Abstract：
:Cooperative hybridization has been used to establish physical linkage between two loci on a DNA strand. Linkage was detected by hybridization to a new type of high-density oligonucleotide array. Each synthesis location on the array contains a mixture of two different probe sequences. Each of the two probes can hybridize independently to a different target sequence, but if the two target sequences are physically linked there is a cooperative increase in hybridization yield. The ability to create and control non-linear effects raises a host of possibilities for applications of oligonucleotide array hybridization. The method has been used to assign linkage in 50:50 mixtures of DNA containing single nucleotide polymorphisms (SNPs) separated by 17, 693, 1350 and 2038 bp and to reconstruct haplotypes. Other potential uses include increasing the specificity of hybridization in mutation detection and gene expression monitoring applications, determining SNP haplotypes, characterizing repetitive sequences, such as short tandem repeats, and aiding contig assembly in sequen-cing by hybridization.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Gentalen E,Chee Mdoi
10.1093/nar/27.6.1485keywords:
subject
Has Abstractpub_date
1999-03-15 00:00:00pages
1485-91issue
6eissn
0305-1048issn
1362-4962pii
gkc272journal_volume
27pub_type
杂志文章abstract：:We introduce M-Coffee, a meta-method for assembling multiple sequence alignments (MSA) by combining the output of several individual methods into one single MSA. M-Coffee is an extension of T-Coffee and uses consistency to estimate a consensus alignment. We show that the procedure is robust to variations in the choice...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl091
更新日期：2006-03-23 00:00:00
abstract：:Current knowledge of parameters affecting RNA stability is very restricted in plants. Here we investigated factors which might contribute to the stability of a particular plant messenger RNA. To this end, insertion and deletion mutants were made in two different exons and an intron of the transcribed region of a well ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.10.2917
更新日期：1990-05-25 00:00:00
abstract：:GeneAlign is a coding exon prediction tool for predicting protein coding genes by measuring the homologies between a sequence of a genome and related sequences, which have been annotated, of other genomes. Identifying protein coding genes is one of most important tasks in newly sequenced genomes. With increasing numbe...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl307
更新日期：2006-07-01 00:00:00
abstract：:A reporter assay was developed to detect and quantify nonsense codon suppression by chemically aminoacylated tRNAs in mammalian cells. It is based on the cellular expression of the enhanced green fluorescent protein (EGFP) as a reporter for the site-specific amino acid incorporation in its sequence using an orthogonal...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gnf128
更新日期：2002-12-01 00:00:00
abstract：:The 279-bp major breakpoint region (mbr) within the 3'-untranslated region (3'-UTR) of the BCL2 gene is a binding site of special AT-rich sequence binding protein 1 (SATB1) that is well known to participate in the long-range regulation of gene transcription. Our previous studies have revealed that the mbr could regula...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr023
更新日期：2011-06-01 00:00:00
abstract：:We have compiled the DNA sequence data for E. coli available from the GENBANK and EMBL data libraries and over a period of several years independently from the literature. This is the fifth listing replacing and increasing the former listings substantially. However, in order to save space this printed version contains...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/21.13.2973
更新日期：1993-07-01 00:00:00
abstract：:The field bean, Vicia faba L. var. minor, possesses two sub-families of 11 S legumin genes named A and B. We isolated from a genomic library a B-type gene (LeB4) and determined its primary DNA sequence. Gene LeB4 codes for a 484 amino acid residue prepropolypeptide, encompassing a signal peptide of 22 amino acid resid...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/14.6.2707
更新日期：1986-03-25 00:00:00
abstract：:All exchangeable protons in a short DNA helix, d(CG)3 sodium salt, have been studied by proton nuclear magnetic resonance. The cytidine and guanosine amino protons have been assigned for the first time. As a function of temperature the cytidine amino protons and the imino protons behave very similarly, their relaxatio...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.21.8269
更新日期：1984-11-12 00:00:00
abstract：:Conflicts between replication and transcription challenge chromosome duplication. Escherichia coli replisome movement along transcribed DNA is promoted by Rep and UvrD accessory helicases with Δrep ΔuvrD cells being inviable under rapid growth conditions. We have discovered that mutations in a tRNA gene, aspT, in an a...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw1254
更新日期：2017-03-17 00:00:00
abstract：:The transmission of genetic information relies on Watson-Crick base pairing between nucleoside phosphates and template bases in template-primer complexes. Enzyme-free primer extension is the purest form of the transmission process, without any chaperon-like effect of polymerases. This simple form of copying of sequenc...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku314
更新日期：2014-06-01 00:00:00
abstract：:iSARST is a web server for efficient protein structural similarity searches. It is a multi-processor, batch-processing and integrated implementation of several structural comparison tools and two database searching methods: SARST for common structural homologs and CPSARST for homologs with circular permutations. iSARS...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp291
更新日期：2009-07-01 00:00:00
abstract：:We have developed a simple method to measure RNA synthesis in real time. In this technique, transcription reactions are performed in the presence of molecular beacons that possess a 2'-O-methylribonucleotide backbone. These probes become fluorescent as they hybridize to nascent RNA during the course of synthesis. We f...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gnh068
更新日期：2004-05-20 00:00:00
abstract：:Comparative analysis of mutants using transfection is complicated by clones exhibiting variable levels of gene expression due to copy number differences and genomic position effects. Recombinase-mediated cassette exchange (RMCE) can overcome these problems by introducing the target gene into pre-determined chromosomal...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gni145
更新日期：2005-10-04 00:00:00
abstract：:We present the results of in vitro binding studies aimed at defining the key recognition elements on the MS2 RNA translational operator (TR) essential for complex formation with coat protein. We have used chemically synthesized operators carrying modified functional groups at defined nucleotide positions, which are es...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/23.13.2512
更新日期：1995-07-11 00:00:00
abstract：:The interactions of HIV-1 reverse transcriptase (HIV-1 RT) with a synthetic 53/19-mer DNA substrate was investigated. For this template-primer HIV-1 RT displayed a Km value of 20 nM. The 53/19-mer competitively inhibited DNA synthesis performed on poly (rC).oligo(dG) with Ki value of 260 nM. This corresponded well to ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/21.17.3943
更新日期：1993-08-25 00:00:00
abstract：:Ribosome biogenesis is a key process for maintaining protein synthetic capacity in dividing or growing cells, and requires coordinated production of ribosomal proteins and ribosomal RNA (rRNA), including the processing of the latter. Signalling through mammalian target of rapamycin complex 1 (mTORC1) activates all the...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku130
更新日期：2014-04-01 00:00:00
abstract：:A novel cytoplasmic gene expression system has been developed. This system differs from other expression systems in that it relies on the co-delivery of plasmid DNA and T7 RNA polymerase (RNAP) during transfection. The plasmid contains a T7 RNAP gene driven by the T7 promoter (T7 autogene) and a functional/reporter ge...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.11.2114
更新日期：1994-06-11 00:00:00
abstract：:The replication control circuit of the FII plasmids R1, R100 and R6-5 involves a small untranslated RNA molecule of about 93 nucleotides. This RNA, designated CopA RNA in plasmid R1, acts in vivo as a post-transcriptional inhibitor of the expression of the RepA protein whose synthesis is required for each round of pla...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/14.6.2523
更新日期：1986-03-25 00:00:00
abstract：:Adenosine-to-inosine (A-to-I) RNA editing is a common post transcriptional modification. It has a critical role in protecting against false activation of innate immunity by endogenous double stranded RNAs and has been associated with various regulatory processes and diseases such as autoimmune and cardiovascular disea...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa305
更新日期：2020-06-19 00:00:00
abstract：:Metabolite-responsive RNA pseudoknots derived from prokaryotic riboswitches have been shown to stimulate -1 programmed ribosomal frameshifting (PRF), suggesting -1 PRF as a promising gene expression platform to extend riboswitch applications in higher eukaryotes. However, its general application has been hampered by d...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw718
更新日期：2016-10-14 00:00:00
abstract：:The principles of mRNA decoding are conserved among all extant life forms. We present an integrative view of all the interaction networks between mRNA, tRNA and rRNA: the intrinsic stability of codon-anticodon duplex, the conformation of the anticodon hairpin, the presence of modified nucleotides, the occurrence of no...
journal_title：Nucleic acids research
pub_type： 杂志文章,评审
doi：10.1093/nar/gkw608
更新日期：2016-09-30 00:00:00
abstract：:Using a bio-oligo pull-down DNA-binding assay we investigated the binding capacity of endogenous, DNA damage-induced p53 in human diploid fibroblasts to several p53-responsive elements (REs) present in p53-regulated genes. During the course of p53 accumulation, we observed a decrease in p53 binding to the GADD45 but n...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/30.11.2340
更新日期：2002-06-01 00:00:00
abstract：:RNA pseudoknots are functional structure elements with key roles in viral and cellular processes. Prediction of a pseudoknotted minimum free energy structure is an NP-complete problem. Practical algorithms for RNA structure prediction including restricted classes of pseudoknots suffer from high runtime and poor accura...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq021
更新日期：2010-04-01 00:00:00
abstract：:Upon HIV-1 infection of a target cell, the viral reverse transcriptase (RT) copies the genomic RNA to synthesize the viral DNA. The genomic RNA is within the incoming HIV-1 core where it is coated by molecules of nucleocapsid (NC) protein that chaperones the reverse transcription process. Indeed, the RT chaperoning pr...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr117
更新日期：2011-07-01 00:00:00
abstract：:Transfection of a human estrogen receptor cDNA expression vector (HEO) into cultured Xenopus kidney cells confers estrogen responsiveness to the recipient cells as demonstrated by the hormone dependent expression of co-transfected Xenopus vitellogenin-CAT chimeric genes. The estrogen stimulation of these vit-CAT genes...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.17.8291
更新日期：1988-09-12 00:00:00
abstract：:Apicoplast, an essential organelle of human malaria parasite Plasmodium falciparum contains a ∼35 kb circular genome and is a possible target for therapy. Proteins required for the replication and maintenance of the apicoplast DNA are not clearly known. Here we report the presence of single-stranded DNA binding protei...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq565
更新日期：2010-11-01 00:00:00
abstract：:Poly 2'0-ethylcytidylic acid (poly (Ce)) was prepared by polymerization of 2'-0-ethylcytidine-5'-pyrophosphate with Escherichia coli polynucleotide phosphorylase in the presence of Mn++, and its properties compared with those of poly (rC), poly (Cm) and poly (dC). The neutral form of pOLY (Ce) exhibits properties simi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/3.3.817
更新日期：1976-03-01 00:00:00
abstract：:Hereditary persistence of fetal hemoglobin (HPFH) is a condition characterized by the continued expression of the fetal globin gene in adulthood. Both deletional and nondeletional forms have been described. We studied one Japanese family with two different nondeletional forms of HPFH. Analysis of polymorphic restricti...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.17.5245
更新日期：1990-09-11 00:00:00
abstract：:When the function of origins of replication in yeast was compromised by placing ARS sequences downstream of strong promoters, ARS activity might have been affected either by transcription or by an altered chromatin configuration induced by the construct. To distinguish between these possibilities, derivatives of the y...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.19.3904
更新日期：1994-09-25 00:00:00
abstract：:Trinucleotide exchange (TriNEx) is a method for generating novel molecular diversity during directed evolution by random substitution of one contiguous trinucleotide sequence for another. Single trinucleotide sequences were deleted at random positions in a target gene using the engineered transposon MuDel that were su...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkn358
更新日期：2008-08-01 00:00:00
