In cell mutational interference mapping experiment (in cell MIME) identifies the 5' polyadenylation signal as a dual regulator of HIV-1 genomic RNA production and packaging.

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：:We present a new coarse grained method for the simulation of duplex DNA. The algorithm uses a generalized multi-harmonic model that can represent any multi-normal distribution of helical parameters, thus avoiding caveats of current mesoscopic models for DNA simulation and representing a breakthrough in the field. The ...

journal_title：Nucleic acids research

authors： Walther J,Dans PD,Balaceanu A,Hospital A,Bayarri G,Orozco M

更新日期：2020-03-18 00:00:00

abstract：:Heteroduplexes between the viral DNA of phiX174 and DNA from the replicative form (RF) of phage G4 were examined by electron microscopy. The single Eco RI site of G4-RF was utilized as a physical marker by preparing the heteroduplexes from the denatured, linear DNA obtained by restricting G4-RF with Eco RI endonucleas...

journal_title：Nucleic acids research

authors： Smiley BL,Warner RC

更新日期：1979-01-01 00:00:00

abstract：:Human cells are, in general, poor recipients of foreign DNA, which has severely hampered the cloning of genes by direct phenotypic correction of deficient human cell lines after DNA mediated gene transfer. In this communication a methodology is presented which largely circumvents this problems. The method relies on th...

journal_title：Nucleic acids research

authors： Belt PB,Jongmans W,de Wit J,Hoeijmakers JH,van de Putte P,Backendorf C

更新日期：1991-09-25 00:00:00

abstract：:Aminoglycosides antibiotics negate dissociation and recycling of the bacterial ribosome's subunits by binding to Helix 69 (H69) of 23S rRNA. The differential binding of various aminoglycosides to the chemically synthesized terminal domains of the Escherichia coli and human H69 has been characterized using spectroscopy...

journal_title：Nucleic acids research

authors： Scheunemann AE,Graham WD,Vendeix FA,Agris PF

更新日期：2010-05-01 00:00:00

abstract：:Topoisomerases (topos) maintain DNA topology and influence DNA transaction processes by catalysing relaxation, supercoiling and decatenation reactions. In the cellular milieu, division of labour between different topos ensures topological homeostasis and control of central processes. In Escherichia coli, DNA gyrase is...

journal_title：Nucleic acids research

authors： Kumar R,Riley JE,Parry D,Bates AD,Nagaraja V

更新日期：2012-11-01 00:00:00

abstract：:UNITE (https://unite.ut.ee/) is a web-based database and sequence management environment for the molecular identification of fungi. It targets the formal fungal barcode-the nuclear ribosomal internal transcribed spacer (ITS) region-and offers all ∼1 000 000 public fungal ITS sequences for reference. These are clustere...

journal_title：Nucleic acids research

authors： Nilsson RH,Larsson KH,Taylor AFS,Bengtsson-Palme J,Jeppesen TS,Schigel D,Kennedy P,Picard K,Glöckner FO,Tedersoo L,Saar I,Kõljalg U,Abarenkov K

更新日期：2019-01-08 00:00:00

abstract：:The chemical synthesis of backbone deuterium labelled [r(CGCGAAU*U*CGCG)]2 (U* = [5'-2H]U) is described. An efficient purification procedure was developed using a polymeric reverse phase (PRP) HPLC column at 60 degrees C. This procedure provided pure RNA dodecamer in the multi-milligram quantities (39% overall yield) ...

journal_title：Nucleic acids research

authors： Khare D,Orban J

更新日期：1992-10-11 00:00:00

abstract：:Direct visualization of DNA and proteins allows researchers to investigate DNA-protein interactions with great detail. Much progress has been made in this area as a result of increasingly sensitive single-molecule fluorescence techniques. At the same time, methods that control the conformation of DNA molecules have be...

journal_title：Nucleic acids research

authors： van Mameren J,Peterman EJ,Wuite GJ

更新日期：2008-08-01 00:00:00

abstract：:To study the role of the poly(A) tail length during the replication of poly(A)-containing plus-strand RNA virus, we have developed a simple reverse transcription polymerase chain reaction (RT-PCR)-based method that substantially improves the previously reported PAT [poly(A) test] assay. In contrast to the PAT assay, t...

journal_title：Nucleic acids research

authors： Kusov YY,Shatirishvili G,Dzagurov G,Gauss-Müller V

更新日期：2001-06-15 00:00:00

abstract：:A successful application is reported of the multivariate curve resolution alternating least-squares method (MCR-ALS) for the analysis of nucleic acid melting and salt-induced transitions. Under conditions where several structures co-exist in a conformational equilibrium, MCR-ALS analysis of the UV and circular dichroi...

journal_title：Nucleic acids research

authors： Jaumot J,Escaja N,Gargallo R,González C,Pedroso E,Tauler R

更新日期：2002-09-01 00:00:00

abstract：:We have compiled the DNA sequence data for E. coli available from the GENBANK and EMBL data libraries and over a period of several years independently from the literature. This is the fifth listing replacing and increasing the former listings substantially. However, in order to save space this printed version contains...

journal_title：Nucleic acids research

authors： Kröger M,Wahl R,Rice P

更新日期：1993-07-01 00:00:00

abstract：:In metazoan cells, only a limited number of mini chromosome maintenance (MCM) complexes are fired during S phase, while the majority remain dormant. Several methods have been used to map replication origins, but such methods cannot identify dormant origins. Herein, we determined MCM7-binding sites in human cells using...

journal_title：Nucleic acids research

authors： Sugimoto N,Maehara K,Yoshida K,Ohkawa Y,Fujita M

更新日期：2018-07-27 00:00:00

abstract：:An R-loop is a DNA:RNA hybrid formed during transcription when a DNA duplex is invaded by a nascent RNA transcript. R-loops accumulate in nucleoli during RNA polymerase I (RNAP I) transcription. Here, we report that mammalian RNase H1 enriches in nucleoli and co-localizes with R-loops in cultured human cells. Co-migra...

journal_title：Nucleic acids research

authors： Shen W,Sun H,De Hoyos CL,Bailey JK,Liang XH,Crooke ST

更新日期：2017-10-13 00:00:00

abstract：:Isopentenyl adenosine derivatives are always located adjacent to the 3' end of the anticodon in transfer RNA and have been implicated in certain biological functions. In the enteric bacterium, E. coli, the derivative is ms2i6A whereas in some plant associated bacteria the derivative is the hydroxylated form, ms2io6A. ...

journal_title：Nucleic acids research

authors： Janzer JJ,Raney JP,McLennan BD

更新日期：1982-09-25 00:00:00

abstract：:The genome stability is maintained by coordinated action of DNA repairs and checkpoints, which delay progression through the cell cycle in response to DNA damage. Rad9 is conserved from yeast to human and functions in cell cycle checkpoint controls. Here, a regulatory mechanism for Rad9 function is reported. In this s...

journal_title：Nucleic acids research

authors： He W,Ma X,Yang X,Zhao Y,Qiu J,Hang H

更新日期：2011-06-01 00:00:00

abstract：:Using an in vitro transcription system for Saccharomyces cerevisiae RNA polymerase I, we have analyzed Pol I promoter deletion mutants and mapped the boundaries of the promoter between positions -155 and +27. The 5'-boundary of the minimal core promoter capable of transcription initiation, however, was found to lie be...

journal_title：Nucleic acids research

authors： Kulkens T,Riggs DL,Heck JD,Planta RJ,Nomura M

更新日期：1991-10-11 00:00:00

abstract：:Conventional chemotherapy remains the primary treatment option for triple-negative breast cancer (TNBC). However, the current chemotherapeutic drugs have limited effects on TNBC, and often lead to serious side effects as well as drug resistance. Thus, more effective therapeutic options are sorely needed. As c-MYC onco...

journal_title：Nucleic acids research

authors： Hu MH,Wu TY,Huang Q,Jin G

更新日期：2019-11-18 00:00:00

abstract：:Twenty AdoMet-dependent methyltransferases (MTases) have been characterized structurally by X-ray crystallography and NMR. These include seven DNA MTases, five RNA MTases, four protein MTases and four small molecule MTases acting on the carbon, oxygen or nitrogen atoms of their substrates. The MTases share a common co...

journal_title：Nucleic acids research

authors： Cheng X,Roberts RJ

更新日期：2001-09-15 00:00:00

abstract：:An important problem in genomics is automatically clustering homologous proteins when only sequence information is available. Most methods for clustering proteins are local, and are based on simply thresholding a measure related to sequence distance. We first show how locality limits the performance of such methods by...

journal_title：Nucleic acids research

authors： Paccanaro A,Casbon JA,Saqi MA

更新日期：2006-03-17 00:00:00

abstract：:Nucleotide excision DNA repair is mechanistically conserved across all kingdoms of life. In prokaryotes, this multi-enzyme process requires six proteins: UvrA-D, DNA polymerase I and DNA ligase. To examine how UvrC locates the UvrB-DNA pre-incision complex at a site of damage, we have labeled UvrB and UvrC with differ...

journal_title：Nucleic acids research

authors： Hughes CD,Wang H,Ghodke H,Simons M,Towheed A,Peng Y,Van Houten B,Kad NM

更新日期：2013-05-01 00:00:00

abstract：:The family of ten-eleven translocation (Tet) dioxygenases is widely distributed across the eukaryotic tree of life, from mammals to the amoeboflagellate Naegleria gruberi. Like mammalian Tet proteins, the Naegleria Tet-like protein, NgTet1, acts on 5-methylcytosine (5mC) and generates 5-hydroxymethylcytosine (5hmC), 5...

journal_title：Nucleic acids research

authors： Hashimoto H,Pais JE,Dai N,Corrêa IR Jr,Zhang X,Zheng Y,Cheng X

更新日期：2015-12-15 00:00:00

abstract：:The Schizosaccharomyces pombe genome is one of the smallest among the free-living eukaryotes. We further reduced the S. pombe gene number by large-scale gene deletion to identify a minimal gene set required for growth under laboratory conditions. The genome-reduced strain has four deletion regions: 168.4 kb in the lef...

journal_title：Nucleic acids research

authors： Sasaki M,Kumagai H,Takegawa K,Tohda H

更新日期：2013-05-01 00:00:00

abstract：:The 5'-cap of spliceosomal small nuclear RNAs, some small nucleolar RNAs and of telomerase RNA was found to be hypermethylated in vivo. The Trimethylguanosine Synthase 1 (TGS1) mediates this conversion of the 7-methylguanosine-cap to the 2,2,7-trimethylguanosine (m(3)G)-cap during maturation of the RNPs. For mammalian...

journal_title：Nucleic acids research

authors： Monecke T,Dickmanns A,Ficner R

更新日期：2009-07-01 00:00:00

abstract：:We have recently described three group I introns inserted into a single gene, orf142, of the staphylococcal bacteriophage Twort and suggested the presence of at least two additional self-splicing introns in this phage genome. Here we report that two previously uncharacterized introns, 429 and 1087 nt in length, interr...

journal_title：Nucleic acids research

authors： Landthaler M,Begley U,Lau NC,Shub DA

更新日期：2002-05-01 00:00:00

abstract：:To successfully infect plants, viruses must counteract small RNA-based host defense responses. During infection of Arabidopsis, Cauliflower mosaic pararetrovirus (CaMV) is transcribed into pregenomic 35S and subgenomic 19S RNAs. The 35S RNA is both reverse transcribed and also used as an mRNA with highly structured 60...

journal_title：Nucleic acids research

authors： Blevins T,Rajeswaran R,Aregger M,Borah BK,Schepetilnikov M,Baerlocher L,Farinelli L,Meins F Jr,Hohn T,Pooggin MM

更新日期：2011-07-01 00:00:00

abstract：:The effect of temperature and primer concentration on oligonucleotide-primed transcription has been studied using the separated strands of a well-defined natural DNA as template. Results were similar to those obtained in the homopolymer-directed model systems. At high temperature and excess primer concentration mainly...

journal_title：Nucleic acids research

authors： Van Kreijl CF,Beelen RH,Borst P

更新日期：1977-02-01 00:00:00

abstract：:The NusA protein is a universally conserved bacterial transcription elongation factor that binds RNA polymerase (RNAP). When functioning independently, NusA enhances intrinsic termination. Paradoxically, NusA stimulates the function of the N and Q antiterminator proteins of bacteriophage λ. The mechanistic basis for N...

journal_title：Nucleic acids research

authors： Wells CD,Deighan P,Brigham M,Hochschild A

更新日期：2016-06-20 00:00:00

abstract：:It is a central issue to elucidate the new type of molecular recognition accompanied by a global structural change of a molecule upon binding to its targets. Here we investigate the driving force for the binding of R12 (a ribonucleic acid aptamer) and P16 (a partial peptide of a prion protein) during which P16 exhibit...

journal_title：Nucleic acids research

authors： Hayashi T,Oshima H,Mashima T,Nagata T,Katahira M,Kinoshita M

更新日期：2014-06-01 00:00:00

abstract：:The primary structure of the E. coli rpoC gene (5321 base pairs) coding the beta'-subunit of RNA polymerase as well as its adjacent segment have been determined. The structure analysis of the peptides obtained by cleavage of the protein with cyanogen bromide and trypsin has confirmed the amino acid sequence of the bet...

journal_title：Nucleic acids research

authors： Ovchinnikov YuA,Monastyrskaya GS,Gubanov VV,Guryev SO,Salomatina IS,Shuvaeva TM,Lipkin VM,Sverdlov ED

更新日期：1982-07-10 00:00:00