Studies on deoxyribonucleases from Saccharomyces cerevisiae. Characterization of two endonuclease activities with a preference for double-stranded DNA.

abstract：:Atomistic molecular dynamics (MD) simulations generate a wealth of information related to the dynamics of proteins. If properly analyzed, this information can lead to new insights regarding protein function and assist wet-lab experiments. Aiming to identify interactions between individual amino acid residues and the r...

journal_title：Nucleic acids research

authors： Serçinoglu O,Ozbek P

更新日期：2018-07-02 00:00:00

abstract：:Adjustable transgene expression is considered key for next-generation molecular interventions in gene therapy scenarios, therapeutic reprogramming of clinical cell phenotypes for tissue engineering and sophisticated gene-function analyses in the post-genomic era. We have designed a portfolio of latest generation self-...

journal_title：Nucleic acids research

authors： Mitta B,Weber CC,Rimann M,Fussenegger M

更新日期：2004-07-16 00:00:00

abstract：:HT1080 cells stably expressing green fluorescent protein (GFP) linked to a 3' terminal AU-rich element (ARE) proved to be a convenient system to study the dynamics of mRNA stability, as changes in mRNA levels are reflected in increased or decreased fluorescence intensity. This study examined whether mRNA stability can...

journal_title：Nucleic acids research

authors： Raineri I,Wegmueller D,Gross B,Certa U,Moroni C

更新日期：2004-02-19 00:00:00

abstract：:We have reported previously (1) two unexpected consequences of the microinjection into fertilized mouse eggs of a recombinant plasmid designated p12B1, carrying a 343 bp insert of non-repetitive mouse DNA. Injected at very low concentrations, this plasmid could be established as an extrachromosomal genetic element. Wh...

journal_title：Nucleic acids research

authors： Blangy A,Léopold P,Vidal F,Rassoulzadegan M,Cuzin F

更新日期：1991-12-01 00:00:00

abstract：:The MIPS Fusarium graminearum Genome Database (FGDB) is a comprehensive genome database on one of the most devastating fungal plant pathogens of wheat and barley. FGDB provides information on two gene sets independently derived by automated annotation of the F.graminearum genome sequence. A complete manually revised g...

journal_title：Nucleic acids research

authors： Güldener U,Mannhaupt G,Münsterkötter M,Haase D,Oesterheld M,Stümpflen V,Mewes HW,Adam G

更新日期：2006-01-01 00:00:00

abstract：:Three peaks of methyltransferase activity specific for MNNG alkylated DNA have been identified from extracts of chemically adapted M. luteus. They are designated as TI to TIII in order to their elution from a Sephadex G-75 column. The first one of these peaks has been purified to homogeneity. TI, is an inducible, unus...

journal_title：Nucleic acids research

authors： Riazuddin S,Athar A,Sohail A

更新日期：1987-11-25 00:00:00

abstract：:Many interacting proteins regulate and/or assist the activities of RAD51, a recombinase which plays a critical role in both DNA repair and meiotic recombination. Yeast two-hybrid screening of a human testis cDNA library revealed a new protein, RAD51AP2 (RAD51 Associated Protein 2), that interacts strongly with RAD51. ...

journal_title：Nucleic acids research

authors： Kovalenko OV,Wiese C,Schild D

更新日期：2006-01-01 00:00:00

abstract：:Next-generation sequencing technologies have made it possible to carry out transcriptome analysis at the single-cell level. Single-cell RNA-sequencing (scRNA-seq) data provide insights into cellular dynamics, including intercellular heterogeneity as well as inter- and intra-cellular fluctuations in gene expression tha...

journal_title：Nucleic acids research

authors： Kubo M,Nishiyama T,Tamada Y,Sano R,Ishikawa M,Murata T,Imai A,Lang D,Demura T,Reski R,Hasebe M

更新日期：2019-05-21 00:00:00

abstract：:In vitro splicing of human beta-globin pre-mRNA can be fully inhibited by treatment of the splicing extract with polyclonal antibodies against hnRNP core proteins prior to the addition of pre-mRNA. Inhibition of the first step in the splicing pathway, cleavage at the 5' splice site and lariat formation, requires more ...

journal_title：Nucleic acids research

authors： Sierakowska H,Szer W,Furdon PJ,Kole R

更新日期：1986-07-11 00:00:00

abstract：:Gel migration and uranyl photoprobing have been used to study the effects of inosine and 2,6-diaminopurine (2,6-DAP) substitution on adenine-tract (A-tract) induced DNA curvature. Using a 10mer repeated sequence including five inosines we show by uranyl photoprobing that a narrow minor groove varying in phase with the...

journal_title：Nucleic acids research

authors： Mollegaard NE,Bailly C,Waring MJ,Nielsen PE

更新日期：1997-09-01 00:00:00

abstract：:The sequence of 110 nucleotides adjacent to the 3'-end of Neurospora crassa 25S-rRNA has been derived by chemical sequencing methods. Sequences present between 40 and 85 nucleotides of the 3'-end were found to complement sequences at the 3'- and 5'-ends of 5.8S-rRNA. Interaction was shown to occur between 5.8S-rRNA an...

journal_title：Nucleic acids research

authors： Kelly JM,Cox RA

更新日期：1981-03-11 00:00:00

abstract：:Although telomeres are not recognized as double-strand breaks (DSBs), some DSB repair proteins are present at telomeres and are required for telomere maintenance. To learn more about the telomeric function of proteins from the homologous recombination (HR) and non-homologous end joining pathways (NHEJ), we have screen...

journal_title：Nucleic acids research

authors： Wei C,Skopp R,Takata M,Takeda S,Price CM

更新日期：2002-07-01 00:00:00

abstract：:DNA methylation is the best-studied epigenetic modification and describes the conversion of cytosine to 5-methylcytosine. The importance of this phenomenon is that aberrant promoter hypermethylation is a common occurrence in cancer and is frequently associated with gene silencing. Various techniques are currently avai...

journal_title：Nucleic acids research

authors： Brena RM,Auer H,Kornacker K,Hackanson B,Raval A,Byrd JC,Plass C

更新日期：2006-02-07 00:00:00

abstract：:Fluorescence anisotropy and fluorescence correlation spectroscopy measurements of rhodamine-labeled DNA oligonucleotide duplexes have been used to determine equilibrium binding constants for DNA binding of the prokaryotic transcription activator protein NtrC. Measurements were made with wild-type NtrC from Escherichia...

journal_title：Nucleic acids research

authors： Sevenich FW,Langowski J,Weiss V,Rippe K

更新日期：1998-03-15 00:00:00

abstract：:H3K4me3 is a histone modification that accumulates at the transcription-start site (TSS) of active genes and is known to be important for transcription activation. The way in which H3K4me3 is regulated at TSS and the actual molecular basis of its contribution to transcription remain largely unanswered. To address thes...

journal_title：Nucleic acids research

authors： Lloret-Llinares M,Pérez-Lluch S,Rossell D,Morán T,Ponsa-Cobas J,Auer H,Corominas M,Azorín F

更新日期：2012-10-01 00:00:00

abstract：:A novel class of RNA-binding proteins, Puf, regulates translation and RNA stability by binding to specific sequences in the 3'-untranslated region of target mRNAs. Members of this protein family share a conserved Puf domain consisting of eight 36 amino acid imperfect repeats. Here we report two Puf family member genes...

journal_title：Nucleic acids research

authors： Cui L,Fan Q,Li J

更新日期：2002-11-01 00:00:00

abstract：:We have developed an improved and rapid genomic engineering procedure for the construction of custom-designed microorganisms. This method, which can be performed in 2 days, permits restructuring of the Escherichia coli genome via markerless deletion of selected genomic regions. The deletion process was mediated by a s...

journal_title：Nucleic acids research

authors： Yu BJ,Kang KH,Lee JH,Sung BH,Kim MS,Kim SC

更新日期：2008-08-01 00:00:00

abstract：:Although secondary structure predictions of an individual RNA sequence have been widely used in a number of sequence analyses of RNAs, accuracy is still limited. Recently, we proposed a method (called 'CentroidHomfold'), which includes information about homologous sequences into the prediction of the secondary structu...

journal_title：Nucleic acids research

authors： Hamada M,Yamada K,Sato K,Frith MC,Asai K

更新日期：2011-07-01 00:00:00

abstract：:Therapeutic oligonucleotides are often modified using the phosphorothioate (PS) backbone modification which enhances stability from nuclease mediated degradation. However, substituting oxygen in the phosphodiester backbone with sulfur introduce chirality into the backbone such that a full PS 16-mer oligonucleotide is ...

journal_title：Nucleic acids research

authors： Østergaard ME,De Hoyos CL,Wan WB,Shen W,Low A,Berdeja A,Vasquez G,Murray S,Migawa MT,Liang XH,Swayze EE,Crooke ST,Seth PP

更新日期：2020-02-28 00:00:00

abstract：:Heterotrimeric eukaryotic/archaeal translation initiation factor 2 (e/aIF2) binds initiator methionyl-tRNA and plays a key role in the selection of the start codon on messenger RNA. tRNA binding was extensively studied in the archaeal system. The γ subunit is able to bind tRNA, but the α subunit is required to reach h...

journal_title：Nucleic acids research

authors： Naveau M,Lazennec-Schurdevin C,Panvert M,Dubiez E,Mechulam Y,Schmitt E

更新日期：2013-01-01 00:00:00

abstract：:The E3 ubiquitin ligase HUWE1/Mule/ARF-BP1 plays an important role in integrating/coordinating diverse cellular processes such as DNA damage repair and apoptosis. A previous study has shown that HUWE1 is required for the early step of DNA damage-induced apoptosis, by targeting MCL-1 for proteasomal degradation. Howeve...

journal_title：Nucleic acids research

authors： Yi J,Lu G,Li L,Wang X,Cao L,Lin M,Zhang S,Shao G

更新日期：2015-05-19 00:00:00

abstract：:Most proteins from higher organisms are known to be multi-domain proteins and contain substantial numbers of intrinsically disordered (ID) regions. To analyse such protein sequences, those from human for instance, we developed a special protein-structure-prediction pipeline and accumulated the products in the Structur...

journal_title：Nucleic acids research

authors： Motono C,Nakata J,Koike R,Shimizu K,Shirota M,Amemiya T,Tomii K,Nagano N,Sakaya N,Misoo K,Sato M,Kidera A,Hiroaki H,Shirai T,Kinoshita K,Noguchi T,Ota M

更新日期：2011-01-01 00:00:00

abstract：:We have developed a web-based resource (available at www.ciliate.org) for researchers studying the model ciliate organism Tetrahymena thermophila. Employing the underlying database structure and programming of the Saccharomyces Genome Database, the Tetrahymena Genome Database (TGD) integrates the wealth of knowledge g...

journal_title：Nucleic acids research

authors： Stover NA,Krieger CJ,Binkley G,Dong Q,Fisk DG,Nash R,Sethuraman A,Weng S,Cherry JM

更新日期：2006-01-01 00:00:00

abstract：:The interplay between aromatic stacking and hydrogen bonding in nucleobases has been investigated via high-level quantum chemical calculations. The experimentally observed stacking arrangement between consecutive bases in DNA and RNA/DNA double helices is shown to enhance their hydrogen bonding ability as opposed to g...

journal_title：Nucleic acids research

authors： Mignon P,Loverix S,Steyaert J,Geerlings P

更新日期：2005-03-23 00:00:00

abstract：:The combination of RNA interference (RNAi) with the tetracycline-controlled transcription activation (tet) system promises to become a powerful method for conditional gene inactivation in cultured cells and in whole organisms. Here, we tested critical sequence elements that originated from miRNA mR-30 for optimal effi...

journal_title：Nucleic acids research

authors： Berger SM,Pesold B,Reber S,Schönig K,Berger AJ,Weidenfeld I,Miao J,Berger MR,Gruss OJ,Bartsch D

更新日期：2010-09-01 00:00:00

abstract：:An improved and simplified protocol for DNA immobilization was developed to enhance DNA-DNA hybridization on microwell plates. Target DNA was immobilized by simple dry-adsorption. Efficiencies of DNA immobilization and retention were enhanced 1.4-6.5 times and 4.2-19.6 times, respectively, compared with a conventional...

journal_title：Nucleic acids research

authors： Hirayama H,Tamaoka J,Horikoshi K

更新日期：1996-10-15 00:00:00

abstract：:Simple modular architecture research tool (SMART) is an online tool (http://smart.embl.de/) for the identification and annotation of protein domains. It provides a user-friendly platform for the exploration and comparative study of domain architectures in both proteins and genes. The current release of SMART contains ...

journal_title：Nucleic acids research

authors： Letunic I,Doerks T,Bork P

更新日期：2009-01-01 00:00:00

abstract：:Double-stranded (ds) oligodeoxynucleotides (29mers) containing an O6-ethylguanine (O6-EtGua) flanked 5' and 3' by different bases (5'..TGT..3'; 5'..CGG..3', 5'..GGT..3'; 5'..GGG..3'; 5'..GGA..3') were synthesized to investigate the binding and repair characteristics of recombinant human O6-alkylguanine-DNA alkyltransf...

journal_title：Nucleic acids research

authors： Bender K,Federwisch M,Loggen U,Nehls P,Rajewsky MF

更新日期：1996-06-01 00:00:00

abstract：:Human 2'-5' oligoadenylate synthetase-1 (OAS1) is central in innate immune system detection of cytoplasmic double-stranded RNA (dsRNA) and promotion of host antiviral responses. However, the molecular signatures that promote OAS1 activation are currently poorly defined. We show that the 3'-end polyuridine sequence of ...

journal_title：Nucleic acids research

authors： Vachon VK,Calderon BM,Conn GL

更新日期：2015-01-01 00:00:00

abstract：:Although a vast amount of life sciences data is generated in the form of images, most scientists still store images on extremely diverse and often incompatible storage media, without any type of metadata structure, and thus with no standard facility with which to conduct searches or analyses. Here we present a solutio...

journal_title：Nucleic acids research

authors： Gonzalez-Couto E,Hayes B,Danckaert A

更新日期：2001-01-01 00:00:00