SMART 6: recent updates and new developments.

abstract：:Human telomerase RNA (hTR) contains several guanine tracts at its 5'-end that can form a G4-quadruplex structure. Previous evidence suggests that a G4-quadruplex within this region disrupts the formation of an important structure within hTR known as the P1 helix, a critical element in defining the template boundary fo...

journal_title：Nucleic acids research

authors： Booy EP,Meier M,Okun N,Novakowski SK,Xiong S,Stetefeld J,McKenna SA

更新日期：2012-05-01 00:00:00

abstract：:Single cell RNA-seq experiments provide valuable insight into cellular heterogeneity but suffer from low coverage, 3' bias and technical noise. These unique properties of single cell RNA-seq data make study of alternative splicing difficult, and thus most single cell studies have restricted analysis of transcriptome v...

journal_title：Nucleic acids research

authors： Welch JD,Hu Y,Prins JF

更新日期：2016-05-05 00:00:00

abstract：:The last 82 nucleotides of the 6.3 kb genomic RNA of plant turnip yellow mosaic virus (TYMV), the so-called 'tRNA-like' domain, presents functional, structural and primary sequence homologies with canonical tRNAs. In particular, one of the stem-loops resembles the TPsi(pseudouridine)-branch of tRNA, except for the pre...

journal_title：Nucleic acids research

authors： Becker HF,Motorin Y,Florentz C,Giegé R,Grosjean H

更新日期：1998-09-01 00:00:00

abstract：:Budding yeast telomerase is mainly activated by Tel1/Mec1 (yeast ATM/ATR) on Cdc13 from late S to G2 phase of the cell cycle. Here, we demonstrated that the telomerase-recruitment domain of Cdc13 is also phosphorylated by Cdk1 at the same cell cycle stage as the Tel1/Mec1-dependent regulation. Phosphor-specific gel an...

journal_title：Nucleic acids research

authors： Tseng SF,Shen ZJ,Tsai HJ,Lin YH,Teng SC

更新日期：2009-06-01 00:00:00

abstract：:The recent publication of the Caenorhabditis elegans cisRED database has provided an extensive catalog of upstream elements that are conserved between nematode genomes. We have performed a secondary analysis to determine which subsequences of the cisRED motifs are found in multiple locations throughout the C. elegans ...

journal_title：Nucleic acids research

authors： Sleumer MC,Mah AK,Baillie DL,Jones SJ

更新日期：2010-05-01 00:00:00

abstract：:Classical simulations of protein flexibility remain computationally expensive, especially for large proteins. A few years ago, we developed a fast method for predicting protein structure fluctuations that uses a single protein model as the input. The method has been made available as the CABS-flex web server and appli...

journal_title：Nucleic acids research

authors： Kuriata A,Gierut AM,Oleniecki T,Ciemny MP,Kolinski A,Kurcinski M,Kmiecik S

更新日期：2018-07-02 00:00:00

abstract：:Gaussian network model (GNM) is a simple yet powerful model for investigating the dynamics of proteins and their complexes. GNM analysis became a broadly used method for assessing the conformational dynamics of biomolecular structures with the development of a user-friendly interface and database, iGNM, in 2005. We pr...

journal_title：Nucleic acids research

authors： Li H,Chang YY,Yang LW,Bahar I

更新日期：2016-01-04 00:00:00

abstract：:Annotation of herpesvirus genomes has traditionally been undertaken through the detection of open reading frames and other genomic motifs, supplemented with sequencing of individual cDNAs. Second generation sequencing and high-density microarray studies have revealed vastly greater herpesvirus transcriptome complexity...

journal_title：Nucleic acids research

authors： O'Grady T,Wang X,Höner Zu Bentrup K,Baddoo M,Concha M,Flemington EK

更新日期：2016-10-14 00:00:00

abstract：:A fiber optic biosensor was used for the fluorimetric detection of T/AT triple-helical DNA formation. The surfaces of two sets of fused silica optical fibers were functionalized with hexaethylene oxide linkers from which decaadenylic acid oligonucleotides were grown in the 3'to 5'and 5'to 3'direction, respectively, us...

journal_title：Nucleic acids research

authors： Uddin AH,Piunno PA,Hudson RH,Damha MJ,Krull UJ

更新日期：1997-10-15 00:00:00

abstract：:2'-Deoxyoligonucleotides with 5-fluorocytosine residues incorporated at specific positions of the nucleotide sequence are tools of great potential in the study of the catalytic mechanism by which DNA cytosine methyltransferases methylate the 5-position of DNA cytosine residues in specific sequence contexts. Chemical s...

journal_title：Nucleic acids research

authors： Schmidt S,Pein CD,Fritz HJ,Cech D

更新日期：1992-05-25 00:00:00

abstract：:The interactions of self-complementary oligonucleotides with a group of metal-mediated DNA-binding drugs, including chromomycin A(3), mithramycin and the novel compound UK-1, were examined via electrospray ionization quadrupole ion trap mass spectrometry. Both chromomycin and mithramycin were shown to bind preferentia...

journal_title：Nucleic acids research

authors： Reyzer ML,Brodbelt JS,Kerwin SM,Kumar D

更新日期：2001-11-01 00:00:00

abstract：:During S phase, the entire genome must be precisely duplicated, with no sections of DNA left unreplicated. Here, we develop a simple mathematical model to describe the probability of replication failing due to the irreversible stalling of replication forks. We show that the probability of complete genome replication i...

journal_title：Nucleic acids research

authors： Newman TJ,Mamun MA,Nieduszynski CA,Blow JJ

更新日期：2013-11-01 00:00:00

abstract：:DNA synthesis of broad host-range plasmid R1162 is initiated from two positions, flanking a large (40 bp stem, 40 bp loop) inverted repeat. Each start-point is located within a highly conserved, but oppositely oriented, 10 base-pair sequence. Synthesis from the two positions converges within the intervening inverted r...

journal_title：Nucleic acids research

authors： Lin LS,Meyer RJ

更新日期：1987-10-26 00:00:00

abstract：:A highly sensitive method to detect traces of aldehyde-containing apurinic/apyrimidinic (AP) sites in nucleic acids has been developed. Based on this method, a novel approach to detect DNA base mismatches recognized by the mismatch repair glycosylase MutY is demonstrated. Open chain aldehydes generated in nucleic acid...

journal_title：Nucleic acids research

authors： Maulik G,Botchway S,Chakrabarti S,Tetradis S,Price B,Makrigiorgos GM

更新日期：1999-03-01 00:00:00

abstract：:A sensitive gel retention assay has been utilized to detect proteins from uninfected Hela nuclei which interact with the adenovirus type 2 enhancer. This assay has been employed to monitor fractionation of nuclear extracts. Three enhancer binding factors were resolved by chromatography on DEAE-Sepharose and one of the...

journal_title：Nucleic acids research

authors： Barrett P,Clark L,Hay RT

更新日期：1987-03-25 00:00:00

abstract：UNLABELLED:Partial cleavage of DNA with the restriction endonuclease NotI (5'...GC/GGCCGC...3') is an important technique for genomic mapping. However, partial genomic cleavage with this enzyme is impaired by the agarose matrix in which the DNA must be suspended. To solve this problem we have purified the blocking meth...

journal_title：Nucleic acids research

authors： Hanish J,McClelland M

更新日期：1990-06-11 00:00:00

abstract：:Using peptide arrays and binding to native histone proteins, we show that the ADD domain of Dnmt3a specifically interacts with the H3 histone 1-19 tail. Binding is disrupted by di- and trimethylation of K4, phosphorylation of T3, S10 or T11 and acetylation of K4. We did not observe binding to the H4 1-19 tail. The ADD...

journal_title：Nucleic acids research

authors： Zhang Y,Jurkowska R,Soeroes S,Rajavelu A,Dhayalan A,Bock I,Rathert P,Brandt O,Reinhardt R,Fischle W,Jeltsch A

更新日期：2010-07-01 00:00:00

abstract：:Two new endonuclease activities, endonuclease B and endonuclease C, obtained from yeast nuclear preparations have been separated and partially characterized. Endonuclease B has a primary requirement for Mn2+ which cannot be replaced by Mg2+ or Ca2+, and makes single-strand scissions in double-stranded DNA. Endonculeas...

journal_title：Nucleic acids research

authors： Pinon R,Leney E

更新日期：1975-07-01 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

authors： Grosjean H,Westhof E

更新日期：2016-09-30 00:00:00

abstract：:Linked-atom molecular modelling was employed to determine the steric and torsional requirements for intercalation of proflavine into a double-stranded region of DNA compatible with adjacent regions of cohelical A-DNA. The optimum intercalation conformation is characterized by the dihedral angles xi and psi becoming tr...

journal_title：Nucleic acids research

authors： Alden CJ,Arnott S

更新日期：1977-11-01 00:00:00

abstract：:RNA polymerase III recognizes and pauses at its terminator, an oligo(dT) tract in non-template DNA, terminates 3' oligo(rU) synthesis within this sequence, and releases the RNA. The pol III subunit Rpc11p (C11) mediates RNA 3'-5' cleavage in the catalytic center of pol III during pausing. The amino and carboxyl region...

journal_title：Nucleic acids research

authors： Iben JR,Mazeika JK,Hasson S,Rijal K,Arimbasseri AG,Russo AN,Maraia RJ

更新日期：2011-08-01 00:00:00

abstract：:Originally identified as an RNA polymerase II interactor, Che-1/AATF (Che-1) has now been recognized as a multifunctional protein involved in cell-cycle regulation and cancer progression, as well as apoptosis inhibition and response to stress. This protein displays a peculiar nucleolar localization and it has recently...

journal_title：Nucleic acids research

authors： Sorino C,Catena V,Bruno T,De Nicola F,Scalera S,Bossi G,Fabretti F,Mano M,De Smaele E,Fanciulli M,Iezzi S

更新日期：2020-06-19 00:00:00

abstract：:An effective tool for the global analysis of both DNA methylation status and protein-chromatin interactions is a microarray constructed with sequences containing regulatory elements. One type of array suited for this purpose takes advantage of the strong association between CpG Islands (CGIs) and gene regulatory regio...

journal_title：Nucleic acids research

authors： Heisler LE,Torti D,Boutros PC,Watson J,Chan C,Winegarden N,Takahashi M,Yau P,Huang TH,Farnham PJ,Jurisica I,Woodgett JR,Bremner R,Penn LZ,Der SD

更新日期：2005-05-23 00:00:00

abstract：:The three chromosomal DNAs of S. pombe have been fractionated by pulsed field gel electrophoresis. The resulting molecular karyotype will greatly speed gene mapping in this organism, and it indicates that the separation range of the technique extends to DNA molecules as large as 9,000,000 base pairs. ...

journal_title：Nucleic acids research

authors： Smith CL,Matsumoto T,Niwa O,Klco S,Fan JB,Yanagida M,Cantor CR

更新日期：1987-06-11 00:00:00

abstract：:Influenza viruses have a segmented viral RNA (vRNA) genome, which is replicated by the viral RNA-dependent RNA polymerase (RNAP). Replication initiates on the vRNA 3' terminus, producing a complementary RNA (cRNA) intermediate, which serves as a template for the synthesis of new vRNA. RNAP structures show the 3' termi...

journal_title：Nucleic acids research

authors： Robb NC,Te Velthuis AJ,Wieneke R,Tampé R,Cordes T,Fodor E,Kapanidis AN

更新日期：2016-12-01 00:00:00

abstract：:In some preparations of DNA dependent RNA polymerase a new enzymatic activity has been found which catalyzes the condensation of two pyrophosphate molecules, liberated in the process of RNA synthesis, to one molecule of orthophosphate and one molecule of Mg (or Mn) - chelate complex with trimetaphosphate. This activit...

journal_title：Nucleic acids research

authors： Volloch VZ,Rits S,Tumerman L

更新日期：1979-04-01 00:00:00

abstract：:Methylthiotransferases (MTTases) are a closely related family of proteins that perform both radical-S-adenosylmethionine (SAM) mediated sulfur insertion and SAM-dependent methylation to modify nucleic acid or protein targets with a methyl thioether group (-SCH(3)). Members of two of the four known subgroups of MTTases...

journal_title：Nucleic acids research

authors： Anton BP,Russell SP,Vertrees J,Kasif S,Raleigh EA,Limbach PA,Roberts RJ

更新日期：2010-10-01 00:00:00

abstract：:Primer design is a fundamental technique that is widely used for polymerase chain reaction (PCR). Although many methods have been proposed for primer design, they require a great deal of manual effort to generate feasible and valid primers, including homology tests on off-target sequences using BLAST-like tools. That ...

journal_title：Nucleic acids research

authors： Kim H,Kang N,Chon KW,Kim S,Lee N,Koo J,Kim MS

更新日期：2015-11-16 00:00:00

abstract：:As more and more high-throughput data has been produced by next-generation sequencing, it is still a challenge to classify RNA transcripts into protein-coding or non-coding, especially for poorly annotated species. We upgraded our original coding potential calculator, CNCI (Coding-Non-Coding Index), to CNIT (Coding-No...

journal_title：Nucleic acids research

authors： Guo JC,Fang SS,Wu Y,Zhang JH,Chen Y,Liu J,Wu B,Wu JR,Li EM,Xu LY,Sun L,Zhao Y

更新日期：2019-07-02 00:00:00

abstract：:Every bulky lesion in DNA can potentially inhibit the Taq DNA polymerase and thereby decrease the amplification produced in the polymerase chain reaction. We investigated the feasibility of using this inhibition to quantify DNA lesions produced by the anticancer drug cisplatin. Products were detected by electrophoresi...

journal_title：Nucleic acids research

authors： Jennerwein MM,Eastman A

更新日期：1991-11-25 00:00:00