DNA multiplex hybridization on microarrays and thermodynamic stability in solution: a direct comparison.

abstract：:A somatic cell hybrid line containing only human chromosome 21 on a mouse background has been used as the source of DNA for construction of a recombinant phage library. Individual phages containing human inserts have been identified. Repeat-free human DNA subclones have been prepared and used to screen for restriction...

journal_title：Nucleic acids research

authors： Watkins PC,Tanzi RE,Gibbons KT,Tricoli JV,Landes G,Eddy R,Shows TB,Gusella JF

更新日期：1985-09-11 00:00:00

abstract：:Prokaryotes use primed CRISPR adaptation to update their memory bank of spacers against invading genetic elements that have escaped CRISPR interference through mutations in their protospacer target site. We previously observed a trend that nucleotide-dependent mismatches between crRNA and the protospacer strongly infl...

journal_title：Nucleic acids research

authors： Künne T,Zhu Y,da Silva F,Konstantinides N,McKenzie RE,Jackson RN,Brouns SJ

更新日期：2018-11-02 00:00:00

abstract：:A sixty base pair DNA duplex containing the nucleotide sequence of the bacteriophage T5 early (T5P25) promoter has been constructed using a combination of chemical synthesis and enzymatic methods. Subsequent to cloning into pBR322, the promoter has been demonstrated to be biologically active being capable of directing...

journal_title：Nucleic acids research

authors： Rommens J,MacKnight D,Pomeroy-Cloney L,Jay E

更新日期：1983-09-10 00:00:00

abstract：:The inducibility of the vir genes (virA, -B, -C, -D, -E, and -G) on pRiA4 was examined at the transcriptional level, and the RNA-starting sites were determined by S1-nuclease mapping and primer-extension experiments. All of these genes were inducible, while virA, -E, and -G were transcribed even under noninducing cond...

journal_title：Nucleic acids research

authors： Aoyama T,Takanami M,Oka A

更新日期：1989-11-11 00:00:00

abstract：:Calf thymus DNA polymerase alpha (pol alpha) and bacteriophage T4 DNA polymerase (pol T4) were exploited as model enzymes to investigate the molecular mechanism of inhibitory action of N2-(p-n-butylphenyl)dGTP (BuPdGTP) and 2-(p-n-butyl-anilino)dATP (BuAdATP) on the BuPdNTP-susceptible alpha polymerase family. Kinetic...

journal_title：Nucleic acids research

authors： Khan NN,Wright GE,Brown NC

更新日期：1991-04-11 00:00:00

abstract：:Adenosine deaminases that act on RNA (ADARs) convert adenosine to inosine within double-stranded regions of RNA, resulting in increased transcriptomic diversity, as well as protection of cellular double-stranded RNA (dsRNA) from silencing and improper immune activation. The presence of dsRNA-binding domains (dsRBDs) i...

journal_title：Nucleic acids research

authors： Rajendren S,Manning AC,Al-Awadi H,Yamada K,Takagi Y,Hundley HA

更新日期：2018-10-12 00:00:00

abstract：:Large-scale sequencing studies discovered substantial genetic variants occurring in enhancers which regulate genes via long range chromatin interactions. Importantly, such variants could affect enhancer regulation by changing transcription factor bindings or enhancer hijacking, and in turn, make an essential contribut...

journal_title：Nucleic acids research

authors： Zhang G,Shi J,Zhu S,Lan Y,Xu L,Yuan H,Liao G,Liu X,Zhang Y,Xiao Y,Li X

更新日期：2018-01-04 00:00:00

abstract：:NetMHC-3.0 is trained on a large number of quantitative peptide data using both affinity data from the Immune Epitope Database and Analysis Resource (IEDB) and elution data from SYFPEITHI. The method generates high-accuracy predictions of major histocompatibility complex (MHC): peptide binding. The predictions are bas...

journal_title：Nucleic acids research

authors： Lundegaard C,Lamberth K,Harndahl M,Buus S,Lund O,Nielsen M

更新日期：2008-07-01 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

authors： Yan Z,Shah PK,Amin SB,Samur MK,Huang N,Wang X,Misra V,Ji H,Gabuzda D,Li C

更新日期：2012-09-01 00:00:00

abstract：:In order to direct antisense oligonucleotides to specific tissues or cell types in vivo, we are exploring the possibility to utilize lipoproteins as transport vehicles. A 16-mer oligonucleotide (ODN) was derivatized at the 5' prime through a 32P phosphate spacer with cholesterol, yielding a 32P-labeled amphiphatic cho...

journal_title：Nucleic acids research

authors： de Smidt PC,Le Doan T,de Falco S,van Berkel TJ

更新日期：1991-09-11 00:00:00

abstract：:Scalable multiplexed amplification technologies are needed for cost-effective large-scale genotyping of genetic markers such as single nucleotide polymorphisms (SNPs). We present SNPWave, a novel SNP genotyping technology to detect various subsets of sequences in a flexible fashion in a fixed detection format. SNPWave...

journal_title：Nucleic acids research

authors： van Eijk MJ,Broekhof JL,van der Poel HJ,Hogers RC,Schneiders H,Kamerbeek J,Verstege E,van Aart JW,Geerlings H,Buntjer JB,van Oeveren AJ,Vos P

更新日期：2004-03-05 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

authors： Mamede R,Vila-Cerqueira P,Silva M,Carriço JA,Ramirez M

更新日期：2021-01-08 00:00:00

abstract：:A common goal in the discovery of rare functional DNA variants via medical resequencing is to incur a relatively lower proportion of false positive base-calls. We developed a novel statistical method for resequencing arrays (SRMA, sequence robust multi-array analysis) to increase the accuracy of detecting rare variant...

journal_title：Nucleic acids research

authors： Wang W,Shen P,Thiyagarajan S,Lin S,Palm C,Horvath R,Klopstock T,Cutler D,Pique L,Schrijver I,Davis RW,Mindrinos M,Speed TP,Scharfe C

更新日期：2011-01-01 00:00:00

abstract：:Due to the importance of protein phosphorylation in cellular control, many researches are undertaken to predict the kinase-specific phosphorylation sites. Referred to our previous work, KinasePhos 1.0, incorporated profile hidden Markov model (HMM) with flanking residues of the kinase-specific phosphorylation sites. H...

journal_title：Nucleic acids research

authors： Wong YH,Lee TY,Liang HK,Huang CM,Wang TY,Yang YH,Chu CH,Huang HD,Ko MT,Hwang JK

更新日期：2007-07-01 00:00:00

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 str...

journal_title：Nucleic acids research

authors： Cho TJ,Park SS

更新日期：1998-03-15 00:00:00

abstract：:The role of TATA elements in the expression of a mammalian promoter was investigated in the fission yeast Schizosaccharomyces pombe, by studying the human adenovirus E2-early promoter. This is a unique dual promoter with two nonconsensus TATA elements directing transcription from two cap sites, +1 and -26. A sequence ...

journal_title：Nucleic acids research

authors： Swaminathan S,Malhotra P,Manohar CF,Dhar R,Thimmapaya B

更新日期：1993-06-11 00:00:00

abstract：:Myotonic dystrophy type 1 (DM1) is caused by the expansion of a (CTG).(CAG) repeat in the DMPK gene on chromosome 19q13.3. At least 17 neurological diseases have similar genetic mutations, the expansion of DNA repeats. In most of these disorders, the disease severity is related to the length of the repeat expansion, a...

journal_title：Nucleic acids research

authors： Hashem VI,Pytlos MJ,Klysik EA,Tsuji K,Khajavi M,Ashizawa T,Sinden RR

更新日期：2004-12-01 00:00:00

abstract：:Hepatocyte Nuclear Factor 4 (HNF-4), a liver-enriched orphan receptor of the nuclear receptor superfamily, is required for the expression of a wide variety of liver-specific genes including apoAI. To explore the possibility that site A of the apoAI gene enhancer might also be the target for HNF-4 without the interfere...

journal_title：Nucleic acids research

authors： Fuernkranz HA,Wang Y,Karathanasis SK,Mak P

更新日期：1994-12-25 00:00:00

abstract：:Four pseudorevertants of a -10 region lacP mutation were isolated. Three of these mutations were found to activate nascent promoters. These mutations were: a -2 G/C----A/T change (-2A) promoting transcription at position +11, a +1 A/T----T/A change (+1T) promoting transcription initiation at position +13, and a +10 C/...

journal_title：Nucleic acids research

authors： Karls R,Schulz V,Jovanovich SB,Flynn S,Pak A,Reznikoff WS

更新日期：1989-05-25 00:00:00

abstract：:Bacteria core RNA polymerase (RNAP) must associate with a sigma factor to recognize promoter sequences. Promoters recognized by the sigma(54) (or sigma(N)) associated RNA polymerase are unique in having conserved positions around -24 and -12 nucleotides upstream from the transcriptional start site. Using DNA microarra...

journal_title：Nucleic acids research

authors： Zhao K,Liu M,Burgess RR

更新日期：2010-03-01 00:00:00

abstract：:A long-range physical map of the centromeric region of human chromosome 7 has been constructed in order to define the region containing sequences with potential involvement in centromere function. The map is centered around alpha satellite DNA, a family of tandemly repeated DNA forming arrays of hundreds to thousands ...

journal_title：Nucleic acids research

authors： Wevrick R,Willard HF

更新日期：1991-05-11 00:00:00

abstract：:A gene encoding a putative DNA helicase from Staphylococcus aureus USA300 was cloned and expressed in Escherichia coli. The protein was purified to over 90% purity by chromatography. The purified enzyme, SauUSI, predominantly cleaves modified DNA containing 5mC and 5-hydroxymethylcytosine. Cleavage of 5mC-modified pla...

journal_title：Nucleic acids research

authors： Xu SY,Corvaglia AR,Chan SH,Zheng Y,Linder P

更新日期：2011-07-01 00:00:00

abstract：:We have recently shown that phosphorothioate (PS) oligodeoxynucleotide (ODN) analogs, unlike their normal congeners, exhibit significant anti-HIV activity (Matsukura et al., (1987) Proc. Natl. Acad. Sci. USA 84, 7706-7710). We now report the syntheses, melting temperatures (Tm), and nuclease susceptibilities of a seri...

journal_title：Nucleic acids research

authors： Stein CA,Subasinghe C,Shinozuka K,Cohen JS

更新日期：1988-04-25 00:00:00

abstract：:Hfq, a bacterial RNA-binding protein, was recently shown to contain the Sm1 motif, a characteristic of Sm and LSm proteins that function in RNA processing events in archaea and eukaryotes. In this report, comparative structural modeling was used to predict a three-dimensional structure of the Hfq core sequence. The pr...

journal_title：Nucleic acids research

authors： Sun X,Zhulin I,Wartell RM

更新日期：2002-09-01 00:00:00

abstract：:Expression of the wild-type p53 tumor suppressor gene has been found to play an important role in the regulation of cellular proliferation and differentiation. In addition, in many transformed cells and primary tumors, the gene has undergone allelic deletions and mutant forms of the p53 gene are expressed at elevated ...

journal_title：Nucleic acids research

authors： Reisman D,Rotter V

更新日期：1993-01-25 00:00:00

abstract：:The three-dimensional structures of two DNA duplexes d(CATGAGTAC). d(GTACXCATG) (1) and d(CATGAGTAC).d(GTACTCATG) (2), where X represents 1-(2'-deoxy-beta-D-ribofuranosyl)-3-nitropyrrole, were solved using high resolution nuclear magnetic resonance spectroscopy and restrained molecular dynamics. Good convergence was o...

journal_title：Nucleic acids research

authors： Klewer DA,Hoskins A,Zhang P,Davisson VJ,Bergstrom DE,LiWang AC

更新日期：2000-11-15 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

authors： de Vries E,van Driel W,Tromp M,van Boom J,van der Vliet PC

更新日期：1985-07-11 00:00:00

abstract：:Most human genes generate multiple transcript isoforms. The differential expression of these isoforms can help specify cell types. Diverse transcript isoforms arise from the use of alternative transcription start sites, polyadenylation sites and splice sites; however, the relative contribution of these processes to is...

journal_title：Nucleic acids research

authors： Reyes A,Huber W

更新日期：2018-01-25 00:00:00

abstract：:Initiation of bacterial DNA replication at oriC is mediated by primosomal proteins that act cooperatively to melt an AT-rich region where the replicative helicase is loaded prior to the assembly of the replication fork. In Bacillus subtilis, the dnaD, dnaB and dnaI genes are essential for initiation of DNA replication...

journal_title：Nucleic acids research

authors： Grainger WH,Machón C,Scott DJ,Soultanas P

更新日期：2010-05-01 00:00:00

abstract：:Helicobacter pylori is a Gram-negative bacterium that colonizes human stomach and causes gastric inflammation. The species is naturally competent and displays remarkable diversity. The presence of a large number of restriction-modification (R-M) systems in this bacterium creates a barrier against natural transformatio...

journal_title：Nucleic acids research

authors： Dwivedi GR,Sharma E,Rao DN

更新日期：2013-03-01 00:00:00