Selective isolation and detailed analysis of intra-RNA cross-links induced in the large ribosomal subunit of E. coli: a model for the tertiary structure of the tRNA binding domain in 23S RNA.

abstract：:Recently, due to the dual roles of DNA and enzyme, DNAzyme has been widely used in the field of DNA circuit, which has a wide range of applications in bio-engineered system, information processing and biocomputing. In fact, the activity of DNAzymes was regulated by subunits assembly, pH control and metal ions triggers...

journal_title：Nucleic acids research

authors： Zheng X,Yang J,Zhou C,Zhang C,Zhang Q,Wei X

更新日期：2019-02-20 00:00:00

abstract：:Rice alpha-amylases are encoded by a multigene family that has previously been classified into 5 hybridization groups. DNA sequence and Southern blot analysis identified three genes (RAmy1A, RAmy1B and RAmy1C) in Group 1 with DNA sequence identity of at least 90%. Hybridization Group 2 is represented by only one gene,...

journal_title：Nucleic acids research

authors： Huang N,Koizumi N,Reinl S,Rodriguez RL

更新日期：1990-12-11 00:00:00

abstract：:No analogous nucleoside triphosphate was found which acts as well as ATP in binding to and supporting catalysis of leucyl-tRNA synthetase from Escherichia coli MRE 600. However, there are numerous nucleotides which are able to replace ATP, but with lower efficiency. The 6-amino group of the adenine ring and the 2'-hyd...

journal_title：Nucleic acids research

authors： Marutzky R,Flossdorf J,Kula MR

更新日期：1976-08-01 00:00:00

abstract：:We have studied the coil-to-helix transition of the DNA oligomer d(C4A4T4C4), using circular dichroism measurements to monitor the formation of A.T base pairs within the central self-complementary A4T4 region and the formation of protonated C.C+ base pairs at the ends of the oligomer. We found that both A.T and C.C+ b...

journal_title：Nucleic acids research

authors： Gray DM,Cui T,Ratliff RL

更新日期：1984-10-11 00:00:00

abstract：:The Est3 subunit of yeast telomerase, which adopts a predicted OB-fold, is essential for telomere replication. To assess the possible contributions that Est3 might make to enzyme catalysis, we compared telomerase activity from wild type and est3-Delta strains of Saccharomyces castellii, which revealed that loss of the...

journal_title：Nucleic acids research

authors： Lee J,Mandell EK,Rao T,Wuttke DS,Lundblad V

更新日期：2010-04-01 00:00:00

abstract：:KRAS is one of the most mutated genes in human cancer. It is controlled by a G4 motif located upstream of the transcription start site. In this paper, we demonstrate that 8-oxoguanine (8-oxoG), being more abundant in G4 than in non-G4 regions, is a new player in the regulation of this oncogene. We designed oligonucleo...

journal_title：Nucleic acids research

authors： Cogoi S,Ferino A,Miglietta G,Pedersen EB,Xodo LE

更新日期：2018-01-25 00:00:00

abstract：:Here we analyze the effect of DNA folding on the performance of short primers and describe a simple technique for assessing hitherto uncertain values of thermodynamic parameters that determine the folding of single-stranded DNA into secondary structure. An 8mer with two degenerate positions is extended simultaneously ...

journal_title：Nucleic acids research

authors： Lvovsky L,Ioshikhes I,Raja MC,Zevin-Sonkin D,Sobolev IA,Liberzon A,Shwartzburd J,Ulanovsky LE

更新日期：1998-12-01 00:00:00

abstract：:The transcriptional shift from repression to activation of target genes is crucial for the fidelity of Notch responses through incompletely understood mechanisms that likely involve chromatin-based control. To activate silenced genes, repressive chromatin marks are removed and active marks must be acquired. Histone H3...

journal_title：Nucleic acids research

authors： Oswald F,Rodriguez P,Giaimo BD,Antonello ZA,Mira L,Mittler G,Thiel VN,Collins KJ,Tabaja N,Cizelsky W,Rothe M,Kühl SJ,Kühl M,Ferrante F,Hein K,Kovall RA,Dominguez M,Borggrefe T

更新日期：2016-06-02 00:00:00

abstract：:PUF proteins, named for Drosophila Pumilio (PUM) and Caenorhabditis elegans fem-3-binding factor (FBF), recognize specific sequences in the mRNAs they bind and control. RNA binding by classical PUF proteins is mediated by a characteristic PUM homology domain (PUM-HD). The Puf1 and Puf2 proteins possess a distinct arch...

journal_title：Nucleic acids research

authors： Qiu C,Dutcher RC,Porter DF,Arava Y,Wickens M,Hall TMT

更新日期：2019-09-19 00:00:00

abstract：:Splicing of mammalian introns requires that the intron possess at least 80 nucleotides. This length requirement presumably reflects the constraints of accommodating multiple snRNPs simultaneously in the same intron. In the free-living nematode, C. elegans, introns typically are 45 to 55 nucleotides in length. In this ...

journal_title：Nucleic acids research

authors： Ogg SC,Anderson P,Wickens MP

更新日期：1990-01-11 00:00:00

abstract：:A DNA fragment d(GCGAAAGCT), known to adopt a stable mini-hairpin structure in solution, has been crystallized in the space group I4(1)22 with the unit-cell dimensions a = b = 53.4 A and c = 54.0 A, and the crystal structure has been determined at 2.5 A resolution. The four nucleotide residues CGAA of the first half o...

journal_title：Nucleic acids research

authors： Sunami T,Kondo J,Kobuna T,Hirao I,Watanabe K,Miura K,Takénaka A

更新日期：2002-12-01 00:00:00

abstract：:An oligonucleotide hybrid is described which possesses two triple helix forming oligonucleotides which have been connected by a flexible polymeric linker chain. As a prototype, binding of this class of oligonucleotide to duplex DNA has been studied using a segment of the HSV-1 D-glycoprotein promoter, which possesses ...

journal_title：Nucleic acids research

authors： Kessler DJ,Pettitt BM,Cheng YK,Smith SR,Jayaraman K,Vu HM,Hogan ME

更新日期：1993-10-11 00:00:00

abstract：:We have used photo-crosslinking to investigate the structure and dynamics of four-way junction hairpin ribozyme constructs. Four phenylazide photo-crosslinkers were coupled to 2'-NH2-modified U+2 in the substrate and irradiated at different Mg2+ concentrations and temperatures. Consistent with the role of divalent met...

journal_title：Nucleic acids research

authors： Borda EJ,Sigurdsson ST

更新日期：2005-02-18 00:00:00

abstract：:Eukaryotic transcription factor B (TFB) proteins are homologous to KsgA/Dim1 ribosomal RNA (rRNA) methyltransferases. The mammalian TFB1, mitochondrial (TFB1M) factor is an essential protein necessary for mitochondrial gene expression. TFB1M mediates an rRNA modification in the small ribosomal subunit and thus plays a...

journal_title：Nucleic acids research

authors： Guja KE,Venkataraman K,Yakubovskaya E,Shi H,Mejia E,Hambardjieva E,Karzai AW,Garcia-Diaz M

更新日期：2013-09-01 00:00:00

abstract：:We report the latest release (version 3.0) of the CATH protein domain database (http://www.cathdb.info). There has been a 20% increase in the number of structural domains classified in CATH, up to 86 151 domains. Release 3.0 comprises 1110 fold groups and 2147 homologous superfamilies. To cope with the increases in di...

journal_title：Nucleic acids research

authors： Greene LH,Lewis TE,Addou S,Cuff A,Dallman T,Dibley M,Redfern O,Pearl F,Nambudiry R,Reid A,Sillitoe I,Yeats C,Thornton JM,Orengo CA

更新日期：2007-01-01 00:00:00

abstract：:The solution structures of two 27 nt RNA hairpins and their complexes with cobalt(III)-hexammine [Co(NH(3))(6)(3+)] were determined by NMR spectroscopy. The RNA hairpins are variants of the P4 region from Escherichia coli RNase P RNA: a U-to-A mutant changing the identity of the bulged nucleotide, and a U-to-C, C-to-U...

journal_title：Nucleic acids research

authors： Schmitz M

更新日期：2004-12-02 00:00:00

abstract：:The Zebrafish Information Network (ZFIN) (https://zfin.org/) is the database for the model organism, zebrafish (Danio rerio). ZFIN expertly curates, organizes, and provides a wide array of zebrafish genetic and genomic data, including genes, alleles, transgenic lines, gene expression, gene function, mutant phenotypes,...

journal_title：Nucleic acids research

authors： Howe DG,Ramachandran S,Bradford YM,Fashena D,Toro S,Eagle A,Frazer K,Kalita P,Mani P,Martin R,Moxon ST,Paddock H,Pich C,Ruzicka L,Schaper K,Shao X,Singer A,Van Slyke CE,Westerfield M

更新日期：2021-01-08 00:00:00

abstract：:DNA helicases are motor proteins that catalyze the unwinding of double-stranded DNA into single-stranded DNA using the free energy from ATP hydrolysis. Single molecule approaches enable us to address detailed mechanistic questions about how such enzymes move processively along DNA. Here, an optical method has been dev...

journal_title：Nucleic acids research

authors： Fili N,Mashanov GI,Toseland CP,Batters C,Wallace MI,Yeeles JT,Dillingham MS,Webb MR,Molloy JE

更新日期：2010-07-01 00:00:00

abstract：:The detailed conformational features and dynamics of the naturally occurring deoxyribotrinucleoside diphosphates d-TpTpT and d-TpTpC have been investigated at 20 degrees C and 80 degrees C in aqueous solution by nuclear magnetic resonance spectroscopy. The observed NMR parameters indicate that the conformational prope...

journal_title：Nucleic acids research

authors： Cheng DM,Dhingra MM,Sarma RH

更新日期：1978-11-01 00:00:00

abstract：:A truly universal nucleobase enables a host of novel applications such as simplified templates for PCR primers, randomized sequencing and DNA based devices. A universal base must pair indiscriminately to each of the canonical bases with little or preferably no destabilization of the overall duplex. In reality, many ca...

journal_title：Nucleic acids research

authors： Spring-Connell AM,Evich MG,Debelak H,Seela F,Germann MW

更新日期：2016-10-14 00:00:00

abstract：:Yeast Dna2 helicase/nuclease is essential for DNA replication and assists FEN1 nuclease in processing a subset of Okazaki fragments that have long single-stranded 5' flaps. It is also involved in the maintenance of telomeres. DNA2 is a gene conserved in eukaryotes, and a putative human ortholog of yeast DNA2 (ScDNA2) ...

journal_title：Nucleic acids research

authors： Masuda-Sasa T,Imamura O,Campbell JL

更新日期：2006-04-04 00:00:00

abstract：:Protein-DNA binding is a fundamental component of gene regulatory processes, but it is still not completely understood how proteins recognize their target sites in the genome. Besides hydrogen bonding in the major groove (base readout), proteins recognize minor-groove geometry using positively charged amino acids (sha...

journal_title：Nucleic acids research

authors： Chiu TP,Rao S,Mann RS,Honig B,Rohs R

更新日期：2017-12-01 00:00:00

abstract：:Human MitBASE is a database collecting human mtDNA variants. This database is part of a greater mitochondrial genome database (MitBASE) funded within the EU Biotech Program. The present paper reports the recent improvements in data structure, data quality and data quantity. As far as the database structure is concerne...

journal_title：Nucleic acids research

authors： Attimonelli M,Cooper JM,D'Elia D,de Montalvo A,De Robertis M,Lehväslaiho H,Malladi SB,Memeo F,Stevens K,Schapira AH,Saccone C

更新日期：1999-01-01 00:00:00

abstract：:Few transcriptional regulatory networks have been described in non-model organisms. In Entamoeba histolytica seminal aspects of pathogenesis are transcriptionally controlled, however, little is known about transcriptional regulatory networks that effect gene expression in this parasite. We used expression data from tw...

journal_title：Nucleic acids research

authors： Hackney JA,Ehrenkaufer GM,Singh U

更新日期：2007-01-01 00:00:00

abstract：:Increasing numbers of proteins, nucleic acids and other molecular entities have been explored as therapeutic targets, hundreds of which are targets of approved and clinical trial drugs. Knowledge of these targets and corresponding drugs, particularly those in clinical uses and trials, is highly useful for facilitating...

journal_title：Nucleic acids research

authors： Zhu F,Han B,Kumar P,Liu X,Ma X,Wei X,Huang L,Guo Y,Han L,Zheng C,Chen Y

更新日期：2010-01-01 00:00:00

abstract：:1,10-Phenanthroline-platinum(II)-ethylenediamine ( PEPt ) forms a crystalline complex with cytidine-3'-phosphate (3'-CMP) and its structure has been determined by X-ray crystallography. 3'-CMP molecules are hemiprotonated and form hydrogen-bonded pairs that stack above and below the phenanthroline-platinum(II) drug mo...

journal_title：Nucleic acids research

authors： Vijay-Kumar S,Sakore TD,Sobell HM

更新日期：1984-04-25 00:00:00

abstract：:DNA molecules with covalently sealed (hairpin) ends are probable intermediates in V(D)J recombination. According to current models hairpin ends are opened to produce short single-stranded extensions that are thought to be precursors of a particular type of extra nucleotides, termed P nucleotides, which are frequently ...

journal_title：Nucleic acids research

authors： Kabotyanski EB,Zhu C,Kallick DA,Roth DB

更新日期：1995-10-11 00:00:00

abstract：:Topoisomerases are ubiquitous proteins found in all three domains of life. They change the topology of DNA via transient breaks on either one or two of the DNA strands to allow passage of another single or double DNA strand through the break. Topoisomerases are classified into two types: type I enzymes cleave one DNA ...

journal_title：Nucleic acids research

authors： Baker NM,Rajan R,Mondragón A

更新日期：2009-02-01 00:00:00

abstract：:Present results provide direct evidence of the nature of a conformational change in DNA when nucleosomes are formed from core histones and poly [d(A-T)]. First, we have found some features which have characteristic aspects of the A like conformation of DNA. Thus, an increased contribution due to a sugar conformation c...

journal_title：Nucleic acids research

authors： Brahms S,Brahmachari SK,Angelier N,Brahms JG

更新日期：1981-10-10 00:00:00

abstract：:Bacterial Hfq is a protein that plays an important role in the regulation of genes in cooperation with sRNAs. Escherichia coli Hfq (EcHfq) has two or more sites that bind RNA(s) including U-rich and/or the poly(A) tail of mRNA. However, functional and structural information about Bacillus subtilis Hfq (BsHfq) includin...

journal_title：Nucleic acids research

authors： Someya T,Baba S,Fujimoto M,Kawai G,Kumasaka T,Nakamura K

更新日期：2012-02-01 00:00:00