Predicting translational diffusion of evolutionary conserved RNA structures by the nucleotide number.

abstract：:The main goal of this review is to provide some guide-lines for choosing a proper method when searching for differentially expressed transcripts. The choice of an approach should depend upon particular features of the experiment and project requirements. We outline some general considerations to help decide between di...

journal_title：Nucleic acids research

authors： Matz MV,Lukyanov SA

更新日期：1998-12-15 00:00:00

abstract：:Metagenomics has been employed to systematically sequence, classify, analyze and manipulate the entire genetic material isolated from environmental samples. Finding genes within metagenomic sequences remains a formidable challenge, and noncoding RNA genes other than those encoding rRNA and tRNA are not well annotated ...

journal_title：Nucleic acids research

authors： Zhu Y,Pulukkunat DK,Li Y

更新日期：2007-01-01 00:00:00

abstract：:It has been inferred from DNA sequence analyses that in echinoderm mitochondria not only the usual asparagine codons AAU and AAC, but also the usual lysine codon AAA, are translated as asparagine by a single mitochondrial (mt) tRNAAsn with the anticodon GUU. Nucleotide sequencing of starfish mt tRNAAsn revealed that t...

journal_title：Nucleic acids research

authors： Tomita K,Ueda T,Watanabe K

更新日期：1999-04-01 00:00:00

abstract：:In the virion core of retroviruses, the genomic RNA is tightly associated with nucleocapsid (NC) protein molecules, forming the nucleocapsid structure. NC protein, a highly basic protein with two zinc fingers, is indispensable for RNA dimerization, encapsidation and the initiation of reverse transcription in avian, mu...

journal_title：Nucleic acids research

authors： Lapadat-Tapolsky M,De Rocquigny H,Van Gent D,Roques B,Plasterk R,Darlix JL

更新日期：1993-02-25 00:00:00

abstract：:Chemically modified siRNAs are expected to have resistance toward nuclease degradation and good thermal stability in duplex formation for in vivo applications. We have recently found that 2'-OMe-4'-thioRNA, a hybrid chemical modification based on 2'-OMeRNA and 4'-thioRNA, has high hybridization affinity for complement...

journal_title：Nucleic acids research

authors： Takahashi M,Nagai C,Hatakeyama H,Minakawa N,Harashima H,Matsuda A

更新日期：2012-07-01 00:00:00

abstract：:MicroRNAs (miRNAs) are approximately 22 nucleotide (nt) long and play important roles in post-transcriptional regulation in both plants and animals. In animals, precursor (pre-) miRNAs are ∼70 nt hairpins produced by Drosha cleavage of long primary (pri-) miRNAs in the nucleus. Exportin-5 (XPO5) transports pre-miRNAs ...

journal_title：Nucleic acids research

authors： Sheng P,Fields C,Aadland K,Wei T,Kolaczkowski O,Gu T,Kolaczkowski B,Xie M

更新日期：2018-06-20 00:00:00

abstract：:The RSC complex of Saccharomyces cerevisiae is closely related to the SWI/SNF complex. Both complexes are involved in remodeling chromatin structure and they share conserved components. The RSC proteins Sth1, Rsc8/Swh3, Sfh1 and Rsc6 are homologs of the SWI/SNF proteins Swi2/Snf2, Swi3, Snf5 and Swp73 respectively. To...

journal_title：Nucleic acids research

authors： Treich I,Ho L,Carlson M

更新日期：1998-08-15 00:00:00

abstract：:The multi-protein complex WRAD, formed by WDR5, RbBP5, Ash2L and Dpy30, binds to the MLL SET domain to stabilize the catalytically active conformation required for histone H3K4 methylation. In addition, the WRAD complex contributes to the targeting of the activated complex to specific sites on chromatin. RbBP5 is cent...

journal_title：Nucleic acids research

authors： Mittal A,Hobor F,Zhang Y,Martin SR,Gamblin SJ,Ramos A,Wilson JR

更新日期：2018-04-20 00:00:00

abstract：:In this article, we characterize histone demethylase activity of the entire family of JmjC+N proteins of Drosophila melanogaster. Our results show that Lid (little imaginal discs), which is structurally homologous to JARID1, demethylates H3K4me3. However, contrary to what would be inferred from its demethylase activit...

journal_title：Nucleic acids research

authors： Lloret-Llinares M,Carré C,Vaquero A,de Olano N,Azorín F

更新日期：2008-05-01 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：:Differential display of mRNA is a simple, sensitive and powerful method to identify differentially expressed gene fragments. The main drawback of differential display is the lack of reproducibility and the inability to read and compare complex gels. This issue results from employing unoptimized primer combinations and...

journal_title：Nucleic acids research

authors： Malhotra K,Foltz L,Mahoney WC,Schueler PA

更新日期：1998-02-01 00:00:00

abstract：:Recently, we described a method for multiplex genome editing by natural transformation (MuGENT). Mutant constructs for MuGENT require large arms of homology (>2000 bp) surrounding each genome edit, which necessitates laborious in vitro DNA splicing. In Vibrio cholerae, we uncover that this requirement is due to cytopl...

journal_title：Nucleic acids research

authors： Dalia TN,Yoon SH,Galli E,Barre FX,Waters CM,Dalia AB

更新日期：2017-07-07 00:00:00

abstract：:A new restriction endonuclease Bse SI has been isolated from Bacillus stearothermophilus Jo10-553. Bse SI recognizes a degenerate hexanucleotide sequence 5'-G(G/T)GC(A/C)C-3' and cleaves DNA to produce 3[prime]-protruding tetranucleotide ends. ...

journal_title：Nucleic acids research

authors： Steponaviciene D,Maneliene Z,Petrusyte M,Janulaitis A

更新日期：1999-07-01 00:00:00

abstract：:MicroRNAs (miRNAs) are short, non-protein coding RNAs that direct the widespread phenomenon of post-transcriptional regulation of metazoan genes. The mature approximately 22-nt long RNA molecules are processed from genome-encoded stem-loop structured precursor genes. Hundreds of such genes have been experimentally val...

journal_title：Nucleic acids research

authors： Gerlach D,Kriventseva EV,Rahman N,Vejnar CE,Zdobnov EM

更新日期：2009-01-01 00:00:00

abstract：:Using sedimentation and cryo electron tomography techniques, the conformations of eukaryotic polyribosomes formed in a long-term cell-free translation system were analyzed over all the active system lifetime (20-30 translation rounds during 6-8 h in wheat germ extract at 25°C). Three distinct types of the conformation...

journal_title：Nucleic acids research

authors： Afonina ZA,Myasnikov AG,Shirokov VA,Klaholz BP,Spirin AS

更新日期：2015-01-01 00:00:00

abstract：:The long interspersed repeated DNA family of rats (LINE or L1Rn family) contains about 40,000 6.7-kilobase (kb) long members (1). LINE members may be currently mobile since their presence or absence causes allelic variation at three single copy loci (2, 3): insulin 1, Moloney leukemia virus integration 2 (Mlvi-2) (4),...

journal_title：Nucleic acids research

authors： Furano AV,Somerville CC,Tsichlis PN,D'Ambrosio E

更新日期：1986-05-12 00:00:00

abstract：:Fluorogenic RNAs that are based on the complex formed by 3,5-difluoro-4-hydroxybenzylidene imidazolinone (DFHBI) derivatives and the RNA aptamer named Spinach were used to engineer a new generation of in vitro and in vivo sensors for bioanalytics. With the resolved crystal structure of the RNA/small molecule complex, ...

journal_title：Nucleic acids research

authors： Ketterer S,Fuchs D,Weber W,Meier M

更新日期：2015-10-30 00:00:00

abstract：:The oncogenic transformation of normal cells into malignant, rapidly proliferating cells requires major alterations in cell physiology. For example, the transformed cells remodel their metabolic processes to supply the additional demand for cellular building blocks. We have recently demonstrated essential metabolic pr...

journal_title：Nucleic acids research

authors： Shaul YD,Yuan B,Thiru P,Nutter-Upham A,McCallum S,Lanzkron C,Bell GW,Sabatini DM

更新日期：2016-01-04 00:00:00

abstract：:Integrating DNA delivery systems hold promise for many applications including treatment of diseases; however, targeted integration is needed for improved safety. The piggyBac (PB) transposon system is a highly active non-viral gene delivery system capable of integrating defined DNA segments into host chromosomes witho...

journal_title：Nucleic acids research

authors： Luo W,Galvan DL,Woodard LE,Dorset D,Levy S,Wilson MH

更新日期：2017-08-21 00:00:00

abstract：:Here we describe a two-stepped photobiotin-based procedure to enrich a target (canine retinal) cDNA library for tissue specific clones without removing those containing repetitive ( SINE ) elements, despite the presence of these elements in the driver population. In a first hybridization excess SINE elements were hybr...

journal_title：Nucleic acids research

authors： Lin CT,Sargan DR

更新日期：1997-11-01 00:00:00

abstract：:We investigated the effects of the antiviral agent distamycin A and of a distamycin derivative (FCE 24517) which possesses antineoplastic activity on the binding of some regulatory proteins to DNA. Both compounds inhibited the binding to DNA of the ubiquitous octamer binding factor OTF 1 and of the erythroid specific ...

journal_title：Nucleic acids research

authors： Broggini M,Ponti M,Ottolenghi S,D'Incalci M,Mongelli N,Mantovani R

更新日期：1989-02-11 00:00:00

abstract：:We have synthesized the tetradecamer GAGCXGATAACAAG containing a part of the sequence of the lactose operator. A guanine base in the sequence is replaced by the adduct of the carcinogen 2-acetylaminofluorene with guanine. Under the standard conditions of de-protection, the fluorene moiety is lost, leaving behind a gua...

journal_title：Nucleic acids research

authors： Stöhrer G,Osband JA,Alvarado-Urbina G

更新日期：1983-08-11 00:00:00

abstract：:The annotation of protein function has become a crucial problem with the advent of sequence and structural genomics initiatives. A large body of evidence suggests that protein structural information is frequently encoded in local sequences, and that folds are mainly made up of a number of simple local units of super-s...

journal_title：Nucleic acids research

authors： Espadaler J,Fernandez-Fuentes N,Hermoso A,Querol E,Aviles FX,Sternberg MJ,Oliva B

更新日期：2004-01-01 00:00:00

abstract：:Achiral pseudonucleosides bearing an anthraquinone moiety have been incorporated into deoxyoligonucleotides in internal, 3' and 5' positions. The ability of these modified deoxyoligonucleotides to hybridize to complementary RNA and DNA was investigated using Tm measurements. The anthraquinone was shown to enhance bind...

journal_title：Nucleic acids research

authors： Lin KY,Matteucci M

更新日期：1991-06-11 00:00:00

abstract：:PPARγ2 is a critical lineage-determining transcription factor that is essential for adipogenic differentiation. Here we report characterization of the three-dimensional structure of the PPARγ2 locus after the onset of adipogenic differentiation and the mechanisms by which it forms. We identified a differentiation-depe...

journal_title：Nucleic acids research

authors： LeBlanc SE,Wu Q,Lamba P,Sif S,Imbalzano AN

更新日期：2016-06-20 00:00:00

abstract：:The activation of a telomere maintenance mechanism is required for cancer development in humans. While most tumors achieve this by expressing the enzyme telomerase, a fraction (5-15%) employs a recombination-based mechanism termed alternative lengthening of telomeres (ALT). Here we show that loss of the single-strande...

journal_title：Nucleic acids research

authors： Grudic A,Jul-Larsen A,Haring SJ,Wold MS,Lønning PE,Bjerkvig R,Bøe SO

更新日期：2007-01-01 00:00:00

abstract：:The three dimensional crystal structure of T5 5'-3' exonuclease was compared with that of two other members of the 5'-3' exonuclease family: T4 ribonuclease H and the N-terminal domain of Thermus aquaticus DNA polymerase I. Though these structures were largely similar, some regions of these enzymes show evidence of si...

journal_title：Nucleic acids research

authors： Artymiuk PJ,Ceska TA,Suck D,Sayers JR

更新日期：1997-11-01 00:00:00

abstract：:After ionising radiation double-strand breaks (dsb) are lethal if not repaired or misrepaired. Cell killing is greatly enhanced by hyperthermia and it is questioned here whether heat not only affects dsb repair capacity but also fidelity in a chromosomal context. dsb repair experiments were designed so as to mainly sc...

journal_title：Nucleic acids research

authors： El-Awady RA,Dikomey E,Dahm-Daphi J

更新日期：2001-05-01 00:00:00

abstract：:Transcription factor decoy binding sites are short DNA sequences that can titrate a transcription factor away from its natural binding site, therefore regulating gene expression. In this study, we harness synthetic transcription factor decoy systems to regulate gene expression for metabolic pathways in Escherichia col...

journal_title：Nucleic acids research

authors： Wang T,Tague N,Whelan SA,Dunlop MJ

更新日期：2021-01-25 00:00:00

abstract：:In this report we have analyzed the role of antisense transcription in the control of LEF1 transcription factor expression. A natural antisense transcript (NAT) is transcribed from a promoter present in the first intron of LEF1 gene and undergoes splicing in mesenchymal cells. Although this locus is silent in epitheli...

journal_title：Nucleic acids research

authors： Beltran M,Aparicio-Prat E,Mazzolini R,Millanes-Romero A,Massó P,Jenner RG,Díaz VM,Peiró S,de Herreros AG

更新日期：2015-07-13 00:00:00