Elastic network models for RNA: a comparative assessment with molecular dynamics and SHAPE experiments.

abstract：:Corynebacterium diphtheriae is a Gram-positive, non-spore forming, non-motile, pleomorphic rod belonging to the genus Corynebacterium and the actinomycete group of organisms. The organism produces a potent bacteriophage-encoded protein exotoxin, diphtheria toxin (DT), which causes the symptoms of diphtheria. This pote...

journal_title：Nucleic acids research

authors： Cerdeño-Tárraga AM,Efstratiou A,Dover LG,Holden MT,Pallen M,Bentley SD,Besra GS,Churcher C,James KD,De Zoysa A,Chillingworth T,Cronin A,Dowd L,Feltwell T,Hamlin N,Holroyd S,Jagels K,Moule S,Quail MA,Rabbinowitsch E

更新日期：2003-11-15 00:00:00

abstract：:The PSI/TM-Coffee web server performs multiple sequence alignment (MSA) of proteins by combining homology extension with a consistency based alignment approach. Homology extension is performed with Position Specific Iterative (PSI) BLAST searches against a choice of redundant and non-redundant databases. The main nove...

journal_title：Nucleic acids research

authors： Floden EW,Tommaso PD,Chatzou M,Magis C,Notredame C,Chang JM

更新日期：2016-07-08 00:00:00

abstract：:A novel method for sequence specific double strand DNA cleavage using PNA (peptide nucleic acid) targeting is described. Nuclease S1 digestion of double stranded DNA gives rise to double strand cleavage at an occupied PNA strand displacement binding site, and under optimized conditions complete cleavage can be obtaine...

journal_title：Nucleic acids research

authors： Demidov V,Frank-Kamenetskii MD,Egholm M,Buchardt O,Nielsen PE

更新日期：1993-05-11 00:00:00

abstract：:A formaldehyde denaturation map of the replicative form of phiX174 DNA is obtained. The RFI DNA was converted into a linear state by restriction endonuclease pst I which introduces into this DNA a single double-stranded break. The map has four clear-cut peaks. Their positions excellently correlate with the peak positi...

journal_title：Nucleic acids research

authors： Karataev GI,Permogorov VI,Vologodskii AV,Frank-Kamenetskii MD

更新日期：1978-07-01 00:00:00

abstract：:Three-dimensional protein structures provide invaluable information for understanding and regulating biological functions of proteins. The GalaxyWEB server predicts protein structure from sequence by template-based modeling and refines loop or terminus regions by ab initio modeling. This web server is based on the met...

journal_title：Nucleic acids research

authors： Ko J,Park H,Heo L,Seok C

更新日期：2012-07-01 00:00:00

abstract：:Digestion of isolated Friend erythroleukemic cell nuclei with DNase I under conditions which selectively destroy the DNA of transcriptionally "active" genes releases into the supernatant fraction proteins of the non-histone "High Mobility Group" (HMGs). Two of these, HMG-14 and HMG-17(identified by solubility in trich...

journal_title：Nucleic acids research

authors： Reeves R,Candido EP

更新日期：1980-05-10 00:00:00

abstract：:Gene expression is a multi-step process involving many layers of regulation. The main regulators of the pathway are DNA and RNA binding proteins. While over the years, a large number of DNA and RNA binding proteins have been identified and extensively studied, it is still expected that many other proteins, some with y...

journal_title：Nucleic acids research

authors： Paz I,Kligun E,Bengad B,Mandel-Gutfreund Y

更新日期：2016-07-08 00:00:00

abstract：:CeR-2 RNA is one of the newly identified Caenorhabditis elegans noncoding RNAs (ncRNAs). The characterization of CeR-2 by RNomic studies has failed to classify it into any known ncRNA family. In this study, we examined the spatiotemporal expression patterns of CeR-2 to gain insight into its function. CeR-2 is expresse...

journal_title：Nucleic acids research

authors： Hokii Y,Sasano Y,Sato M,Sakamoto H,Sakata K,Shingai R,Taneda A,Oka S,Himeno H,Muto A,Fujiwara T,Ushida C

更新日期：2010-09-01 00:00:00

abstract：:Various in vivo mutagenesis methods have been developed to facilitate fast and efficient continuous evolution of proteins in cells. However, they either modify the DNA region that does not match the target gene, or suffer from low mutation rates. Here, we report a mutator, eMutaT7 (enhanced MutaT7), with very fast in ...

journal_title：Nucleic acids research

authors： Park H,Kim S

更新日期：2021-01-06 00:00:00

abstract：:A very high rate of multidrug resistance (MDR) seen among Gram-negative bacteria such as Escherichia, Klebsiella, Salmonella, Shigella, etc. is a major threat to public health and safety. One of the major virulent determinants of Gram-negative bacteria is capsular polysaccharide or K antigen located on the bacterial o...

journal_title：Nucleic acids research

authors： Kunduru BR,Nair SA,Rathinavelan T

更新日期：2016-01-04 00:00:00

abstract：:PAHdb (http://www.mcgill.ca/pahdb ) is a curated relational database (Fig. 1) of nucleotide variation in the human PAH cDNA (GenBank U49897). Among 328 different mutations by state (Fig. 2) the majority are rare mutations causing hyperphenylalaninemia (HPA) (OMIM 261600), the remainder are polymorphic variants without...

journal_title：Nucleic acids research

authors： Nowacki PM,Byck S,Prevost L,Scriver CR

更新日期：1998-01-01 00:00:00

abstract：:PubChem (http://pubchem.ncbi.nlm.nih.gov) is a public repository for biological activity data of small molecules and RNAi reagents. The mission of PubChem is to deliver free and easy access to all deposited data, and to provide intuitive data analysis tools. The PubChem BioAssay database currently contains 500,000 des...

journal_title：Nucleic acids research

authors： Wang Y,Xiao J,Suzek TO,Zhang J,Wang J,Zhou Z,Han L,Karapetyan K,Dracheva S,Shoemaker BA,Bolton E,Gindulyte A,Bryant SH

更新日期：2012-01-01 00:00:00

abstract：:The 1.7 Å X-ray crystal structure of the B-DNA dodecamer, [d(CGCGAATTCGCG)]₂ (DDD)-bound non-covalently to a platinum(II) complex, [{Pt(NH₃)₃}₂-µ-{trans-Pt(NH₃)₂(NH₂(CH₂)₆NH₂)₂}](NO₃)₆ (1, TriplatinNC-A,) shows the trinuclear cation extended along the phosphate backbone and bridging the minor groove. The square planar...

journal_title：Nucleic acids research

authors： Komeda S,Moulaei T,Chikuma M,Odani A,Kipping R,Farrell NP,Williams LD

更新日期：2011-01-01 00:00:00

abstract：:7,8-Dihydro-8-oxo-deoxyguanosine (8oxodG) is a highly premutagenic DNA lesion due to its ability to mispair with adenine. Schizosaccharomyces pombe lacks homologs for relevant enzymes that repair 8oxodG, which suggests that this lesion could be persistent and must be tolerated. Here we show that SpPol4, the unique Pol...

journal_title：Nucleic acids research

authors： Sastre-Moreno G,Sánchez A,Esteban V,Blanco L

更新日期：2014-09-01 00:00:00

abstract：:Genomic studies have indicated that certain bacterial lineages such as the Bacteroidetes lack Shine-Dalgarno (SD) sequences, and yet with few exceptions ribosomes of these organisms carry the canonical anti-SD (ASD) sequence. Here, we show that ribosomes purified from Flavobacterium johnsoniae, a representative of the...

journal_title：Nucleic acids research

authors： Jha V,Roy B,Jahagirdar D,McNutt ZA,Shatoff EA,Boleratz BL,Watkins DE,Bundschuh R,Basu K,Ortega J,Fredrick K

更新日期：2021-01-11 00:00:00

abstract：:VIDA is a new virus database that organizes open reading frames (ORFs) from partial and complete genomic sequences from animal viruses. Currently VIDA includes all sequences from GenBank for Herpesviridae, Coronaviridae and Arteriviridae. The ORFs are organized into homologous protein families, which are identified on...

journal_title：Nucleic acids research

authors： Albà MM,Lee D,Pearl FM,Shepherd AJ,Martin N,Orengo CA,Kellam P

更新日期：2001-01-01 00:00:00

abstract：:To study the effect of intron size on splicing efficiency we have varied the size of the avian leukosis virus (ALV) env mRNA intron in a cloned ALV genome. This was accomplished by deletion of ALV sequences or insertion of phage lambda DNA. The effect of these modifications on splicing was analyzed by microinjection o...

journal_title：Nucleic acids research

authors： Cullen BR,Kopchick JJ,Stacey DW

更新日期：1982-10-11 00:00:00

abstract：:In this report we have analyzed the role of antisense transcription in the control of LEF1 transcription factor expression. A natural antisense transcript (NAT) is transcribed from a promoter present in the first intron of LEF1 gene and undergoes splicing in mesenchymal cells. Although this locus is silent in epitheli...

journal_title：Nucleic acids research

authors： Beltran M,Aparicio-Prat E,Mazzolini R,Millanes-Romero A,Massó P,Jenner RG,Díaz VM,Peiró S,de Herreros AG

更新日期：2015-07-13 00:00:00

abstract：:The satellite RNA of tobacco ringspot virus (STobRV RNA) replicates and becomes encapsidated in association with tobacco ringspot virus. Previous results show that the infected tissue produces multimeric STobRV RNAs of both polarities. RNA that is complementary to encapsidated STobRV RNA, designated as having the (-) ...

journal_title：Nucleic acids research

authors： Buzayan JM,Hampel A,Bruening G

更新日期：1986-12-22 00:00:00

abstract：:Expression of the matrix metalloproteinase (MMP) gene stromelysin-3 ( ST3 ) has been shown to be tightly associated with cell migration and apoptosis inmammals and amphibians. This contrasts with most other MMP genes. We demonstrate here that the Xenopus ST3 gene also has a structure distinct from other MMP genes, wit...

journal_title：Nucleic acids research

authors： Li J,Liang VC,Sedgwick T,Wong J,Shi YB

更新日期：1998-06-15 00:00:00

abstract：:During telomere replication in yeast, chromosome ends acquire a long single-stranded extension of the strand making the 3' end. Previous work showed that these 3' tails are generated late in S-phase, when conventional replication is virtually complete. In addition, the extensions were also observed in cells that lacke...

journal_title：Nucleic acids research

authors： Dionne I,Wellinger RJ

更新日期：1998-12-01 00:00:00

abstract：:Accumulating evidence has demonstrated that transcriptional regulation is affected by DNA methylation. Understanding the perturbation of DNA methylation-mediated regulation between transcriptional factors (TFs) and targets is crucial for human diseases. However, the global landscape of DNA methylation-mediated transcr...

journal_title：Nucleic acids research

authors： Wang Z,Yin J,Zhou W,Bai J,Xie Y,Xu K,Zheng X,Xiao J,Zhou L,Qi X,Li Y,Li X,Xu J

更新日期：2020-03-18 00:00:00

abstract：:Sequence-specific interactions between aminoacyl-tRNA synthetases and their cognate tRNAs ensure both accurate RNA recognition and the efficient catalysis of aminoacylation. The effects of tRNA(Trp)variants on the aminoacylation reaction catalyzed by wild-type Escherichia coli tryptophanyl-tRNA synthe-tase (TrpRS) hav...

journal_title：Nucleic acids research

authors： Ibba M,Sever S,Praetorius-Ibba M,Söll D

更新日期：1999-09-15 00:00:00

abstract：:Non-coding RNA regulatory elements are important for viral replication, making them promising targets for therapeutic intervention. However, regulatory RNA is challenging to detect and characterise using classical structure-function assays. Here, we present in cell Mutational Interference Mapping Experiment (in cell M...

journal_title：Nucleic acids research

authors： Smyth RP,Smith MR,Jousset AC,Despons L,Laumond G,Decoville T,Cattenoz P,Moog C,Jossinet F,Mougel M,Paillart JC,von Kleist M,Marquet R

更新日期：2018-05-18 00:00:00

abstract：:Site-specific DNA double-strand breaks have been used to generate knock-in through the homology-dependent or -independent pathway. However, low efficiency and accompanying negative impacts such as undesirable indels or tumorigenic potential remain problematic. In this study, we present an enhanced reduced-risk genome ...

journal_title：Nucleic acids research

authors： He X,Chen W,Liu Z,Yu G,Chen Y,Cai YJ,Sun L,Xu W,Zhong L,Gao C,Chen J,Zhang M,Yang S,Yao Y,Zhang Z,Ma F,Zhang CC,Lu HP,Yu B,Cheng TL,Qiu J,Sheng Q,Zhou HM,Lv ZR,Yan J,Zhou Y,Qiu Z,Cui Z,Zhang X,Me

更新日期：2020-06-04 00:00:00

abstract：:Human La protein is an essential factor in the biology of both coding and non-coding RNAs. In the nucleus, La binds primarily to 3' oligoU containing RNAs, while in the cytoplasm La interacts with an array of different mRNAs lacking a 3' UUU(OH) trailer. An example of the latter is the binding of La to the IRES domain...

journal_title：Nucleic acids research

authors： Martino L,Pennell S,Kelly G,Bui TT,Kotik-Kogan O,Smerdon SJ,Drake AF,Curry S,Conte MR

更新日期：2012-02-01 00:00:00

abstract：:Reagents for proteome research must of necessity be generated by high throughput methods. Aptamers are potentially useful as reagents to identify and quantitate individual proteins, yet are currently produced for the most part by manual selection procedures. We have developed automated selection methods, but must stil...

journal_title：Nucleic acids research

authors： Cox JC,Hayhurst A,Hesselberth J,Bayer TS,Georgiou G,Ellington AD

更新日期：2002-10-15 00:00:00

abstract：:A method is presented for the purification of mRNAs and the identification of structural gene sequences in recombinant DNA molecules. RNA is hybridized to double-stranded linear DNA such that R-loops are formed between most DNAs and their complementary RNA sequences. These R-loops are purified from unhybridized RNAs b...

journal_title：Nucleic acids research

authors： Woolford JL Jr,Rosbash M

更新日期：1979-06-11 00:00:00

abstract：:We have isolated and characterized DNA probes that detect homologies between the X and Y chromosomes. Clone St25 is derived from the q13-q22 region of the X chromosome and recognizes a 98% homologous sequence on the Y chromosome. Y specific fragments were present in DNAs from 5 Yq-individuals and from 4 out of 7 XX ma...

journal_title：Nucleic acids research

authors： Koenig M,Moisan JP,Heilig R,Mandel JL

更新日期：1985-08-12 00:00:00

abstract：:Applications of conditional gene expression, whether for therapeutic or basic research purposes, are increasingly requiring mammalian gene control systems that exhibit far tighter control properties. While numerous approaches have been used to improve the widely used Tet-regulatory system, many applications, particula...

journal_title：Nucleic acids research

authors： Greber D,El-Baba MD,Fussenegger M

更新日期：2008-09-01 00:00:00