:00:00
abstract::Nucleotide excision DNA repair is mechanistically conserved across all kingdoms of life. In prokaryotes, this multi-enzyme process requires six proteins: UvrA-D, DNA polymerase I and DNA ligase. To examine how UvrC locates the UvrB-DNA pre-incision complex at a site of damage, we have labeled UvrB and UvrC with differ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt177
更新日期:2013-05-01 00:00:00
abstract::The DNA replication, plasmid segregation and transactivation functions of Epstein-Barr nuclear antigen 1 (EBNA1) require the binding of EBNA1 to specific DNA recognition sites in the two non-contiguous functional elements of the Epstein-Barr virus latent origin of replication, oriP . EBNA1 molecules bound to these ele...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.19.4462
更新日期:1998-10-01 00:00:00
abstract::The bHLH transcription factor MyoD, the prototypical master regulator of differentiation, directs a complex program of gene expression during skeletal myogenesis. The up-regulation of the cdk inhibitor p57kip2 plays a critical role in coordinating differentiation and growth arrest during muscle development, as well as...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks619
更新日期:2012-09-01 00:00:00
abstract::We present the sequences of five additional human U2 pseudogenes which are very similar to the U2.13 pseudogene reported previously [Van Arsdell et al. (1981) Cell 26, 11-17]. All six U2 pseudogenes preserve the 5' end of the mature U2 snRNA sequence, and all six are flanked by nearly perfect direct repeats that diffe...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.3.1463
更新日期:1984-02-10 00:00:00
abstract::The crystal structure of d(CATGGGCCCATG)(2) shows unique stacking patterns of a stable B<-->A-DNA intermediate. We evaluated intrinsic base stacking energies in this crystal structure using an ab initio quantum mechanical method. We found that all crystal base pair steps have stacking energies close to their values in...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.24.4893
更新日期:2000-12-15 00:00:00
abstract::Allele-specific DNA methylation, histone acetylation and histone methylation are recognized as epigenetic characteristics of imprinted genes and imprinting centers (ICs). These epigenetic modifications are also used to regulate tissue-specific gene expression. Epigenetic differences between alleles can be significant ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh671
更新日期:2004-06-24 00:00:00
abstract::Mismatch Repair (MMR) is closely linked to DNA replication; however, other than the role of the replicative sliding clamp (PCNA) in various MMR functions, the linkage between DNA replication and MMR has been difficult to investigate. Here we use an in vitro DNA replication system based on simian virus 40, to investiga...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm943
更新日期:2008-01-01 00:00:00
abstract::The molecular mechanisms that underlie the neurological manifestations of patients with inherited diseases of vitamin B12 (cobalamin) metabolism remain to date obscure. We observed transcriptomic changes of genes involved in RNA metabolism and endoplasmic reticulum stress in a neuronal cell model with impaired cobalam...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky634
更新日期:2018-09-06 00:00:00
abstract::Sequence-dependent variation in structure and dynamics of a DNA duplex, collectively referred to as 'DNA shape', critically impacts interactions between DNA and proteins. Here, a method based on the technique of site-directed spin labeling was developed to experimentally map shapes of two DNA duplexes that contain res...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku695
更新日期:2014-10-01 00:00:00
abstract::Explicit solvent molecular dynamics (MD) was used to describe the intrinsic flexibility of the helix 42-44 portion of the 23S rRNA (abbreviated as Kt-42+rGAC; kink-turn 42 and GTPase-associated center rRNA). The bottom part of this molecule consists of alternating rigid and flexible segments. The first flexible segmen...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm245
更新日期:2007-01-01 00:00:00