Crosslinking transfer RNA and messenger RNA at the ribosomal decoding region: identification of the site of reaction on the messenger RNA.

abstract：:Mismatch repair is a highly conserved cellular pathway responsible for repairing mismatched dsDNA. Errors are detected by the MutS enzyme, which most likely senses altered mechanical property of damaged dsDNA rather than a specific molecular pattern. While the curved shape of dsDNA in crystallographic MutS/DNA structu...

journal_title：Nucleic acids research

authors： Bouchal T,Durník I,Illík V,Réblová K,Kulhánek P

更新日期：2020-11-18 00:00:00

abstract：:Mitochondrial proteins remain the subject of intense research interest due to their implication in an increasing number of different conditions including mitochondrial and metabolic disease, cancer, and neuromuscular degenerative and age-related disorders. However, the mitochondrial proteome has yet to be accurately a...

journal_title：Nucleic acids research

authors： Smith AC,Robinson AJ

更新日期：2016-01-04 00:00:00

abstract：:A crucial component of the human mitochondrial DNA replisome is the ring-shaped helicase TWINKLE-a phage T7-gene 4-like protein expressed in the nucleus and localized in the human mitochondria. Our previous studies showed that despite being a helicase, TWINKLE has unique DNA annealing activity. At the time, the implic...

journal_title：Nucleic acids research

authors： Sen D,Patel G,Patel SS

更新日期：2016-05-19 00:00:00

abstract：:The unknown modified nucleotide G*, isolated from both Schizosaccharomyces pombe and Torulopsis utilis initiator tRNAs(Met), has been identified as an O-ribosyl-(1"----2')-guanosine-5"-phosphate, called Gr(p), by means of HPLC, UV-absorption, mass spectrometry and periodate oxidation procedures. By comparison with the...

journal_title：Nucleic acids research

authors： Glasser AL,Desgres J,Heitzler J,Gehrke CW,Keith G

更新日期：1991-10-11 00:00:00

abstract：:A simple and rapid procedure to isolate clones carrying sequences from a specific region of the polytene chromosome of Drosophila is demonstrated. The procedure involves microdissection of the region of interest, amplification of the DNA by PCR using a primer designed to prime the synthesis nonspecifically, labeling o...

journal_title：Nucleic acids research

authors： Wesley CS,Ben M,Kreitman M,Hagag N,Eanes WF

更新日期：1990-02-11 00:00:00

abstract：:Cdc48/p97 is an evolutionary conserved ubiquitin-dependent chaperone involved in a broad array of cellular functions due to its ability to associate with multiple cofactors. Aside from its role in removing RNA polymerase II from chromatin after DNA damage, little is known about how this AAA-ATPase is involved in the t...

journal_title：Nucleic acids research

authors： Bonizec M,Hérissant L,Pokrzywa W,Geng F,Wenzel S,Howard GC,Rodriguez P,Krause S,Tansey WP,Hoppe T,Dargemont C

更新日期：2014-01-01 00:00:00

abstract：:Boundary elements partition eukaryotic chromatin into active and repressive domains, and can also block regulatory interactions between domains. Boundary elements act via diverse mechanisms making accurate feature-based computational predictions difficult. Therefore, we developed an unbiased algorithm that predicts th...

journal_title：Nucleic acids research

authors： Wang J,Lunyak VV,Jordan IK

更新日期：2012-01-01 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：:A requirement for specific RNA folding is that the free-energy landscape discriminate against non-native folds. While tertiary interactions are critical for stabilizing the native fold, they are relatively non-specific, suggesting additional mechanisms contribute to tertiary folding specificity. In this study, we use ...

journal_title：Nucleic acids research

authors： Mustoe AM,Al-Hashimi HM,Brooks CL 3rd

更新日期：2016-01-08 00:00:00

abstract：:The CRISPR system has become a powerful biological tool with a wide range of applications. However, improving targeting specificity and accurately predicting potential off-targets remains a significant goal. Here, we introduce a web-based CR: ISPR/Cas9 O: ff-target P: rediction and I: dentification T: ool (CROP-IT) th...

journal_title：Nucleic acids research

authors： Singh R,Kuscu C,Quinlan A,Qi Y,Adli M

更新日期：2015-10-15 00:00:00

abstract：:Several authors have suggested or inferred that modest changes in microRNA expression can potentiate or impinge on their capacity to mediate gene repression, and that doing so could play a significant role in diseases. Such interpretations are based on several assumptions, namely: (i) changes in microRNA expression co...

journal_title：Nucleic acids research

authors： Mayya VK,Duchaine TF

更新日期：2015-09-03 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：:Analysis of intergenic sequences for purposes such as the investigation of transcriptional signals or the identification of small RNA genes is frequently complicated by traditional biological database structures. Genome data is commonly treated as chromosome-length sequence records, detailed by gene calls demarcating ...

journal_title：Nucleic acids research

authors： Ray WC,Daniels CJ

更新日期：2003-01-01 00:00:00

abstract：:How DNA sequence variation influences gene expression remains poorly understood. Diploid organisms have two homologous copies of their DNA sequence in the same nucleus, providing a rich source of information about how genetic variation affects a wealth of biochemical processes. However, few computational methods have ...

journal_title：Nucleic acids research

authors： Chou SP,Danko CG

更新日期：2019-06-20 00:00:00

abstract：:Escherichia coli leucyl-tRNA synthetase (LeuRS) aminoacylates up to six different class II tRNA(leu) molecules. Each has a distinct anticodon and varied nucleotides in other regions of the tRNA. Attempts to construct a minihelix RNA that can be aminoacylated with leucine have been unsuccessful. Herein, we describe the...

journal_title：Nucleic acids research

authors： Larkin DC,Williams AM,Martinis SA,Fox GE

更新日期：2002-05-15 00:00:00

abstract：:From a recombinant lambda phage, we have determined a 387 bp sequence containing a mouse lysine tRNA gene. The putative lys tRNA (anticodon UUU) differs from rabbit liver lys tRNA at five positions. The flanking regions of the mouse gene are not generally homologous to published human and Drosophila lys tRNA genes. Ho...

journal_title：Nucleic acids research

authors： Han JH,Harding JD

更新日期：1983-04-11 00:00:00

abstract：:The selective and potent inhibition of mitochondrial translation in Saccharomyces cerevisiae by pentamidine suggests a novel antimicrobial action for this drug. Electrophoresis mobility shift assay, T1 ribonuclease footprinting, hydroxyl radical footprinting and isothermal titration calorimetry collectively demonstrat...

journal_title：Nucleic acids research

authors： Sun T,Zhang Y

更新日期：2008-03-01 00:00:00

abstract：:DNA-PKcs and Ku are essential components of the complex that catalyzes non-homologous end joining (NHEJ) of DNA double-strand breaks (DSBs). Ku, a heterodimeric protein, binds to DNA ends and facilitates recruitment of the catalytic subunit, DNA-PKcs. We have investigated the effect of DNA strand orientation and seque...

journal_title：Nucleic acids research

authors： Pawelczak KS,Andrews BJ,Turchi JJ

更新日期：2005-01-07 00:00:00

abstract：:During the last years, the demand for custom-made cDNA chips/arrays as well as whole genome chips is increasing rapidly. The efficient selection of gene-specific primers/oligomers is of the utmost importance for the successful production of such chips. We developed GenomePRIDE, a highly flexible and scalable software ...

journal_title：Nucleic acids research

authors： Haas SA,Hild M,Wright AP,Hain T,Talibi D,Vingron M

更新日期：2003-10-01 00:00:00

abstract：:The chicken erythroid proteins binding to the histone H5 5' promoter and 3' erythroid-specific enhancer regions were identified. In DNase I footprinting and gel mobility shift experiments with immature adult erythrocyte nuclear extracts, we have demonstrated the binding of proteins to the GC-box, a high affinity Sp1 b...

journal_title：Nucleic acids research

authors： Sun JM,Penner CG,Davie JR

更新日期：1992-12-11 00:00:00

abstract：:Nuclei isolated from cultured mouse and rat cell lines initiated pre-rRNA chains at the correct site and with the correct nucleotide specificity (A for mouse, G for rat). Nucleic acid filter hybridization and S1 nuclease mapping were used to analyze the RNA products initiated with nucleoside (beta-S)triphosphates. Ini...

journal_title：Nucleic acids research

authors： Zhang ZY,Thompson EA,Stallcup MR

更新日期：1984-11-12 00:00:00

abstract：:Transfection of a human estrogen receptor cDNA expression vector (HEO) into cultured Xenopus kidney cells confers estrogen responsiveness to the recipient cells as demonstrated by the hormone dependent expression of co-transfected Xenopus vitellogenin-CAT chimeric genes. The estrogen stimulation of these vit-CAT genes...

journal_title：Nucleic acids research

authors： Seiler-Tuyns A,Mérillat AM,Haefliger DN,Wahli W

更新日期：1988-09-12 00:00:00

abstract：:A refined map for the linear arrangement of histones along DNA in nucleosomal core particles has been determined by DNA-protein crosslinking. On one strand of 145-bp core DNA, histones are aligned in the following order: (5') H2B25,35-H455,65-H375,85,95/H488-H2B105,11 5-H2A118-H3135,145/H2A145 (3') (the subscripts giv...

journal_title：Nucleic acids research

authors： Bavykin SG,Usachenko SI,Lishanskaya AI,Shick VV,Belyavsky AV,Undritsov IM,Strokov AA,Zalenskaya IA,Mirzabekov AD

更新日期：1985-05-24 00:00:00

abstract：:A method is described which allows selection of sequences which can substitute for the normal AATAAA hexanucleotide involved in polyadenylation of SV40 late mRNAs. Plaques were generated from viral DNA lacking the motif, forcing acquisition of substitute sequences. Four variants were characterized. All displayed wild-...

journal_title：Nucleic acids research

authors： Swimmer C,Shenk T

更新日期：1985-11-25 00:00:00

abstract：:The minor groove binding asymmetric cyanine dye 4-[(3-methyl-6-(benzothiazol-2-yl)-2,3-dihydro- (benzo-1,3-thiazole)-2-methylidene)]-1-methyl-pyridin ium iodide (BEBO) is tested as sequence non- specific label in real-time PCR. The fluorescence intensity of BEBO increases upon binding to double-stranded DNA allowing e...

journal_title：Nucleic acids research

authors： Bengtsson M,Karlsson HJ,Westman G,Kubista M

更新日期：2003-04-15 00:00:00

abstract：:ATR functions as a master regulator of the DNA-damage response. ATR activation requires the ATR activator, topoisomerase IIβ-binding protein 1 (TopBP1). However, the underlying mechanism of TopBP1 regulation and how its regulation affects DNA replication remain unknown. Here, we report a specific interaction between T...

journal_title：Nucleic acids research

authors： Feng H,Lu J,Song X,Thongkum A,Zhang F,Lou L,Reizes O,Almasan A,Gong Z

更新日期：2020-11-04 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：:We have used gel retardation analysis to show that human DNA topoisomerase IIbeta can bind a 40 bp linear duplex containing a single DNA topoisomerase IIbeta cleavage site. Furthermore, we demonstrate for the first time that human DNA topoisomerase IIbeta binds to four-way junction DNA. This supports previous suggesti...

journal_title：Nucleic acids research

authors： West KL,Austin CA

更新日期：1999-02-15 00:00:00

abstract：:Three copies of a highly repetitive DNA sequence B1 which is complementary to the most abundant class of mouse fold-back RNA have been cloned in pBR322 plasmid and sequenced by the method of Maxam and Gilbert. All the three have a length of about 130 base pairs and are very similar in their base sequence. The deviatio...

journal_title：Nucleic acids research

authors： Krayev AS,Kramerov DA,Skryabin KG,Ryskov AP,Bayev AA,Georgiev GP

更新日期：1980-03-25 00:00:00

abstract：:RJ2.2.5, a mutant derived from the human B-lymphoma cell, Raji, is unable to express the MHC class II genes because of a recessive transcriptional defect attributed to the lack of an activator function. We report the isolation of a RJ2.2.5 revertant, namely AR, in which the expression of the mRNAs encoded by these gen...

journal_title：Nucleic acids research

authors： Ombra MN,Perfetto C,Autiero M,Anzisi AM,Pasquinelli R,Maffei A,Del Pozzo G,Guardiola J

更新日期：1993-02-11 00:00:00