Plant intron sequences: evidence for distinct groups of introns.

abstract：:Light is a major external factor in regulating seed germination. Photoreceptor phytochrome B (PHYB) plays a predominant role in promoting seed germination in the initial phase after imbibition, partially by repressing phytochrome-interacting factor1 (PIF1). However, the mechanism underlying the PHYB-PIF1-mediated tran...

journal_title：Nucleic acids research

authors： Gu D,Chen CY,Zhao M,Zhao L,Duan X,Duan J,Wu K,Liu X

更新日期：2017-07-07 00:00:00

abstract：:A highly repetitive DNA sequence from tilapia (Oreochromis mossambicus/hornorum) has been cloned and sequenced. It is a tandemly arrayed sequence of 237 bp and constitutes 7% of the fish genome. The copy number of the repeat is approximately 3 x 10(5) per haploid genome. DNA sequence analysis of 7 cloned repeats revea...

journal_title：Nucleic acids research

authors： Wright JM

更新日期：1989-07-11 00:00:00

abstract：:DNA replication of phi29 and related phages takes place via a strand displacement mechanism, a process that generates large amounts of single-stranded DNA (ssDNA). Consequently, phage-encoded ssDNA-binding proteins (SSBs) are essential proteins during phage phi29-like DNA replication. In the present work we analyze th...

journal_title：Nucleic acids research

authors： Gascón I,Lázaro JM,Salas M

更新日期：2000-05-15 00:00:00

abstract：:Protein classification by machine learning algorithms is now widely used in structural and functional annotation of proteins. The Protein Classification Benchmark collection (http://hydra.icgeb.trieste.it/benchmark) was created in order to provide standard datasets on which the performance of machine learning methods ...

journal_title：Nucleic acids research

authors： Sonego P,Pacurar M,Dhir S,Kertész-Farkas A,Kocsor A,Gáspári Z,Leunissen JA,Pongor S

更新日期：2007-01-01 00:00:00

abstract：:In this study, we show that silencing of CITED2 using small-hairpin RNA (shCITED2) induced DNA damage and reduction of ERCC1 gene expression in HEK293, HeLa and H1299 cells, even in the absence of cisplatin. In contrast, ectopic expression of ERCC1 significantly reduced intrinsic and induced DNA damage levels, and res...

journal_title：Nucleic acids research

authors： Liu YC,Chang PY,Chao CC

更新日期：2015-12-15 00:00:00

abstract：:Upon endocytosis, most oligodeoxynucleotides (ODNs) accumulate in vesicular compartments; a tiny number of them cross the vesicle membrane, reach the cytosol and by passive diffusion enter the nucleus where they are entrapped. So far, the compartment in which an antisense ODN interacts with its mRNA target has not bee...

journal_title：Nucleic acids research

authors： Meunier L,Mayer R,Monsigny M,Roche AC

更新日期：1999-07-01 00:00:00

abstract：:We have previously investigated the role of the N-terminal region of ribosomal protein S4 to participate in 30S ribosome assembly and function (1-3). In this report we extend these studies to the two fragments produced by the chemical cleavage of protein S4 at the tryptophan residue 167. We find that the carboxyl term...

journal_title：Nucleic acids research

authors： Changchien LM,Craven GR

更新日期：1985-09-11 00:00:00

abstract：:Recent studies indicate that controlling the nuclear decondensation and intra-nuclear localization of plasmid DNA (pDNA) would result in an increased transfection efficiency. In the present study, we established a technology for imaging the nuclear condensation/decondensation status of pDNA in nuclear subdomains using...

journal_title：Nucleic acids research

authors： Shaheen SM,Akita H,Yamashita A,Katoono R,Yui N,Biju V,Ishikawa M,Harashima H

更新日期：2011-04-01 00:00:00

abstract：:Multicellular organismal development is controlled by a complex network of transcription factors, promoters and enhancers. Although reliable computational and experimental methods exist for enhancer detection, prediction of their target genes remains a major challenge. On the basis of available literature and ChIP-seq...

journal_title：Nucleic acids research

authors： Rödelsperger C,Guo G,Kolanczyk M,Pletschacher A,Köhler S,Bauer S,Schulz MH,Robinson PN

更新日期：2011-04-01 00:00:00

abstract：:Oligodeoxyribonucleotides containing N4-methoxycytosine (mo4C), N4-methoxy-5-methylcytosine (mo4m5C) and other base-analogues were synthesised and used to compare the stabilities of duplexes containing mo4C.A and mo4C.G base pairs with those containing normal and mismatch pairs. The Tm values and other thermodynamic p...

journal_title：Nucleic acids research

authors： Anand NN,Brown DM,Salisbury SA

更新日期：1987-10-26 00:00:00

abstract：:Two hexamer DNA fragments containing a carcinogenic modified base, O6-methyl guanine, have been synthesized by a solid-phase phosphotriester method, in which the unmodified guanine residues present were O6 protected with the 4-nitrophenylethyl group. These two alkylated oligonucleotides were found to have similar Tm's...

journal_title：Nucleic acids research

authors： Kuzmich S,Marky LA,Jones RA

更新日期：1983-05-25 00:00:00

abstract：:Release of phosphorothioate antisense oligonucleotides (PS-ASOs) from late endosomes (LEs) is a rate-limiting step and a poorly defined process for productive intracellular ASO drug delivery. Here, we examined the role of Golgi-endosome transport, specifically M6PR shuttling mediated by GCC2, in PS-ASO trafficking and...

journal_title：Nucleic acids research

authors： Liang XH,Sun H,Hsu CW,Nichols JG,Vickers TA,De Hoyos CL,Crooke ST

更新日期：2020-02-20 00:00:00

abstract：:The available reagents for the attachment of functional moieties to plasmid DNA are limiting. Most reagents bind plasmid DNA in a non-sequence- specific manner, with undefined stoichiometry, and affect DNA charge and delivery properties or involve chemical modifications that abolish gene expression. The design and abi...

journal_title：Nucleic acids research

authors： Hertoghs KM,Ellis JH,Catchpole IR

更新日期：2003-10-15 00:00:00

abstract：:A growing number of whole genome sequencing projects, in combination with development of phylogenetic methods for reconstructing gene evolution, have provided us with a window into genomes that existed millions, and even billions, of years ago. Ancestral Genomes (http://ancestralgenomes.org) is a resource for comprehe...

journal_title：Nucleic acids research

authors： Huang X,Albou LP,Mushayahama T,Muruganujan A,Tang H,Thomas PD

更新日期：2019-01-08 00:00:00

abstract：:The thermal stabilities of RNA:DNA hybrids are substantially greater than those of DNA:DNA duplexes in aqueous electrolyte solutions containing high concentrations of formamide. Association rates to form DNA:DNA duplexes and DNA:RNA hybrids have been measured in these solvents. There is a temperature range in which DN...

journal_title：Nucleic acids research

authors： Casey J,Davidson N

更新日期：1977-01-01 00:00:00

abstract：:Ribosome biogenesis is a dynamic multistep process, many features of which are still incompletely documented. Here, we show that changes in this pathway can be captured and annotated by means of a graphic set of pre-rRNA ratios, a technique we call Ratio Analysis of Multiple Precursors (RAMP). We find that knocking do...

journal_title：Nucleic acids research

authors： Wang M,Anikin L,Pestov DG

更新日期：2014-01-01 00:00:00

abstract：:By subtractive screening of a library made from mRNA of lipopolysaccharide (LPS)-stimulated mouse B lymphocytes we isolated cDNA-clones encoding the ribosomal protein L7. Human L7 mRNA was cloned from activated T-lymphocytes. Although no specific function of L7 in the translation apparatus is known as yet, it should b...

journal_title：Nucleic acids research

authors： Hemmerich P,von Mikecz A,Neumann F,Sözeri O,Wolff-Vorbeck G,Zoebelein R,Krawinkel U

更新日期：1993-01-25 00:00:00

abstract：:Naturally occurring RNAs are known to exhibit a high degree of modularity, whereby specific structural modules (or motifs) can be mixed and matched to create new molecular architectures. The modular nature of RNA also affords researchers the ability to characterize individual structural elements in controlled syntheti...

journal_title：Nucleic acids research

authors： Mitchell C,Polanco JA,DeWald L,Kress D,Jaeger L,Grabow WW

更新日期：2019-07-09 00:00:00

abstract：:Translesion synthesis (TLS) employs low fidelity polymerases to replicate past damaged DNA in a potentially error-prone process. Regulatory mechanisms that prevent TLS-associated mutagenesis are unknown; however, our recent studies suggest that the PCNA-binding protein Spartan plays a role in suppression of damage-ind...

journal_title：Nucleic acids research

authors： Kim MS,Machida Y,Vashisht AA,Wohlschlegel JA,Pang YP,Machida YJ

更新日期：2013-02-01 00:00:00

abstract：:Active DNA demethylation is crucial for epigenetic control, but the underlying enzymatic mechanisms are incompletely understood. REPRESSOR OF SILENCING 1 (ROS1) is a 5-methylcytosine (5-meC) DNA glycosylase/lyase that initiates DNA demethylation in plants through a base excision repair process. The enzyme binds DNA no...

journal_title：Nucleic acids research

authors： Parrilla-Doblas JT,Ponferrada-Marín MI,Roldán-Arjona T,Ariza RR

更新日期：2013-10-01 00:00:00

abstract：:ColE1 derivative plasmids were constructed in which the natural promoter that primes replication or, in addition, the region coding for the RNA I control element had been deleted. In all of these molecules priming of the origin was effected by read-through transcription from constitutive or inducible (lacUV5) promoter...

journal_title：Nucleic acids research

authors： Panayotatos N

更新日期：1984-03-26 00:00:00

abstract：:DNA tandem repeats (TRs) are ubiquitous genomic features which consist of two or more adjacent copies of an underlying pattern sequence. The copies may be identical or approximate. Variable number of tandem repeats or VNTRs are polymorphic TR loci in which the number of pattern copies is variable. In this paper we des...

journal_title：Nucleic acids research

authors： Gelfand Y,Hernandez Y,Loving J,Benson G

更新日期：2014-08-01 00:00:00

abstract：:The effect of amino groups attached at positions 2 and 8 of the hypoxanthine moiety in the structure, reactivity and stability of DNA duplexes and triplexes is studied by means of quantum mechanical calculations, as well as extended molecular dynamics (MD) and thermodynamic integration (MD/TI) simulations. Theoretical...

journal_title：Nucleic acids research

authors： Cubero E,Güimil-García R,Luque FJ,Eritja R,Orozco M

更新日期：2001-06-15 00:00:00

abstract：:Equilibrative nucleoside transporters (ENTs) are a recently characterized and poorly understood group of membrane proteins that are important in the uptake of endogenous nucleosides required for nucleic acid and nucleoside triphosphate synthesis. Despite their central importance in cellular metabolism and nucleoside a...

journal_title：Nucleic acids research

authors： Sankar N,Machado J,Abdulla P,Hilliker AJ,Coe IR

更新日期：2002-10-15 00:00:00

abstract：:Oligo(dG).oligo(dC)- or short poly(dG).poly(dC)-containing fragments were enriched and cloned by means of Mg2+-dependent triplex affinity capture and subsequent cloning procedures. A library constructed after three cycles of enrichment showed that approximately 80% of the clones in the supercoiled form formed a comple...

journal_title：Nucleic acids research

authors： Nishikawa N,Kanda N,Oishi M,Kiyama R

更新日期：1997-05-01 00:00:00

abstract：:The eukaryotic genome evolves under the dual constraint of maintaining coordinated gene transcription and performing effective DNA replication and cell division, the coupling of which brings about inevitable DNA topological tension. DNA supercoiling is resolved and, in some cases, even harnessed by the genome through ...

journal_title：Nucleic acids research

authors： Tsochatzidou M,Malliarou M,Papanikolaou N,Roca J,Nikolaou C

更新日期：2017-06-02 00:00:00

abstract：:The Nucleolar Proteome Database (NOPdb) archives data on >700 proteins that were identified by multiple mass spectrometry (MS) analyses from highly purified preparations of human nucleoli, the most prominent nuclear organelle. Each protein entry is annotated with information about its corresponding gene, its domain st...

journal_title：Nucleic acids research

authors： Leung AK,Trinkle-Mulcahy L,Lam YW,Andersen JS,Mann M,Lamond AI

更新日期：2006-01-01 00:00:00

abstract：:An endo-exonuclease has been purified from cultured monkey (CV-1) cells. The enzyme which was purified to near homogeneity to be a 65 kDa monomeric protein. The single-strand DNase activity is endonucleolytic and nonprocessive, whereas the double-strand DNase activity is exonucleolytic and processive. The enzyme was a...

journal_title：Nucleic acids research

authors： Couture C,Chow TY

更新日期：1992-08-25 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：:Bacillus subtilis LrpC is a sequence-independent DNA-binding and DNA-bending protein, which binds both single-stranded (ss) and double-stranded (ds) DNA and facilitates the formation of higher order protein-DNA complexes in vitro. LrpC binds at different sites within the same DNA molecule promoting intramolecular liga...

journal_title：Nucleic acids research

authors： López-Torrejón G,Martínez-Jiménez MI,Ayora S

更新日期：2006-01-10 00:00:00