Abstract：
:We have carried out an extended set of standard and enhanced-sampling MD simulations (for a cumulative simulation time of 620 μs) with the aim to study folding landscapes of the rGGGUUAGGG and rGGGAGGG parallel G-hairpins (PH) with propeller loop. We identify folding and unfolding pathways of the PH, which is bridged with the unfolded state via an ensemble of cross-like structures (CS) possessing mutually tilted or perpendicular G-strands interacting via guanine-guanine H-bonding. The oligonucleotides reach the PH conformation from the unfolded state via a conformational diffusion through the folding landscape, i.e. as a series of rearrangements of the H-bond interactions starting from compacted anti-parallel hairpin-like structures. Although isolated PHs do not appear to be thermodynamically stable we suggest that CS and PH-types of structures are sufficiently populated during RNA guanine quadruplex (GQ) folding within the context of complete GQ-forming sequences. These structures may participate in compact coil-like ensembles that involve all four G-strands and already some bound ions. Such ensembles can then rearrange into the fully folded parallel GQs via conformational diffusion. We propose that the basic atomistic folding mechanism of propeller loops suggested in this work may be common for their formation in RNA and DNA GQs.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Havrila M,Stadlbauer P,Kührová P,Banáš P,Mergny JL,Otyepka M,Šponer Jdoi
10.1093/nar/gky712subject
Has Abstractpub_date
2018-09-28 00:00:00pages
8754-8771issue
17eissn
0305-1048issn
1362-4962pii
5079693journal_volume
46pub_type
杂志文章abstract：:IS200 is found throughout Enterobacteriaceae and transposes at a notoriously low frequency. In addition to the transposase protein (TnpA), IS200 encodes an uncharacterized Hfq-binding sRNA that is encoded opposite to the tnpA 5'UTR. In the current work we asked if this sRNA represses tnpA expression. We show here that...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv584
更新日期：2015-07-27 00:00:00
abstract：:A 2.1-kb cDNA clone representing a new member of the protease inhibitor family was isolated from a human liver cDNA library. The inhibitor, named human Leuserpin 2 (hLS2), comprises 480 amino acids and contains a leucine residue at its putative reactive center. HLS2 is about 25-28% homologous to three human members of...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/14.2.1073
更新日期：1986-01-24 00:00:00
abstract：:Two dimensional PEI-cellulose thin layer chromatography can resolve sequentially degraded oligonucleotide fragments of tRNA. This technique entails the sequential degradation of the oligonucleotide with snake venom phosphodiesterase in the presence of bacterial alkaline phosphatase, and periodate oxidation followed by...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/4.10.3563
更新日期：1977-10-01 00:00:00
abstract：:From gene expression to nanotechnology, understanding and controlling DNA requires a detailed knowledge of its higher order structure and dynamics. Here we take advantage of the environment-sensitive photoisomerization of cyanine dyes to probe local and global changes in DNA structure. We report that a covalently atta...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky887
更新日期：2018-11-30 00:00:00
abstract：:We have established a sensitive, monoclonal antibody (Mab)-based procedure permitting the selective enrichment of sequences containing the miscoding alkylation product O6-ethylguanine (O6-EtGua) from mammalian DNA. H5 rat hepatoma cells were reacted with the N-nitroso carcinogen N-ethyl-N-nitrosourea in vitro, to give...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.16.4467
更新日期：1991-08-25 00:00:00
abstract：:AR9 is a giant Bacillus subtilis phage whose uracil-containing double-stranded DNA genome encodes distant homologs of β and β' subunits of bacterial RNA polymerase (RNAP). The products of these genes are thought to assemble into two non-canonical multisubunit RNAPs - a virion RNAP (vRNAP) that is injected into the hos...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx264
更新日期：2017-06-02 00:00:00
abstract：:The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org) is an expertly curated database of literature-derived functional information for the model organism budding yeast, Saccharomyces cerevisiae. SGD constantly strives to synergize new types of experimental data and bioinformatics predictions with existin...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx1112
更新日期：2018-01-04 00:00:00
abstract：:For the rapid and sensitive detection of p53 'hot spot' mutations, we combined polymerase chain reaction based single-strand conformational polymorphism (PCR-SSCP) analysis with sequence specific-clamping by peptide nucleic acids (PNAs) in a one-step reaction tube protocol. For this purpose, we designed two PNA molecu...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.5.1356
更新日期：1998-03-01 00:00:00
abstract：:YY1 is ubiquitously expressed zinc finger DNA binding protein. It can act as a transcriptional repressor or activator and, when binding at the initiator element, as a component of the basal transcription complex. Binding sites for YY1 have been reported in a wide variety of promoters and they exhibit substantial diver...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/23.21.4457
更新日期：1995-11-11 00:00:00
abstract：:A simple and efficient method is described to introduce structurally pre-determined mutations into recombinant genomes of filamentous phage M13. The method rests on gapped duplex DNA (gdDNA) molecules of the phage M13 genome as the key intermediate. In this gdDNA, the (+) and the (shorter) (-) strand carry different g...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.24.9441
更新日期：1984-12-21 00:00:00
abstract：:Synchronous plasmodia of Physarum polycephalum in DNA synthesis were pulse-labelled with [oH]- thymidine for time periods of 15 seconds up to 9 minutes, or given a 30 seconds pulse followed by chase periods of 9 minutes up to 6 hours. Sedimentation analysis in alkaline sucrose gradients revealed at least five species ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/2.8.1381
更新日期：1975-08-01 00:00:00
abstract：:Members of the pentatricopeptide repeat domain (PPR) protein family bind RNA and are important for post-transcriptional control of organelle gene expression in unicellular eukaryotes, metazoans and plants. They also have a role in human pathology, as mutations in the leucine-rich PPR-containing (LRPPRC) gene cause sev...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku1132
更新日期：2014-12-16 00:00:00
abstract：:O-GLYCBASE is a revised database of information on glycoproteins and their O-linked glycosylation sites. Entries are compiled and revised from the literature, and from the sequence databases. Entries include information about species, sequence, glycosylation sites and glycan type and is fully cross-referenced. Compare...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.1.387
更新日期：1998-01-01 00:00:00
abstract：:Stable protein complexes, including those formed with RNA, are major building blocks of every living cell. Escherichia coli has been the leading bacterial organism with respect to global protein-protein networks. Yet, there has been no global census of RNA/protein complexes in this model species of microbiology. Here,...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa676
更新日期：2020-09-18 00:00:00
abstract：:Infrared Spectroscopy was used to determine the numbers of base pairs for yeast 5S RNA and 5.8S RNA. The spectra were recorded at 20 degrees C and 50 degrees C, where tertiary interactions are assumed to be of less importance. It may be concluded that the structure of both RNAs is highly ordered and that there are lar...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/9.15.3851
更新日期：1981-08-11 00:00:00
abstract：:G-DNA, a polymorphic family of four-stranded DNA structures, has been proposed to play roles in a variety of biological processes including telomere function, meiotic recombination and gene regulation. Here we report the purification and cloning of TGP1, a G-DNA specific binding protein from Tetrahymena thermophila. T...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.7.1613
更新日期：1998-04-01 00:00:00
abstract：:We have sequenced the external transcribed spacer (ETS) of a ribosomal transcription unit from Xenopus laevis, together with sections of the preceding non-transcribed spacer. Our analysis was carried out on the same cloned transcription unit as that from which the internal transcribed spacers (ITS) were previously seq...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/10.7.2387
更新日期：1982-04-10 00:00:00
abstract：:The MspI restriction-modification system, which recognizes the sequence 5'-CCGG-3', has been previously cloned and sequenced (1). We subcloned the methyltransferase gene (M.MspI) downstream of the ptac promoter in the multicopy vector pUC119 and overexpressed it in E. coli. Upon induction with IPTG, M.MspI constitutes...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.7.1579
更新日期：1992-04-11 00:00:00
abstract：:Characterization of the epigenetic status of individual cells remains a challenge. Current sequencing approaches have limited coverage, and it is difficult to assign an epigenetic status to the transcription state of individual gene alleles in the same cell. To address these limitations, a targeted microscopy-based ep...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkab009
更新日期：2021-01-28 00:00:00
abstract：:This paper describes a computer program designed to look for similarities between pairs of nucleic or amino acid sequences. The program looks both for segments of perfect identity or for regions where, using a scoring matrix, a minimum value is exceeded. The results of comparisons are presented as a matrix which is di...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/10.9.2951
更新日期：1982-05-11 00:00:00
abstract：:The human Microprocessor complex cleaves primary microRNA (miRNA) transcripts (pri-miRNAs) to initiate miRNA synthesis. Microprocessor consists of DROSHA (an RNase III enzyme), and DGCR8. DROSHA contains two RNase III domains, RIIIDa and RIIIDb, which simultaneously cleave the 3p- and 5p-strands of pri-miRNAs, respect...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa018
更新日期：2020-03-18 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
pub_type： 杂志文章,评审
doi：10.1093/nar/29.18.3784
更新日期：2001-09-15 00:00:00
abstract：:The U1A protein is a sequence-specific RNA binding protein found in the U1 snRNP particle where it binds to stem/loop II of U1 snRNA. U1A contains two 'RNP' or 'RRM' (RNA Recognition Motif) domains, which are common to many RNA-binding proteins. The N-terminal RRM has been shown to bind specifically to the U1 RNA stem...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.16.4283
更新日期：1992-08-25 00:00:00
abstract：:A recently reported cDNA clone coding for human promyelocytic L apoferritin, shows some differences with a liver L apoferritin cDNA. We have investigated if these differences are due to the expression of different genes or to an alternative transcription of an unique gene. In this paper we report data suggesting that ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/14.7.2863
更新日期：1986-04-11 00:00:00
abstract：:A complete physical map of the spinach mitochondrial genome has been established. The entire sequence content of 327 kilobase pairs (kb) is postulated to occur as a single circular molecule. Two directly repeated elements of approximately 6 kb, located on this "master chromosome", are proposed to participate in an int...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/14.14.5651
更新日期：1986-07-25 00:00:00
abstract：:Homing endonucleases recognize long target DNA sequences generating an accurate double-strand break that promotes gene targeting through homologous recombination. We have modified the homodimeric I-CreI endonuclease through protein engineering to target a specific DNA sequence within the human RAG1 gene. Mutations in ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq801
更新日期：2011-01-01 00:00:00
abstract：:Bacteria from the genus Streptomyces are very important for the production of natural bioactive compounds such as antibiotic, antitumour or immunosuppressant drugs. Around two-thirds of all known natural antibiotics are produced by these bacteria. An enormous quantity of crucial data related to this genus has been gen...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks1253
更新日期：2013-01-01 00:00:00
abstract：:We characterize a component of the E. coli bacterial nucleoid H1a, which accumulates in stationary phase. This protein, identical with the major component of a plasmid-protein complex previously isolated in our laboratory, has a pI close to 7.5. Acrylamide gel electrophoresis and sedimentation in sucrose gradient have...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.13.5321
更新日期：1984-07-11 00:00:00
abstract：:The interactions of HIV-1 reverse transcriptase (HIV-1 RT) with a synthetic 53/19-mer DNA substrate was investigated. For this template-primer HIV-1 RT displayed a Km value of 20 nM. The 53/19-mer competitively inhibited DNA synthesis performed on poly (rC).oligo(dG) with Ki value of 260 nM. This corresponded well to ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/21.17.3943
更新日期：1993-08-25 00:00:00
abstract：:The lesion bypass pathway, which is regulated by monoubiquitination of proliferating cell nuclear antigen (PCNA), is essential for resolving replication stalling due to DNA lesions. This process is important for preventing genomic instability and cancer development. Previously, it was shown that cells deficient in tum...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq1337
更新日期：2011-05-01 00:00:00
