Structural properties and gene-silencing activity of chemically modified DNA-RNA hybrids with parallel orientation.

abstract：:Virulence factor database (VFDB) was set up in 2004 dedicated for providing current knowledge of virulence factors (VFs) from various medical significant bacterial pathogens to facilitate pathogenomic research. Nowadays, complete genome sequences of almost all the major pathogenic microbes have been determined, which ...

journal_title：Nucleic acids research

authors： Yang J,Chen L,Sun L,Yu J,Jin Q

更新日期：2008-01-01 00:00:00

abstract：:Deep mutational scanning has been used to create high-resolution DNA sequence maps that illustrate the functional consequences of large numbers of point mutations. However, this approach has not yet been applied to libraries of genes created by random circular permutation, an engineering strategy that is used to creat...

journal_title：Nucleic acids research

authors： Atkinson JT,Jones AM,Zhou Q,Silberg JJ

更新日期：2018-07-27 00:00:00

abstract：:We have used in vitro site-directed mutagenesis with synthetic DNA oligonucleotides to introduce single nucleotide mutations in yeast mtDNA. In addition to the expected DNA alterations we also recovered with high frequency mutants with large deletions and insertions which arose through interaction with the synthetic D...

journal_title：Nucleic acids research

authors： Osinga KA,Van der Bliek AM,Van der Horst G,Groot Koerkamp MJ,Tabak HF,Veeneman GH,Van Boom JH

更新日期：1983-12-20 00:00:00

abstract：:Homologous recombination is essential for the preservation of genome stability, thereby preventing cancer. The recombination protein RAD51 drives DNA strand exchange, which requires the assembly, rearrangement and disassembly of a RAD51 filament on DNA, coupled to ATP binding and hydrolysis. This process is facilitate...

journal_title：Nucleic acids research

authors： Holthausen JT,van Loenhout MT,Sanchez H,Ristic D,van Rossum-Fikkert SE,Modesti M,Dekker C,Kanaar R,Wyman C

更新日期：2011-08-01 00:00:00

abstract：:Cells respond to DNA damage by activating both cellular growth arrest and DNA repair processes. In Saccharomyces cerevesiae the RAD9 gene controls DNA damage-mediated cell cycle arrest that is known to allow efficient repair. To ascertain whether RAD9 plays a role in DNA repair per se, the removal of UV-induced photol...

journal_title：Nucleic acids research

authors： Al-Moghrabi NM,Al-Sharif IS,Aboussekhra A

更新日期：2001-05-15 00:00:00

abstract：:The mitochondrial DNA of Neurospora crassa has a heterogeneous intramolecular base distribution. A contiguous piece, representing at least 30% of the total genome, has a G+C content that is 6% lower than the overall G+C content of the DNA. The genes for both ribosomal RNAs are contained in the remaining, relatively G+...

journal_title：Nucleic acids research

authors： Terpstra P,Holtrop M,Kroon A

更新日期：1977-01-01 00:00:00

abstract：:In the poly(A)+RNA isolated from the ciliate Paramecium primaurelia is found a discrete and abundant mRNA species of high molecular weight (corresponding to about 9,000 nucleotides). This mRNA species has size and abundance characteristics that identify it tentatively as the message coding for the variant cell-surface...

journal_title：Nucleic acids research

authors： Sommerville J

更新日期：1983-11-11 00:00:00

abstract：:Polyploidy, the presence of multiple sets of chromosomes that are similar but not identical, complicates both chromosome walking and assembly of sequence-ready contigs for many plant taxa including a large number of economically-significant crops. Traditional 'dot-blot hybridization' or PCR-based assays for identifyin...

journal_title：Nucleic acids research

authors： Lin YR,Draye X,Qian X,Ren S,Zhu LH,Tomkins J,Wing RA,Li Z,Paterson AH

更新日期：2000-04-01 00:00:00

abstract：:Here we employ a set of RNA Polymerase II (Pol II) activity mutants to determine the consequences of increased or decreased Pol II catalysis on gene expression in Saccharomyces cerevisiae. We find that alteration of Pol II catalytic rate, either fast or slow, leads to decreased Pol II occupancy and apparent reduction ...

journal_title：Nucleic acids research

authors： Malik I,Qiu C,Snavely T,Kaplan CD

更新日期：2017-05-05 00:00:00

abstract：:By means of a combination of ion-exchange and sequence-specific affinity chromatography techniques, we have purified to homogeneity two protein complexes binding in a human DNA region (B48) previously recognized to contain a DNA replication origin. The DNA sequence used for the protein purification (B48 binding site) ...

journal_title：Nucleic acids research

authors： Tóth EC,Marusic L,Ochem A,Patthy A,Pongor S,Giacca M,Falaschi A

更新日期：1993-07-11 00:00:00

abstract：:The beta protein encoded by the Streptococcus pyogenes plasmid pSM19035 is a site-specific recombinase involved in both resolution of plasmid multimers into monomers and DNA inversion. It has been proposed that the DNA region to which the beta recombinase binds to mediate recombination includes a promoter from which o...

journal_title：Nucleic acids research

authors： Rojo F,Alonso JC

更新日期：1994-05-25 00:00:00

abstract：:Analyses of secondary structures proposed for ribosomal RNA's show that, of the different kinds of base pairs directly adjoining the ends of postulated double-helical regions, only A-G with A at the 5' end significantly exceeds the number expected for a random base distribution. An A(syn)-G(trans) hydrogen-bonded base...

journal_title：Nucleic acids research

authors： Traub W,Sussman JL

更新日期：1982-04-24 00:00:00

abstract：:Integration of foreign genes into plant genomes by the Agrobacterium T-DNA transfer system has been considered to occur at random. It has been speculated that the chromosomal structure of the integration site might affect the expression pattern of the introduced genes. To gain insight into the molecular structure of T...

journal_title：Nucleic acids research

authors： Dietz A,Kay V,Schlake T,Landsmann J,Bode J

更新日期：1994-07-25 00:00:00

abstract：:Alternative splicing and polyadenylation were observed pervasively in eukaryotic messenger RNAs. These alternative isoforms could either be consequences of physiological regulation or stochastic noise of RNA processing. To quantify the extent of stochastic noise in splicing and polyadenylation, we analyzed the alterna...

journal_title：Nucleic acids research

authors： Hon CC,Weber C,Sismeiro O,Proux C,Koutero M,Deloger M,Das S,Agrahari M,Dillies MA,Jagla B,Coppee JY,Bhattacharya A,Guillen N

更新日期：2013-02-01 00:00:00

abstract：:The sequence requirements for specific and efficient transcription from the 16S/23S rRNA promoter of Sulfolobus shibatae were analysed by point mutations and by cassette mutations using an in vitro transcription system. The examination of the box A-containing distal promoter element (DPE) showed the great importance o...

journal_title：Nucleic acids research

authors： Hain J,Reiter WD,Hüdepohl U,Zillig W

更新日期：1992-10-25 00:00:00

abstract：:A novel class of RNA-binding proteins, Puf, regulates translation and RNA stability by binding to specific sequences in the 3'-untranslated region of target mRNAs. Members of this protein family share a conserved Puf domain consisting of eight 36 amino acid imperfect repeats. Here we report two Puf family member genes...

journal_title：Nucleic acids research

authors： Cui L,Fan Q,Li J

更新日期：2002-11-01 00:00:00

abstract：:Molecular mechanisms that regulate gene expression can occur either before or after transcription. The information for post-transcriptional regulation can lie within the sequence or structure of the RNA transcript and it has been proposed that G-quadruplex nucleic acid sequence motifs may regulate translation as well ...

journal_title：Nucleic acids research

authors： Huppert JL,Bugaut A,Kumari S,Balasubramanian S

更新日期：2008-11-01 00:00:00

abstract：:We have isolated a second gene (MLS1), which in addition to DAL7, encodes malate synthase from S. cerevisiae. Expression of the two genes is specific for their physiological roles in carbon and nitrogen metabolism. Expression of MLS1, which participates in the utilization of non-fermentable carbon sources, is sensitiv...

journal_title：Nucleic acids research

authors： Hartig A,Simon MM,Schuster T,Daugherty JR,Yoo HS,Cooper TG

更新日期：1992-11-11 00:00:00

abstract：:We report the synthesis of new phosphoramidite building blocks and their use for the modification of oligonucleotides with hydrazides. The reaction of these hydrazide oligonucleotides with active esters and aldehydes is demonstrated for solution conjugation and immobilization. Compared with the established amino modif...

journal_title：Nucleic acids research

authors： Raddatz S,Mueller-Ibeler J,Kluge J,Wäss L,Burdinski G,Havens JR,Onofrey TJ,Wang D,Schweitzer M

更新日期：2002-11-01 00:00:00

abstract：:TRF1, a duplex telomeric DNA-binding protein, plays an important role in telomere metabolism. We have previously reported that a fraction of endogenous TRF1 can stably exist free of telomere chromatin when it is phosphorylated at T371 by Cdk1; however, the role of this telomere-free (pT371)TRF1 has yet to be fully cha...

journal_title：Nucleic acids research

authors： McKerlie M,Walker JR,Mitchell TR,Wilson FR,Zhu XD

更新日期：2013-12-01 00:00:00

abstract：:In many viruses and transposons, expression of some genes requires alternative reading of the genetic code, also called recoding. Such events depend on specific mRNA sequences and can lead to read through of an in-frame stop codon or to +1 or -1 frameshifting. Here, we addressed the issue of conservation of recoding r...

journal_title：Nucleic acids research

authors： Stahl G,Bidou L,Rousset JP,Cassan M

更新日期：1995-05-11 00:00:00

abstract：:We have developed a highly sensitive method for DNA analysis on 3D gel element microarrays, a technique we call multiplex microarray-enhanced PCR (MME-PCR). Two amplification strategies are carried out simultaneously in the reaction chamber: on or within gel elements, and in bulk solution over the gel element array. M...

journal_title：Nucleic acids research

authors： Pemov A,Modi H,Chandler DP,Bavykin S

更新日期：2005-01-20 00:00:00

abstract：:Transposable elements (TEs) comprise a large proportion of long non-coding RNAs (lncRNAs). Here, we employed CRISPR to delete a short interspersed nuclear element (SINE) in Malat1, a cancer-associated lncRNA, to investigate its significance in cellular physiology. We show that Malat1 with a SINE deletion forms diffuse...

journal_title：Nucleic acids research

authors： Nguyen TM,Kabotyanski EB,Reineke LC,Shao J,Xiong F,Lee JH,Dubrulle J,Johnson H,Stossi F,Tsoi PS,Choi KJ,Ellis AG,Zhao N,Cao J,Adewunmi O,Ferreon JC,Ferreon ACM,Neilson JR,Mancini MA,Chen X,Kim J,Ma L,Li W,Ro

更新日期：2020-03-18 00:00:00

abstract：:The gene for the thymidine kinase (TK) of Herpes simplex virus type 1 (HSV-1) is located in the KpnI m and BamHI p fragments of the genome (Wigler et al., Cell 11, 223-232 (1977)). These fragments have been inserted into the EcoRI and BamHI sites, respectively, of plasmid pBR322, and propagated in E.coli. The TK gene ...

journal_title：Nucleic acids research

authors： Wilkie NM,Clements JB,Boll W,Mantei N,Lonsdale D,Weissmann C

更新日期：1979-10-25 00:00:00

abstract：:Plastid mRNA stability is tightly regulated by external signals such as light. We have investigated the biochemical mechanism responsible for the dark-induced decrease of relative half-lives for mRNAs encoding photosynthetic proteins. Protein fractions isolated from plastids of light-grown and dark-adapted plants corr...

journal_title：Nucleic acids research

authors： Baginsky S,Gruissem W

更新日期：2002-10-15 00:00:00

abstract：:Zinc fingers are small protein domains in which zinc plays a structural role contributing to the stability of the domain. Zinc fingers are structurally diverse and are present among proteins that perform a broad range of functions in various cellular processes, such as replication and repair, transcription and transla...

journal_title：Nucleic acids research

authors： Krishna SS,Majumdar I,Grishin NV

更新日期：2003-01-15 00:00:00

abstract：:Circular DNA aptamers are powerful candidates for therapeutic applications given their dramatically enhanced biostability. Herein we report the first effort to evolve circular DNA aptamers that bind a human protein directly in serum, a complex biofluid. Targeting human thrombin, this strategy has led to the discovery ...

journal_title：Nucleic acids research

authors： Mao Y,Gu J,Chang D,Wang L,Yao L,Ma Q,Luo Z,Qu H,Li Y,Zheng L

更新日期：2020-11-04 00:00:00

abstract：:The sequencing of the full transcriptome (RNA-seq) has become the preferred choice for the measurement of genome-wide gene expression. Despite its widespread use, challenges remain in RNA-seq data analysis. One often-overlooked aspect is normalization. Despite the fact that a variety of factors or 'batch effects' can ...

journal_title：Nucleic acids research

authors： Peixoto L,Risso D,Poplawski SG,Wimmer ME,Speed TP,Wood MA,Abel T

更新日期：2015-09-18 00:00:00

abstract：:Defects in the posttranscriptional modifications of mitochondrial tRNAs have been linked to human diseases, but their pathophysiology remains elusive. In this report, we investigated the molecular mechanism underlying a deafness-associated tRNAIle 4295A>G mutation affecting a highly conserved adenosine at position 37,...

journal_title：Nucleic acids research

authors： Meng F,Zhou M,Xiao Y,Mao X,Zheng J,Lin J,Lin T,Ye Z,Cang X,Fu Y,Wang M,Guan MX

更新日期：2021-01-25 00:00:00

abstract：:We present a study of how substituent groups of naturally occurring and modified nucleotide bases affect the degree of hydration of right-handed B-DNA and left-handed Z-DNA. A comparison of poly(dG-dC) and poly(dG-dm5C) titrations with the lipotropic salts of the Hofmeister series infers that the methyl stabilization ...

journal_title：Nucleic acids research

authors： Kagawa TF,Howell ML,Tseng K,Ho PS

更新日期：1993-12-25 00:00:00