Allosteric DNAzyme-based DNA logic circuit: operations and dynamic analysis.

abstract：:Sets of genes expressed in the same tissue are believed to be under the regulation of a similar set of transcription factors, and can thus be assumed to contain similar structural patterns in their regulatory regions. Here we present a study of the structural patterns in promoters of genes expressed specifically in 26...

journal_title：Nucleic acids research

authors： Vandenbon A,Nakai K

更新日期：2010-01-01 00:00:00

abstract：:Transcription driven by the proviral promoter of the Human T-cell Leukemia Virus type I (HTLV-I) is tightly regulated by the Tax1 transactivator. This viral protein potently induces the enhancer activity of a 21 bp motif repeated three times in the promoter. We have previously shown that this induction results from th...

journal_title：Nucleic acids research

authors： Lombard-Platet G,Jalinot P

更新日期：1993-08-25 00:00:00

abstract：:To elucidate the response to oxidative stress in eukaryotic cells, the effect of an oxidized nucleotide, 8-oxo-2'-deoxyguanosine 5'-triphosphate (8-oxo-dGTP), generated from dGTP with an active oxygen, on DNA synthesis was studied using a cell-free DNA replication system derived from Xenopus egg lysates with a single-...

journal_title：Nucleic acids research

authors： Kai T,Matsunaga R,Eguchi M,Kamiya H,Kasai H,Suzuki M,Izuta S

更新日期：2002-01-15 00:00:00

abstract：:Rad18 is a ubiquitin E3 ligase that monoubiquitinates PCNA on stalled replications forks. This allows recruitment of damage-tolerant polymerases for damage bypass and DNA repair. In this activity, the Rad18 protein has to interact with Rad6, the E2 ubiquitin-conjugating enzyme, ubiquitin, PCNA and DNA. Here we analyze...

journal_title：Nucleic acids research

authors： Notenboom V,Hibbert RG,van Rossum-Fikkert SE,Olsen JV,Mann M,Sixma TK

更新日期：2007-01-01 00:00:00

abstract：:Streptomyces bldA gene, which encodes a tRNA corresponding to a very minor leucine codon, UUA, regulates pleiotropic gene expression which is involved in sporulation and secondary metabolism. The unique structural feature of this tRNA is the lack of GG sequence in dihydrouridine loop (D-loop) that generally is conserv...

journal_title：Nucleic acids research

authors： Ueda Y,Kumagai I,Miura K

更新日期：1992-08-11 00:00:00

abstract：:Retroviral particles contain a dimeric RNA genome, which serves as template for the generation of double-stranded DNA by reverse transcription. Transfer between RNA strands during DNA synthesis is governed by both sequence similarity between templates and structural features of the dimeric RNA. A kissing hairpin, beli...

journal_title：Nucleic acids research

authors： Mikkelsen JG,Rasmussen SV,Pedersen FS

更新日期：2004-01-09 00:00:00

abstract：:The vitamin D receptor mediates the signal of 1 alpha, 25-dihydroxyvitamin D3 by binding to vitamin D responsive elements in DNA as a homodimer or as a heterodimer composed of one vitamin D receptor subunit and one retinoid X receptor subunit. We have mapped the dimerization interfaces of the vitamin D receptor that i...

journal_title：Nucleic acids research

authors： Nishikawa J,Kitaura M,Imagawa M,Nishihara T

更新日期：1995-02-25 00:00:00

abstract：:A general approach for the synthesis of oligonucleotide-triplet phosphoramidites and the synthesis of four such blocks are described. A strategy was devised to minimize the number of dimer precursors needed for synthesis of a complete set of triplet-amidite blocks encoding all 20 amino acids. Whereas synthesis of 20 t...

journal_title：Nucleic acids research

authors： Ono A,Matsuda A,Zhao J,Santi DV

更新日期：1995-11-25 00:00:00

abstract：:The possibility of cloning large segments of DNA in cosmid vectors offers distinct advantages, in particular for the study of multigene families. Large size fragments of mouse embryo DNA were successfully cloned in the cosmid pHC 79. Twelve recombinants hybridizing specifically to an immunoglobulin kappa chain variabl...

journal_title：Nucleic acids research

authors： Cattaneo R,Gorski J,Mach B

更新日期：1981-06-25 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：:The nucleotide sequence for human argininosuccinate synthetase cDNA was determined by analysis of six clones isolated from a single experiment. The sequence covered 1623 nucleotides including 76 bases of poly(A) and contained a 1236 nucleotide open reading frame encoding a protein of 46,434 daltons. In one cDNA isolat...

journal_title：Nucleic acids research

authors： Bock HG,Su TS,O'Brien WE,Beaudet AL

更新日期：1983-09-24 00:00:00

abstract：:Mature tRNAPhe from Escherichia coli and the transcript of its gene lacking modified nucleotides were compared by a variety of physical techniques. Melting experiments revealed that at a low Mg2+level the transcript was partially denatured, while the mature tRNA possessed intact tertiary interactions. Mg2+binding to b...

journal_title：Nucleic acids research

authors： Serebrov V,Vassilenko K,Kholod N,Gross HJ,Kisselev L

更新日期：1998-06-01 00:00:00

abstract：:DAXX displays complex biological functions. Remarkably, DAXX overexpression is a common feature in diverse cancers, which correlates with tumorigenesis, disease progression and treatment resistance. Structurally, DAXX is modular with an N-terminal helical bundle, a docking site for many DAXX interactors (e.g. p53 and ...

journal_title：Nucleic acids research

authors： Mahmud I,Liao D

更新日期：2019-09-05 00:00:00

abstract：:Improving the accuracy of prediction of gene starts is one of a few remaining open problems in computer prediction of prokaryotic genes. Its difficulty is caused by the absence of relatively strong sequence patterns identifying true translation initiation sites. In the current paper we show that the accuracy of gene s...

journal_title：Nucleic acids research

authors： Besemer J,Lomsadze A,Borodovsky M

更新日期：2001-06-15 00:00:00

abstract：:A stable conformer of Escherichia coli tRNA(Glu), obtained in the absence of Mg(2+), is inactive in the aminoacylation reaction. Probing it with diethylpyrocarbonate, dimethyl sulfate and ribonuclease V1 revealed that it has a hairpin structure with two internal loops; the helical segments at both extremities have the...

journal_title：Nucleic acids research

authors： Madore E,Florentz C,Giegé R,Lapointe J

更新日期：1999-09-01 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：:The nucleotide sequence of the chick beta-actin gene was determined. The gene contains 5 introns; 4 interrupt the translated region at codons 41/42, 120/122, 267, 327/328 and a large intron occurs in the 5' untranslated region. The gene has a 97 nucleotide 5'-untranslated region and a 594 nucleotide 3'-untranslated re...

journal_title：Nucleic acids research

authors： Kost TA,Theodorakis N,Hughes SH

更新日期：1983-12-10 00:00:00

abstract：:The HIV-1 viral infectivity factor (Vif) allows productive infection of non-permissive cells (including most natural HIV-1 targets) by counteracting the cellular cytosine deaminases APOBEC-3G (hA3G) and hA3F. The Vif-induced degradation of these restriction factors by the proteasome has been extensively studied, but l...

journal_title：Nucleic acids research

authors： Mercenne G,Bernacchi S,Richer D,Bec G,Henriet S,Paillart JC,Marquet R

更新日期：2010-01-01 00:00:00

abstract：:Cooperative hybridization has been used to establish physical linkage between two loci on a DNA strand. Linkage was detected by hybridization to a new type of high-density oligonucleotide array. Each synthesis location on the array contains a mixture of two different probe sequences. Each of the two probes can hybridi...

journal_title：Nucleic acids research

authors： Gentalen E,Chee M

更新日期：1999-03-15 00:00:00

abstract：:HORMA domain-containing proteins (HORMADs) play an essential role in meiosis in many organisms. The meiotic HORMADs, including yeast Hop1, mouse HORMAD1 and HORMAD2, and Arabidopsis ASY1, assemble along chromosomes at early prophase and the closure motif at their C-termini has been hypothesized to be instrumental for ...

journal_title：Nucleic acids research

authors： Yang C,Hu B,Portheine SM,Chuenban P,Schnittger A

更新日期：2020-11-18 00:00:00

abstract：:Laser microirradiation is a powerful tool for real-time single-cell analysis of the DNA damage response (DDR). It is often found, however, that factor recruitment or modification profiles vary depending on the laser system employed. This is likely due to an incomplete understanding of how laser conditions/dosages affe...

journal_title：Nucleic acids research

authors： Saquilabon Cruz GM,Kong X,Silva BA,Khatibzadeh N,Thai R,Berns MW,Yokomori K

更新日期：2016-02-18 00:00:00

abstract：:Genetic screens in Saccharomyces cerevisiae have identified the roles of ribosome components, tRNAs and translation factors in translational fidelity. These screens rely on the suppression of altered start codons, nonsense codons or frameshift mutations in genes involved in amino acid or nucleotide metabolism. Many of...

journal_title：Nucleic acids research

authors： Magazinnik T,Anand M,Sattlegger E,Hinnebusch AG,Kinzy TG

更新日期：2005-08-12 00:00:00

abstract：:Isopentenyl adenosine derivatives are always located adjacent to the 3' end of the anticodon in transfer RNA and have been implicated in certain biological functions. In the enteric bacterium, E. coli, the derivative is ms2i6A whereas in some plant associated bacteria the derivative is the hydroxylated form, ms2io6A. ...

journal_title：Nucleic acids research

authors： Janzer JJ,Raney JP,McLennan BD

更新日期：1982-09-25 00:00:00

abstract：:Elucidating the dynamic organization of nuclear RNA foci is important for understanding and manipulating these functional sites of gene expression in both physiological and pathological states. However, such studies have been difficult to establish in vivo as a result of the absence of suitable RNA imaging methods. He...

journal_title：Nucleic acids research

authors： Oomoto I,Suzuki-Hirano A,Umeshima H,Han YW,Yanagisawa H,Carlton P,Harada Y,Kengaku M,Okamoto A,Shimogori T,Wang DO

更新日期：2015-10-30 00:00:00

abstract：:Large-scale sequencing studies discovered substantial genetic variants occurring in enhancers which regulate genes via long range chromatin interactions. Importantly, such variants could affect enhancer regulation by changing transcription factor bindings or enhancer hijacking, and in turn, make an essential contribut...

journal_title：Nucleic acids research

authors： Zhang G,Shi J,Zhu S,Lan Y,Xu L,Yuan H,Liao G,Liu X,Zhang Y,Xiao Y,Li X

更新日期：2018-01-04 00:00:00

abstract：:Genome editing using clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) predominantly induces non-homologous end joining (NHEJ), which generates random insertions or deletions, whereas homology-directed repair (HDR), which generates precise recombination products, is ...

journal_title：Nucleic acids research

authors： Kato-Inui T,Takahashi G,Hsu S,Miyaoka Y

更新日期：2018-05-18 00:00:00

abstract：:Modification of chromatin and related transcription factors by histone deacetylases (HDACs) is one of the major strategies for controlling gene expression in eukaryotes. The HDAC domains of class IIa HDACs repress the respective target genes by interacting with the C-terminal region of the silencing mediator for retin...

journal_title：Nucleic acids research

authors： Park SY,Kim GS,Hwang HJ,Nam TH,Park HS,Song J,Jang TH,Lee YC,Kim JS

更新日期：2018-12-14 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：:The k-junction is a structural motif in RNA comprising a three-way helical junction based upon kink turn (k-turn) architecture. A computer program written to examine relative helical orientation identified the three-way junction of the Arabidopsis TPP riboswitch as an elaborated k-turn. The Escherichia coli TPP ribosw...

journal_title：Nucleic acids research

authors： Wang J,Daldrop P,Huang L,Lilley DM

更新日期：2014-04-01 00:00:00

abstract：:In kinetoplastid protozoa, mitochondrial (mt) mRNAs are post-transcriptionally edited by insertion and deletion of uridylate residues, the information being provided by guide (g)RNAs. Currently popular mechanisms for the editing process envisage a series of consecutive 'cut-and-paste' reactions, carried out by a compl...

journal_title：Nucleic acids research

authors： Blom D,Burg Jv,Breek CK,Speijer D,Muijsers AO,Benne R

更新日期：2001-07-15 00:00:00