An archaeal Rad54 protein remodels DNA and stimulates DNA strand exchange by RadA.

abstract：:Many small RNAs contribute essential activities to eukaryotic cells. In mammalian genomes dispersed repetitive sequences which exhibit homology to small RNAs often exist as pseudogenes which can complicate identification, localization, and analysis of the authentic gene. We mapped a productive human 7SK small nuclear ...

journal_title：Nucleic acids research

authors： Driscoll CT,Darlington GJ,Maraia RJ

更新日期：1994-03-11 00:00:00

abstract：:We present a theory of pluralistic and stochastic gene regulation. To bridge the gap between empirical studies and mathematical models, we integrate pre-existing observations with our meta-analyses of the ENCODE ChIP-Seq experiments. Earlier evidence includes fluctuations in levels, location, activity, and binding of ...

journal_title：Nucleic acids research

authors： Salas EN,Shu J,Cserhati MF,Weeks DP,Ladunga I

更新日期：2016-06-02 00:00:00

abstract：:Redefinition of UAG, UAA and UGA to specify a standard amino acid occurs in response to recoding signals present in a minority of mRNAs. This 'read-through' is in competition with termination and is utilized for gene expression. One of the recoding signals known to stimulate read-through is a hexanucleotide sequence o...

journal_title：Nucleic acids research

authors： Harrell L,Melcher U,Atkins JF

更新日期：2002-05-01 00:00:00

abstract：:We have determined the sequence of 80 nucleotides adjacent to 3' poly(A) of both (middle and bottom component) cowpea mosaic virus RNAs, using dideoxynucleotide termination of reverse transcription. Sequence conservation is indicated, there being about 80% homology between the first 65 bases of each RNA. Although both...

journal_title：Nucleic acids research

authors： Davies JW,Stanley J,Van Kammen A

更新日期：1979-09-25 00:00:00

abstract：:We have isolated the mouse MyoD1 gene flanked by its promoter region by screening a genomic library with synthetic oligonucleotides. The structural gene is interrupted by two G + C rich introns. Transfection of the cloned gene inserted into an expression vector converts fibroblasts to myoblasts. Sequence analysis of a...

journal_title：Nucleic acids research

authors： Zingg JM,Alva GP,Jost JP

更新日期：1991-12-11 00:00:00

abstract：:Primer Design Assistant (PDA) is a web interface primer design service combined with thermodynamic theory to evaluate the fitness of primers. It runs in a Linux-Apache-MySQL-PHP structure on a PC equipped with dual CPU (Intel Pentium III 1.4 GHz) and 512 Mb of RAM. A succinct user interface of PDA is accomplished by b...

journal_title：Nucleic acids research

authors： Chen SH,Lin CY,Cho CS,Lo CZ,Hsiung CA

更新日期：2003-07-01 00:00:00

abstract：:The crystal structure of the DNA dodecamer duplex CATGGGCCCATG lies on a structural continuum along the transition between A- and B-DNA. The dodecamer possesses the normal vector plot and inclination values typical of B-DNA, but has the crystal packing, helical twist, groove width, sugar pucker, slide and x-displaceme...

journal_title：Nucleic acids research

authors： Ng HL,Dickerson RE

更新日期：2002-09-15 00:00:00

abstract：:As an approach to gene therapy for the respiratory manifestations of cystic fibrosis (CF), in vivo plasmid-mediated direct transfer of the normal CF transmembrane conductance regulator (CFTR) gene to the airway epithelium was investigated in mice. To evaluate the feasibility of this strategy, pRSVL, a plasmid composed...

journal_title：Nucleic acids research

authors： Yoshimura K,Rosenfeld MA,Nakamura H,Scherer EM,Pavirani A,Lecocq JP,Crystal RG

更新日期：1992-06-25 00:00:00

abstract：:Histone proteins are synthesized in large amounts during S-phase to package the newly replicated DNA, and are among the most stable proteins in the cell. The replication-dependent (RD)-histone mRNAs expressed during S-phase end in a conserved stem-loop rather than a polyA tail. In addition, there are replication-indep...

journal_title：Nucleic acids research

authors： Lyons SM,Cunningham CH,Welch JD,Groh B,Guo AY,Wei B,Whitfield ML,Xiong Y,Marzluff WF

更新日期：2016-11-02 00:00:00

abstract：:The structural simplicity and ability to capture serial correlations make Markov models a popular modeling choice in several genomic analyses, such as identification of motifs, genes and regulatory elements. A critical, yet relatively unexplored, issue is the determination of the order of the Markov model. Most biolog...

journal_title：Nucleic acids research

authors： Narlikar L,Mehta N,Galande S,Arjunwadkar M

更新日期：2013-02-01 00:00:00

abstract：:p53 as an effector of nucleolar stress is well defined, but p53 independent mechanisms are largely unknown. Like p53, the NF-κB transcription factor plays a critical role in maintaining cellular homeostasis under stress. Many stresses that stimulate NF-κB also disrupt nucleoli. However, the link between nucleolar func...

journal_title：Nucleic acids research

authors： Chen J,Lobb IT,Morin P,Novo SM,Simpson J,Kennerknecht K,von Kriegsheim A,Batchelor EE,Oakley F,Stark LA

更新日期：2018-07-06 00:00:00

abstract：:Detection of cancer-associated somatic mutations has broad applications for oncology and precision medicine. However, this becomes challenging when cancer-derived DNA is in low abundance, such as in impure tissue specimens or in circulating cell-free DNA. Next-generation sequencing (NGS) is particularly prone to techn...

journal_title：Nucleic acids research

authors： Wang TT,Abelson S,Zou J,Li T,Zhao Z,Dick JE,Shlush LI,Pugh TJ,Bratman SV

更新日期：2019-09-05 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

authors： Wilson R,McGuire C,Mohun T,DMDD Project.

更新日期：2016-01-04 00:00:00

abstract：:An attempt has been made to correlate differential scanning calorimetry melting profiles of 5S rRNAs from lupin seeds (L.s.) and wheat germ (W.g.) with their structure. It is suggested that the observed differences in thermal unfolding are due to differences in RNA nucleotide sequence and as a consequence in higher or...

journal_title：Nucleic acids research

authors： Barciszewski J,Bratek-Wiewiórowska MD,Górnicki P,Naskret-Barciszewska M,Wiewiórowski M,Zielenkiewicz A,Zielenkiewicz W

更新日期：1988-01-25 00:00:00

abstract：:Antigenic variation of the pilus is an essential component of Neisseria gonorrhoeae pathogenesis. Unidirectional recombination of silent pilin DNA into an expressed pilin gene allows for substantial sequence variation of this highly immunogenic surface structure. While the RecA protein is required for pilin gene recom...

journal_title：Nucleic acids research

authors： Wainwright LA,Frangipane JV,Seifert HS

更新日期：1997-04-01 00:00:00

abstract：:This paper describes the sequence of 257 nucleotides from the 3' end of RNA 2 of barley stripe mosaic virus ( BSMV , strain Argentina Mild) including an internal oligo (A) tract localized at a distance of 236 nucleotides from the 3' end, and the 3' terminal tRNA-like structure accepting tyrosine. This sequence is show...

journal_title：Nucleic acids research

authors： Kozlov YuV,Rupasov VV,Adyshev DM,Belgelarskaya SN,Agranovsky AA,Mankin AS,Morozov SYu,Dolja VV,Atabekov JG

更新日期：1984-05-11 00:00:00

abstract：:DNA double stranded breaks (DSBs) are one of the most deleterious types of DNA lesions. The main pathways responsible for repairing these breaks in eukaryotic cells are homologous recombination (HR) and non-homologous end-joining (NHEJ). However, a third group of still poorly characterized DSB repair pathways, collect...

journal_title：Nucleic acids research

authors： Kostyrko K,Mermod N

更新日期：2016-04-07 00:00:00

abstract：:Sox proteins belong to the HMG box superfamily of DNA-binding proteins and are found throughout the animal kingdom. They are involved in the regulation of such diverse developmental processes as germ layer formation, organ development and cell type specifi-cation. Hence, deletion or mutation of Sox proteins often resu...

journal_title：Nucleic acids research

authors： Wegner M

更新日期：1999-03-15 00:00:00

abstract：:Plants have large diverse families of small secreted proteins (SSPs) that play critical roles in the processes of development, differentiation, defense, flowering, stress response, symbiosis, etc. Oryza sativa is one of the major crops worldwide and an excellent model for monocotyledonous plants. However, there had no...

journal_title：Nucleic acids research

authors： Pan B,Sheng J,Sun W,Zhao Y,Hao P,Li X

更新日期：2013-01-01 00:00:00

abstract：:The inherent properties of DNA as a stable polymer with unique affinity for partner molecules determined by the specific Watson-Crick base pairing makes it an ideal component in self-assembling structures. This has been exploited for decades in the design of a variety of artificial substrates for investigations of DNA...

journal_title：Nucleic acids research

authors： Andersen FF,Knudsen B,Oliveira CL,Frøhlich RF,Krüger D,Bungert J,Agbandje-McKenna M,McKenna R,Juul S,Veigaard C,Koch J,Rubinstein JL,Guldbrandtsen B,Hede MS,Karlsson G,Andersen AH,Pedersen JS,Knudsen BR

更新日期：2008-03-01 00:00:00

abstract：:A RNA interference (RNAi) like mechanism is involved in elimination of thousands of DNA segments from the developing somatic macronucleus of Tetrahymena, yet how specific internal eliminated sequences (IESs) are recognized remains to be fully elucidated. To define requirements for DNA rearrangement, we performed mutag...

journal_title：Nucleic acids research

authors： Kowalczyk CA,Anderson AM,Arce-Larreta M,Chalker DL

更新日期：2006-01-01 00:00:00

abstract：:Herpes simplex type 1 virus (HSV-1) and bacteriophage λ capsids undergo considerable structural changes during self-assembly and DNA packaging. The initial steps of viral capsid self-assembly require weak, non-covalent interactions between the capsid subunits to ensure free energy minimization and error-free assembly....

journal_title：Nucleic acids research

authors： Sae-Ueng U,Liu T,Catalano CE,Huffman JB,Homa FL,Evilevitch A

更新日期：2014-08-01 00:00:00

abstract：:Control of RNA processing plays a major role in HIV-1 gene expression. To explore the role of several hnRNP proteins in this process, we carried out a siRNA screen to examine the effect of depletion of hnRNPs A1, A2, D, H, I and K on HIV-1 gene expression. While loss of hnRNPs H, I or K had little effect, depletion of...

journal_title：Nucleic acids research

authors： Lund N,Milev MP,Wong R,Sanmuganantham T,Woolaway K,Chabot B,Abou Elela S,Mouland AJ,Cochrane A

更新日期：2012-04-01 00:00:00

abstract：:Single-walled carbon nanotubes (SWNTs) have been considered as the leading candidate for nanodevice applications ranging from gene therapy and novel drug delivery to membrane separations. The miniaturization of DNA-nanotube devices for biological applications requires fully understanding DNA-nanotube interaction mecha...

journal_title：Nucleic acids research

authors： Li X,Peng Y,Qu X

更新日期：2006-08-02 00:00:00

abstract：:The analysis of chromatin fine structure and transcription factor occupancy of differentially expressed genes by in vivo footprinting and ligation-mediated-PCR (LMPCR) is a powerful tool to understand the impact of chromatin on gene expression. However, as with all PCR-based techniques, the accuracy of the experiments...

journal_title：Nucleic acids research

authors： Ingram R,Gao C,Lebon J,Liu Q,Mayoral RJ,Sommer SS,Hoogenkamp M,Riggs AD,Bonifer C

更新日期：2008-02-01 00:00:00

abstract：:The properties of the interaction of 5-fluorocytosine-containing DNA with the EcoRII methyltransferase were studied. The DNA used was either a polymer synthesized in vitro, or a 20-mer containing one CCA/TGG sequence. The DNA could be methylated by the enzyme. In the process the enzyme formed a tight binding adduct wi...

journal_title：Nucleic acids research

authors： Friedman S,Ansari N

更新日期：1992-06-25 00:00:00

abstract：:Bacteriophage Mu has one of the best studied, most efficient and largest transposition machineries of the prokaryotic world. To harness this attractive integration machinery for use in mammalian cells, we cloned the coding sequences of the phage factors MuA and MuB in a eukaryotic expression cassette and fused them to...

journal_title：Nucleic acids research

authors： Schagen FH,Rademaker HJ,Cramer SJ,van Ormondt H,van der Eb AJ,van de Putte P,Hoeben RC

更新日期：2000-12-01 00:00:00

abstract：:The Blocks Database contains multiple alignments of conserved regions in protein families which can be searched by e-mail (blocks@blocks.fhcrc.org) and World Wide Web (http://blocks.fhcrc.org/ ) servers to classify protein and nucleotide sequences. Recent enhancements to the servers include: (i) improved calculation o...

journal_title：Nucleic acids research

authors： Henikoff JG,Pietrokovski S,Henikoff S

更新日期：1997-01-01 00:00:00

abstract：:Polyketide synthases (PKSs) catalyze biosynthesis of a diverse family of pharmaceutically important secondary metabolites. Bioinformatics analysis of sequence and structural features of PKS proteins plays a crucial role in discovery of new natural products by genome mining, as well as in design of novel secondary meta...

journal_title：Nucleic acids research

authors： Anand S,Prasad MV,Yadav G,Kumar N,Shehara J,Ansari MZ,Mohanty D

更新日期：2010-07-01 00:00:00

abstract：:Initiation of sporulation in Bacillus subtilis is controlled by several regulators which affect activation by phosphorylation of the key response regulator Spo0A or transcription of Spo0A-P-dependent genes. In vivo overexpression of one of these regulators, sinR , results in suppression of transcription from the Spo0A...

journal_title：Nucleic acids research

authors： Cervin MA,Lewis RJ,Brannigan JA,Spiegelman GB

更新日期：1998-08-15 00:00:00