Abstract：
:One surprisingly common element of RNA secondary structure consists of a hairpin capped by a four-base loop (or the tetraloop). Recently the 3-D structures of two RNA-tetraloops have been determined by NMR-studies. Both structures have a similar architecture: the first and the last bases of the loop form a hydrogen bonded pair which is stacked on the stem base pair. We have analysed the ability of tetraloops, with the other combinations of the first and the fourth bases, to adopt such a 'diloop' conformation using computer modelling. The analysis has shown that the 'diloop' conformation has many covalent and steric constraints which give a possibility for reliable structural predictions. As a result, a set of the tetraloop 3-D structures in which hydrogen bonded pairing of the first and the last bases does not cause covalent and steric hindrances has been selected. In most cases several predicted 3-D structures corresponded to one tetraloop sequence. Taking into consideration the folding pathway of RNA hairpins we have resolved this ambiguity and predicted the most probable 3-D structure for every possible nucleotide sequence of the tetraloop. On the basis of these results a conclusion has been drawn on the possible reasons of the tetraloop phylogenetic preference.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Kajava A,Rüterjans Hdoi
10.1093/nar/21.19.4556subject
Has Abstractpub_date
1993-09-25 00:00:00pages
4556-62issue
19eissn
0305-1048issn
1362-4962journal_volume
21pub_type
杂志文章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
pub_type： 杂志文章
doi：10.1093/nar/gky199
更新日期：2018-04-20 00:00:00
abstract：:The 3'-untranslated region (UTR) of tobacco mosaic virus (TMV), which terminates in a tRNA-like structure, functionally substitutes for a poly(A) tail in both plant and animal cells. The addition of the TMV 3'-UTR to chimeric mRNA constructs increases their expression up to 100-fold, increasing both translational effi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.18.5031
更新日期：1991-09-25 00:00:00
abstract：:MolProbity is a general-purpose web server offering quality validation for 3D structures of proteins, nucleic acids and complexes. It provides detailed all-atom contact analysis of any steric problems within the molecules as well as updated dihedral-angle diagnostics, and it can calculate and display the H-bond and va...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm216
更新日期：2007-07-01 00:00:00
abstract：:A fluoride-cleavable phosphoramidite for biotinylation was designed, synthesized and coupled efficiently to the 5'-end of DNA on an automatic synthesizer. The diisopropylsilyl acetal functionality was used to link the biotin moiety through a tertiary hydroxide group to the 5'-end of DNA. This linkage proved to be comp...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg130
更新日期：2003-01-15 00:00:00
abstract：:We report the isolation of a novel human POU domain encoding gene named RDC-1. The POU domain of the RDC-1 encoded protein is highly related to the POU domain potentially encoded by the rat brain-3 sequence and to that of the Drosophila I-POU protein; outside of the POU region, RDC-1 is unrelated to any previously cha...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.18.4919
更新日期：1992-09-25 00:00:00
abstract：:4'-Acylated thymidines represent a new class of DNA chain terminators, since they have been shown to act as post-incorporation chain-terminating nucleotides despite the presence of a free 3'-hydroxyl group. Here, we describe the action of the 4'-acetyl- (MeTTP) and 4'-propanoylthymidine 5'-triphosphate (EtTTP) on HIV-...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.17.4063
更新日期：1998-09-01 00:00:00
abstract：:A minizyme is a hammerhead ribozyme with short oligonucleotide linkers instead of stem-loop II. In a previous study we demonstrated that a minizyme with high activity forms a dimeric structure with a common stem II. Because of their dimeric structure, minizymes are potentially capable of cleaving a substrate at two di...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/24.12.2302
更新日期：1996-06-15 00:00:00
abstract：:Major efforts are underway to elucidate the spatial distribution of ribosomal RNAs (rRNAs) in the ribosome. An especially informative approach is the identification of likely base-base tertiary interactions within the RNA by phylogenetic comparison. Herein evidence is presented for three heretofore unrecognized candid...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/17.6.2215
更新日期：1989-03-25 00:00:00
abstract：:We present a multi-laboratory effort to describe the structural and dynamical properties of duplex B-DNA under physiological conditions. By processing a large amount of atomistic molecular dynamics simulations, we determine the sequence-dependent structural properties of DNA as expressed in the equilibrium distributio...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz905
更新日期：2019-12-02 00:00:00
abstract：:In this paper we develop a new method for genotyping Affymetrix single nucleotide polymorphism (SNP) array. The method is based on (i) using multiple arrays at the same time to determine the genotypes and (ii) a model that relates intensities of individual SNPs to each other. The latter point allows us to annotate SNP...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl475
更新日期：2006-01-01 00:00:00
abstract：:A vector system is presented that allows generation of E. coli co-expression clones by a standardized, robust cloning procedure. The number of co-expressed proteins is not limited. Five 'pQLink' vectors for expression of His-tag and GST-tag fusion proteins as well as untagged proteins and for cloning by restriction en...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm067
更新日期：2007-01-01 00:00:00
abstract：:IGF2 mRNA-binding protein 1 (IMP1) is a key regulator of messenger RNA (mRNA) metabolism and transport in organismal development and, in cancer, its mis-regulation is an important component of tumour metastasis. IMP1 function relies on the recognition of a diverse set of mRNA targets that is mediated by the combinator...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz136
更新日期：2019-05-07 00:00:00
abstract：:The Trypanosoma brucei exoribonuclease, TbDSS-1, has been implicated in multiple aspects of mitochondrial RNA metabolism. Here, we investigate the role of TbDSS-1 in RNA processing and surveillance by analyzing 12S rRNA processing intermediates in TbDSS-1 RNAi cells. RNA fragments corresponding to leader sequence upst...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm690
更新日期：2008-01-01 00:00:00
abstract：:Active DNA demethylation (ADDM) in mammals occurs via hydroxylation of 5-methylcytosine (5mC) by TET and/or deamination by AID/APOBEC family enzymes. The resulting 5mC derivatives are removed through the base excision repair (BER) pathway. At present, it is unclear how the cell manages to eliminate closely spaced 5mC ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw059
更新日期：2016-05-05 00:00:00
abstract：:A new method for evaluating some complex characteristics of the primary structure of E.coli promoters is proposed. The method, of nonparametric statistical significance, selects important conserved single-base positions in combination with 2-base coupling relations of identity and complementarity. The extended consens...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/17.12.4799
更新日期：1989-06-26 00:00:00
abstract：:Human immunodeficiency virus-1 (HIV-1) leader RNA, which contains double-stranded regions due to inverted repeats, was shown to activate the dsRNA-dependent enzymes associated with the interferon system. HIV-1 leader RNA produced in vitro using SP6 RNA polymerase was characterized using probes for antisense and sense-...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/17.3.969
更新日期：1989-02-11 00:00:00
abstract：:Microbial enzymes have many known applications as biocatalysts in biotechnology, agriculture, medical and other industries. However, only a few enzymes are currently employed for such commercial applications. In this scenario, the current onslaught of metagenomic data provides a new unexplored treasure trove of genomi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp1001
更新日期：2010-01-01 00:00:00
abstract：:Increased cytochrome P450 2E1 (CYP2E1) expression is the main cause of oxidative stress, which exacerbates alcoholic liver diseases (ALDs). Estrogen-related receptor gamma (ERRγ) induces CYP2E1 expression and contributes to enhancing alcohol-induced liver injury. Retinoic acid-related orphan receptor alpha (RORα) has ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv1034
更新日期：2016-02-18 00:00:00
abstract：:The alternation/deficiency in activation-3 (ADA3) is an essential component of the human p300/CBP-associated factor (PCAF) and yeast Spt-Ada-Gcn5-acetyltransferase (SAGA) histone acetyltransferase complexes. These complexes facilitate transactivation of target genes by association with transcription factors and modifi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq269
更新日期：2010-09-01 00:00:00
abstract：:Two new endonuclease activities, endonuclease B and endonuclease C, obtained from yeast nuclear preparations have been separated and partially characterized. Endonuclease B has a primary requirement for Mn2+ which cannot be replaced by Mg2+ or Ca2+, and makes single-strand scissions in double-stranded DNA. Endonculeas...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/2.7.1023
更新日期：1975-07-01 00:00:00
abstract：:Modification of chromatin and related transcription factors by histone deacetylases (HDACs) is one of the major strategies for controlling gene expression in eukaryotes. The HDAC domains of class IIa HDACs repress the respective target genes by interacting with the C-terminal region of the silencing mediator for retin...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky926
更新日期：2018-12-14 00:00:00
abstract：:Biological and chemical DNA fragmentation generates DNA molecules with a variety of termini, including blunt ends and single-stranded overhangs. We have developed a Next Generation Sequencing (NGS) assay, XACTLY, to interrogate the termini of fragmented DNA, information traditionally lost in standard NGS library prepa...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa128
更新日期：2020-05-07 00:00:00
abstract：:The smallest catalytic RNA identified to date is a manganese-dependent ribozyme that requires only a complex between GAAA and UUU to effect site-specific cleavage. We show here that this ribozyme occurs naturally in the 3'-UTR of Vg1 and beta-actin mRNAs. In accord with earlier studies with model RNAs, cleavage occurs...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkn530
更新日期：2008-10-01 00:00:00
abstract：:A 30 nt RNA with a sequence designed to form an intramolecular triple helix was analyzed by one-and two-dimensional NMR spectroscopy and UV absorption measurements. NMR data show that the RNA contains seven pyrimidine-purine-pyrimidine base triples stabilized by Watson-Crick and Hoogsteen interactions. The temperature...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/24.14.2841
更新日期：1996-07-15 00:00:00
abstract：:The erbAalpha gene encodes two alpha-thyroid hormone receptor isoforms, TRalpha1 and TRalpha2, which arise from alternatively processed mRNAs, erbAalpha1 (alpha1) and erb alpha2 (alpha2). The splicing and alternative polyadenylation patterns of these mRNAs resemble that of mRNAs encoding different forms of immunoglobu...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/25.21.4296
更新日期：1997-11-01 00:00:00
abstract：:LocDB is a manually curated database with experimental annotations for the subcellular localizations of proteins in Homo sapiens (HS, human) and Arabidopsis thaliana (AT, thale cress). Currently, it contains entries for 19,604 UniProt proteins (HS: 13,342; AT: 6262). Each database entry contains the experimentally der...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq927
更新日期：2011-01-01 00:00:00
abstract：:A previously elaborated technique for fixing a chosen partially melted state of DNA with glyoxal was used in a study of the melting process of the replicative form (RF III) of phi X174 DNA. Electron-microscopic maps corresponding to five points of the melting curve of RF III were obtained and compared with the theoret...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/10.6.1867
更新日期：1982-03-25 00:00:00
abstract：:A positive cis-acting DNA element in the near 5'-upstream region of the CYP2B1/B2 genes in rat liver was found to play an important role in the transcription of these genes. An oligonucleotide covering -69 to -98 nt mimicked the gel mobility shift pattern given by the fragment -179 to +29 nt, which was earlier found a...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.3.557
更新日期：1992-02-11 00:00:00
abstract：:In spermidine-condensed calf thymus DNA preparations, torus-shaped condensates were shown by transmission electron microscopy to exist under the hydrated conditions of the freeze fracture experiment. Using extremely low Pt metal deposition levels (9 A Pt/C) high-contrast replicas of the spermidine-DNA toruses were obt...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/11.6.1839
更新日期：1983-03-25 00:00:00
abstract：:A simple method, primer specific and mispair extension analysis (PSMEA) with pfu DNA polymerase was developed for genotyping. PSMEA is based on the unique properties of 3'-->5' exonuclease proofreading activity. In the presence of an incomplete set of dNTPs, pfu was found to be extremely discriminative in nucleotide i...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.21.5013
更新日期：1998-11-01 00:00:00
