Visualizing helicases unwinding DNA at the single molecule level.

abstract：:Endonuclease III from Escherichia coli, yeast (yNtg1p and yNtg2p) and human and E.coli endonuclease VIII have a wide substrate specificity, and recognize oxidation products of both thymine and cytosine. DNA containing single dihydrouracil (DHU) and tandem DHU lesions were used as substrates for these repair enzymes. I...

journal_title：Nucleic acids research

authors： Venkhataraman R,Donald CD,Roy R,You HJ,Doetsch PW,Kow YW

更新日期：2001-01-15 00:00:00

abstract：:Highly regulated induction systems enabling dose-dependent and reversible fine-tuning of protein expression output are beneficial for engineering complex biosynthetic pathways. To address this, we developed PhiReX, a novel red/far-red light-regulated protein expression system for use in Saccharomyces cerevisiae. PhiRe...

journal_title：Nucleic acids research

authors： Hochrein L,Machens F,Messerschmidt K,Mueller-Roeber B

更新日期：2017-09-06 00:00:00

abstract：:Nonsense-mediated mRNA decay (NMD) is a molecular pathway of mRNA surveillance that ensures rapid degradation of mRNAs containing premature translation termination codons (PTCs) in eukaryotes. NMD has been shown to also regulate normal gene expression and thus emerged as one of the key post-transcriptional mechanisms ...

journal_title：Nucleic acids research

authors： Viegas MH,Gehring NH,Breit S,Hentze MW,Kulozik AE

更新日期：2007-01-01 00:00:00

abstract：:Transcriptionally non-co-linear (NCL) transcripts can originate from trans-splicing (trans-spliced RNA; 'tsRNA') or cis-backsplicing (circular RNA; 'circRNA'). While numerous circRNAs have been detected in various species, tsRNAs remain largely uninvestigated. Here, we utilize integrative transcriptome sequencing of p...

journal_title：Nucleic acids research

authors： Chuang TJ,Chen YJ,Chen CY,Mai TL,Wang YD,Yeh CS,Yang MY,Hsiao YT,Chang TH,Kuo TC,Cho HH,Shen CN,Kuo HC,Lu MY,Chen YH,Hsieh SC,Chiang TW

更新日期：2018-04-20 00:00:00

abstract：:Alternative splicing generates multiple transcript and protein isoforms from a single gene and controls transcript intracellular localization and stability by coupling to mRNA export and nonsense-mediated mRNA decay (NMD). RNA interference (RNAi) is a potent mechanism to modulate gene expression. However, its interact...

journal_title：Nucleic acids research

authors： Fuchs A,Riegler S,Ayatollahi Z,Cavallari N,Giono LE,Nimeth BA,Mutanwad KV,Schweighofer A,Lucyshyn D,Barta A,Petrillo E,Kalyna M

更新日期：2021-01-25 00:00:00

abstract：:The loss of the tumour suppressor E-cadherin (Cdh1) is a key event during tumourigenesis and epithelial-mesenchymal transition (EMT). Transforming growth factor-β (TGFβ) triggers EMT by inducing the expression of non-histone chromatin protein High Mobility Group A2 (HMGA2). We have previously shown that HMGA2, togethe...

journal_title：Nucleic acids research

authors： Tan EJ,Kahata K,Idås O,Thuault S,Heldin CH,Moustakas A

更新日期：2015-01-01 00:00:00

abstract：:Much effort has long been devoted to unraveling the coordinated cellular response to genotoxic insults. In view of the difficulty of obtaining human biological samples of homogeneous origin, I have established a set of stable human clones where one DNA repair gene has been stably silenced by means of RNA interference....

journal_title：Nucleic acids research

authors： Biard DS

更新日期：2007-01-01 00:00:00

abstract：:Communication between distantly spaced genomic regions is one of the key features of gene regulation in eukaryotes. Chromatin per se can stimulate efficient enhancer-promoter communication (EPC); however, the role of chromatin structure and dynamics in this process remains poorly understood. Here we show that nucleoso...

journal_title：Nucleic acids research

authors： Nizovtseva EV,Clauvelin N,Todolli S,Polikanov YS,Kulaeva OI,Wengrzynek S,Olson WK,Studitsky VM

更新日期：2017-04-07 00:00:00

abstract：:Chromatin footprinting in Drosophila tissue culture cells has detected the binding of a non-histone protein at +8 of the distal Adh RNA start site, on a 10-bp direct repeat motif abutting a nucleosome positioned over the inactive Adh distal promoter. Alternatively the active promoter is bound by a transcription initia...

journal_title：Nucleic acids research

authors： Benyajati C,Ewel A,McKeon J,Chovav M,Juan E

更新日期：1992-09-11 00:00:00

abstract：:The splicing factor Sam68 is upregulated in many human cancers, including prostate cancer (PCa) where it promotes cell proliferation and survival. Nevertheless, in spite of its frequent upregulation in cancer, the mechanism(s) underlying its expression are largely unknown. Herein, bioinformatics analyses identified th...

journal_title：Nucleic acids research

authors： Caggiano C,Pieraccioli M,Panzeri V,Sette C,Bielli P

更新日期：2019-07-09 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：:Non-homologous DNA end joining (NHEJ) is considered the major pathway of double-strand break (DSB) repair in mammalian cells and depends, among other things, on the DNA end-binding Ku70/80 hetero-dimer. To investigate the function of Ku in NHEJ we have compared the ability of cell-free extracts from wild-type CHO-K1 c...

journal_title：Nucleic acids research

authors： Feldmann E,Schmiemann V,Goedecke W,Reichenberger S,Pfeiffer P

更新日期：2000-07-01 00:00:00

abstract：:Transgenic mice have proven to be an effective expression system for studying developmental control of the human fetal and adult beta-globin genes. In the current work we are interested in developing the transgenic mouse system for the study of the human embryonic beta-globin gene, epsilon. An epsilon-globin gene cons...

journal_title：Nucleic acids research

authors： Shih DM,Wall RJ,Shapiro SG

更新日期：1990-09-25 00:00:00

abstract：:A new series of DNA bis-intercalators is reported in which acridine moieties are connected by rigid and extended pyridine-based linkers of varied length. Cross-linking of DNA by bis-intercalation is inferred from the unwinding and folding of linear DNA induced by the compounds; after ligation and removal of the bis-in...

journal_title：Nucleic acids research

authors： Annan NK,Cook PR,Mullins ST,Lowe G

更新日期：1992-03-11 00:00:00

abstract：:The interactions of archetypical nucleic acid ligands with the HIV-1 polypurine tract (PPT) RNA:DNA hybrid, as well as analogous DNA:DNA, RNA:RNA and swapped hybrid substrates, were used to probe structural features of the PPT that contribute to its specific recognition and processing by reverse transcriptase (RT). Re...

journal_title：Nucleic acids research

authors： Turner KB,Brinson RG,Yi-Brunozzi HY,Rausch JW,Miller JT,Le Grice SF,Marino JP,Fabris D

更新日期：2008-05-01 00:00:00

abstract：:The Chinese hamster cell line, DC-3F, is heterozygous at the DHFR locus, and each allele can be distinguished on the basis of a unique DNA restriction pattern, protein isoelectric profile and in the abundancy of the DHFR mRNAs it expresses. Although each allele produces four transcripts, 1000, 1650 and 2150 nucleotide...

journal_title：Nucleic acids research

authors： Scotto KW,Yang H,Davide JP,Melera PW

更新日期：1992-12-25 00:00:00

abstract：:Actin is a major cytoskeletal protein in eukaryotes. Recent studies suggest more diverse functional roles for this protein. Actin mRNA is known to be localized to neuronal synapses and undergoes rapid deadenylation during early developmental stages. However, its 3'-untranslated region (UTR) is not characterized and th...

journal_title：Nucleic acids research

authors： Ghosh T,Soni K,Scaria V,Halimani M,Bhattacharjee C,Pillai B

更新日期：2008-11-01 00:00:00

abstract：:Gene Ontology (GO) is the most widely accepted attempt to construct a unified and structured vocabulary for the description of genes and their products in any organism. Annotation by GO terms is performed in most of the current genome projects, which besides generality has the advantage of being very convenient for co...

journal_title：Nucleic acids research

authors： Hennig S,Groth D,Lehrach H

更新日期：2003-07-01 00:00:00

abstract：:Eukaryotic RNases H from Saccharomyces cerevisiae , Schizosaccharomyces pombe and Crithidia fasciculata , unlike the related Escherichia coli RNase HI, contain a non-RNase H domain with a common motif. Previously we showed that S.cerevisiae RNase H1 binds to duplex RNAs (either RNA-DNA hybrids or double-stranded RNA) ...

journal_title：Nucleic acids research

authors： Cerritelli SM,Fedoroff OY,Reid BR,Crouch RJ

更新日期：1998-04-01 00:00:00

abstract：:The accurate calculation of protein/nucleic acid-ligand interactions or condensed phase properties by force field-based methods require a precise description of the energetics of intermolecular interactions. Despite the progress made in force fields, small molecule parameterization remains an open problem due to the m...

journal_title：Nucleic acids research

authors： Dodda LS,Cabeza de Vaca I,Tirado-Rives J,Jorgensen WL

更新日期：2017-07-03 00:00:00

abstract：:It has recently been demonstrated that nucleobase-density profiles of typical mRNA coding sequences exhibit a complementary relationship with nucleobase-interaction propensity profiles of their cognate protein sequences. This finding supports the idea that the genetic code developed in response to direct binding inter...

journal_title：Nucleic acids research

authors： Hlevnjak M,Zagrovic B

更新日期：2015-03-31 00:00:00

abstract：:Augmented biological activity in vitro has been demonstrated in oligonucleotides (oligos) modified to provide nuclease resistance, to enhance cellular uptake or to increase target affinity. How chemical modification affects the duration of effect of an oligo with potent activity has not been investigated directly. We ...

journal_title：Nucleic acids research

authors： Tam RC,Li Y,Noonberg S,Hwang DG,Lui G,Hunt CA,Garovoy MR

更新日期：1994-03-25 00:00:00

abstract：:The U1 snRNP-specific protein C contains an N-terminal zinc finger-like CH motif which is required for the binding of the U1C protein to the U1 snRNP particle. Recently a similar motif was reported to be essential for in vivo homodimerization of the yeast splicing factor PRP9. In the present study we demonstrate that ...

journal_title：Nucleic acids research

authors： Gunnewiek JM,van Aarssen Y,Wassenaar R,Legrain P,van Venrooij WJ,Nelissen RL

更新日期：1995-12-11 00:00:00

abstract：:This work presents the Apo-Holo DataBase (AH-DB, http://ahdb.ee.ncku.edu.tw/ and http://ahdb.csbb.ntu.edu.tw/), which provides corresponding pairs of protein structures before and after binding. Conformational transitions are commonly observed in various protein interactions that are involved in important biological f...

journal_title：Nucleic acids research

authors： Chang DT,Yao TJ,Fan CY,Chiang CY,Bai YH

更新日期：2012-01-01 00:00:00

abstract：:We propose a novel mechanism of gene regulation in Mycobacterium tuberculosis where the protein Rv1222 inhibits transcription by anchoring RNA polymerase (RNAP) onto DNA. In contrast to our existing knowledge that transcriptional repressors function either by binding to DNA at specific sequences or by binding to RNAP,...

journal_title：Nucleic acids research

authors： Rudra P,Prajapati RK,Banerjee R,Sengupta S,Mukhopadhyay J

更新日期：2015-07-13 00:00:00

abstract：:The mRNA export complex TREX (TREX) is known to contain Aly, UAP56, Tex1 and the THO complex, among which UAP56 is required for TREX assembly. Here, we systematically investigated the role of each human TREX component in TREX assembly and its association with the mRNA. We found that Tex1 is essentially a subunit of th...

journal_title：Nucleic acids research

authors： Chi B,Wang Q,Wu G,Tan M,Wang L,Shi M,Chang X,Cheng H

更新日期：2013-01-01 00:00:00

abstract：:The alternation/deficiency in activation-3 (ADA3) is an essential component of the human p300/CBP-associated factor (PCAF) and yeast Spt-Ada-Gcn5-acetyltransferase (SAGA) histone acetyltransferase complexes. These complexes facilitate transactivation of target genes by association with transcription factors and modifi...

journal_title：Nucleic acids research

authors： Li CW,Ai N,Dinh GK,Welsh WJ,Chen JD

更新日期：2010-09-01 00:00:00

abstract：:SITEHOUND-web (http://sitehound.sanchezlab.org) is a binding-site identification server powered by the SITEHOUND program. Given a protein structure in PDB format SITEHOUND-web will identify regions of the protein characterized by favorable interactions with a probe molecule. These regions correspond to putative ligand...

journal_title：Nucleic acids research

authors： Hernandez M,Ghersi D,Sanchez R

更新日期：2009-07-01 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：:Short interfering RNAs (siRNAs) are valuable reagents for sequence-specific inhibition of gene expression via the RNA interference (RNAi) pathway. Although it has been proposed that the relative thermodynamic stability at the 5'-ends of siRNAs plays a crucial role in siRNA strand selection, we demonstrate here that a ...

journal_title：Nucleic acids research

authors： Sano M,Sierant M,Miyagishi M,Nakanishi M,Takagi Y,Sutou S

更新日期：2008-10-01 00:00:00