Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “RNA structure”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,045 records · Page 58Linked to original sources
PubMed2005

Regulation of the structure of RNA assemblies through RNA tertiary interactions.

We have previously shown that RNA building blocks containing two or three stem-loops based on the dimerization initiation site (DIS) connected by short linkers can be assembled into various one- and two-dimensional structures. Here, in an attempt to regulate the conformation of the RNA assemblies by adjusting the rigidity of the RNA building block, we have introduced the triple-helical scaffold (THS) into the linker region connecting two DIS-based stem-loops. As a result, linear and circular assemblies could be selectively formed with RNA building blocks containing the wild-type and mutant THS sequences, respectively. The results demonstrate how the conformation of RNA assemblies may be regulated by external factors, thereby expanding the utility of RNA-based nanostructures.

Dimerization↗
PubMed1979

Purification and subunit structure of RNA polymerase II from the pea.

DNA-dependent RNA polymerase II (EC 2.7.7.6) from pea seedlings (Pisum sativum var. Alaska) has been purified to homogeneity, as judged by native polyacrylamide electrophoresis. The procedure includes polyethyleneimine precipitation and elution, ammonium sulfate precipitation, DEAE-Sephadex chromatography, phosphocellulose chromatography, and heparin-Sepharose chromatography. The enzyme purified almost to homogeneity has a specific activity of 200 nmol/mg per 15 min at 30 degrees C with denatured calf thymus DNA as template. The enzyme activity is 50% inhibited in the presence of 0.05 migrograms/ml of alpha-amanitin. Polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate indicates that pea RNA polymerase II is composed of eight subunits with molecular weights and molar ratios (in parentheses) of 170 000 (0.9), 140 000 (1.0), 43 000 (1.5), 26 000 (2.0), 22 500 (1.2), 21 500 (0.6), 18 500 (1.6) and 17 500 (2.3). The structure is closely similar to that of cauliflower RNA polymerase II.

DNA-Directed RNA Polymerases↗
PubMed1997

The hepatitis B virus posttranscriptional regulatory element contains a highly stable RNA secondary structure.

Hepatitis B virus (HBV) transcripts contain a sequence known as the posttranscriptional regulatory element (PRE). This element was shown to facilitate the nuclear export of the S gene transcripts, to partially substitute for the human immunodeficiency virus (HIV-1) Rev-response element (RRE), and to bind two cellular factors. Within the genetically defined PRE (approximately 450 nucleotides), we identified a highly stable secondary structural element of 313 nucleotides in length termed PRE313. The energy values of the PRE313 are similar to those of the RRE of HIV-1 and significantly lower than those of other portions of HBV RNA. A comparison of human HBV subtypes shows strong conservation of the PRE313 in terms of energy and structure, providing further evidence for the biological significance of the genetically defined PRE and the PRE313 in particular. The structural model for the PRE313 described in this study may help in identifying crucial components of the transport mechanism of transcripts of HBV.

Base Sequence↗
PubMed1984

RNA secondary structure and translation inhibition: analysis of mutants in the rplJ leader.

We have carried out measurements of the stable binding of the ribosomal protein (r-protein) complex L10-L7/L12 to mutant forms of the mRNA leader of the rplJ operon of Escherichia coli. One of the point mutations, base 1548, which lies within the L10-L7/L12-protected region, almost completely abolishes in vitro formation of a stable complex of L10-L7/L12 with rplJ mRNA leader, and a second point mutation, base 1634, strongly reduces it. These observations constitute strong support for the proposition that L10-L7/L12 binds to the rplJ leader in bringing about translational feedback. To account for the action of these and other mutations, and to explain the mechanism of translation feedback inhibition, we suggest a secondary structure model involving alternate forms of the rplJ mRNA leader.

DNA-Directed RNA Polymerases↗
PubMed2004

Structure of RNA aptamer for HIV Tat complexed with Tat-derived peptide.

An RNA aptamer containing two binding sites exhibits extremely high affinity to the HIV Tat protein. We previously reported the structure of the aptamer complexed with argininamide as the simplest analogue of Tat. Here, we have analyzed the structure of the aptamer complexed with the partial peptide of Tat, RKKRR. The profile of chemical sift perturbations for the aptamer upon complex formation with RKKRR revealed that RKKRR can be a realistic analogue of Tat to address the interactions between the arginine-rich motif of Tat and the aptamer. It was suggested that the aptamer interacts with different arginine residues of RKKRR simultaneously at the two binding sites, which can explain the extremely high affinity to Tat.

Amino Acid Sequence↗
PubMed2000

Rational selection of antisense oligonucleotide sequences.

The purpose of this review is to identify rational selection procedures for the identification of optimal antisense oligonucleotide sequences. The review is firstly focused on how to find optimal hybridization sites, and secondly on how to select sequences that bind to structured RNA. The methods reviewed range from the more empirical testing of large numbers of mRNA complementary sequences to the more systematic techniques, i.e. RNase H mapping, use of combinatorial arrays and prediction of secondary structure of mRNA by computational methods. Structures that bind to structured RNA, i.e. aptastrucs and tethered oligonucleotide probes, and foldback triplex-forming oligonucleotides are also discussed. Relating to selection of antisense sequences by aid of computational analysis, valuable www addresses are given along with examples of folded structures of mRNA.

Base Sequence↗
PubMed1992

Mutant prohead RNAs in the in vitro packaging of bacteriophage phi 29 DNA-gp3.

The 174-base prohead RNA encoded by bacteriophage phi 29 of Bacillus subtilis, essential for packaging of the DNA-gp3 (DNA-gene product 3) complex, was expressed efficiently from the cloned gene. Computer programs for RNA structure analysis were used to fold hypothetical RNA mutants and thus to target mutagenesis of the RNA for studies of structure and function. Five mutants of the RNA were then produced by oligonucleotide-directed mutagenesis that were altered in the primary sequence at selected sites; two of these mutants were predicted to be altered in secondary structure from a model established previously by a phylogenetic analysis. The binding of the 32P end-labeled mutant RNAs to RNA-free proheads was comparable with that of the wild-type RNA. However, the capability of the mutant RNAs to reconstitute RNA-free proheads for DNA-gp3 packaging in the defined in vitro system and for assembly of phage in RNA-free extracts was variable, depending upon the alteration. Changes of highly conserved bases that retained the predicted secondary structure of the RNA model were tolerated to a much greater extent than changes predicted to alter the RNA secondary structure.

Bacteriophages↗
PubMed1989

An RNA secondary structure switch between the inactive and active conformations of the Escherichia coli 30 S ribosomal subunit.

Psoralen cross-linking was used to produce intramolecular cross-links in the Escherichia coli 16 S ribosomal RNA in the inactive and active forms of the 30 S subunit. A number of psoralen cross-links were made in the inactive form that were not made in the active form. The most frequent of these cross-links was sequenced by a series of techniques and identified as C-924 to U-1532. In this region, a three-base complementary, (921-923).(1532-1534), forms a site where psoralen can stack and produce a cross-link between C-924 and U-1532. When psoralen monoadducts were placed on inactive subunits and the conformation was switched to the active form before cross-linking, a new cross-link involving U-1393 was detected. U-1393 is part of the complementarity, (923-925).(1391-1393), that has previously been proposed as being an element of the functional secondary structure on the basis of sequence comparison. The complementarity between (921-923).(1532-1534) occurs in most nonmitochondrial small subunit RNAs; however, there are several counter examples in which it does not occur. This suggests that this alternate secondary structure interaction is not necessary for the function of the 30 S subunit.

Base Sequence↗
PubMed1974

Studies on the reverse transcriptase of RNA tumor viruses. Structural relatedness of two subunits of avian RNA tumor viruses.

The structural relationship of the small (alpha) and large (beta) subunits of reverse transcriptase isolated from two avian RNA tumor viruses has been examined by tryptic peptide analysis. Comparison of the tryptic hydrolysates of the isolated subunits by two-dimensional separation on thin-layer cellulose plates indicates that (i) the alpha subunit of reverse transcriptase of avian myeloblastosis virus is structurally related to the beta subunit; (ii) the alpha and beta subunits of the enzyme of Rous sarcoma virus also appear to be related; and (iii) there appears to be an extensive amino-acid sequence homology between reverse transcriptases of avian myeloblastosis virus and Rous sarcoma virus. Evidence is also presented that both alpha and beta subunits can be identified in purified avian myeloblastosis virions.

Amino Acid Sequence↗
PubMed2003

Synthesis of Seoul virus RNA and structural proteins in cultured cells.

Seoul virus is a hantavirus that causes hemorrhagic fever with renal syndrome (HFRS). The virion has a tripartite (S, M, and L) negative-stranded RNA genome, which is characteristic of the family Bunyaviridae. However, the molecular basis of virus replication is not well known. We established a Northern blot hybridization (NB) procedure using digoxygenin-labeled RNA probes, to quantitate the hantaviral plus- and minus-strand RNAs separately. Virus RNA replication was analyzed in infected Vero E6 cells. When the Vero E6 cells were infected with Seoul virus strain KI-83-262 (KI) at m.o.i. = 0.25, the plus-strand RNA was detected within 1 h post-infection (hpi), and the minus-strand RNA was detected subsequently. Using laser confocal microscopy, the nucleocapsid protein (NP) was detected within 2 hpi, and accumulated as scattered granules in the cytoplasm until 24 hpi. In contrast, the G2 protein first appeared at 8 hpi, was immediately transported to the Golgi, and accumulated in the Golgi until 24 hpi. Infectious virus particles were released into the medium at 24 h hpi. These findings indicate that hantavirus RNA replication starts with the appearance of NP at 2 hpi, glycoproteins then accumulate gradually in the Golgi, and virion formation is initiated once the viral RNAs and proteins have accumulated.

Animals↗
PubMed1970

Studies of transfer RNA tertiary structure by singlet-singlet energy transfer.

This distance between a base next to the anticodon of tRNA and the 3' CpCpA terminus of the molecule has been estimated by singlet-singlet energy transfer experiments. The energy donor was the Y base of unknown structure found in yeast tRNA(phe). Three different energy acceptors were used: acriflavine, proflavinyl acetic acid hydrazide, and 9-hydrazino acridine. These were attached to the periodate-oxidized 3' end of the tRNA. R(0)'s between 24 and 30 A were calculated for the three chromophore couples by assuming that the relative orientation of donor and acceptor is random. This assumption is supported by the consistency of the experimental results with all three acceptors and by studies of the fluorescence depolarization of Y. The energy transfer observed both by quenching of Y and enhanced activation of the acceptors is quite small, indicating that the anticodon is more than 40 A away from the amino acid accepting terminus. This places severe restrictions on the type of tertiary structure possible for tRNA.

Acridines↗
PubMed2005

Internal ribosome entry segment-mediated translation during apoptosis: the role of IRES-trans-acting factors.

During apoptosis, there is a reduction in translation initiation caused by caspase cleavage of several of the factors required for the cap-dependent scanning mechanism. Under these circumstances, many proteins that are required for apoptosis are instead translated by the alternative method of internal ribosome entry. This mechanism requires the formation of a complex RNA structural element and in the presence of internal ribosome entry segment (IRES)-trans-acting factors (ITAFs), the ribosome is recruited to the RNA. The interactions of several ITAFs with IRESs have been investigated in detail, and several mechanisms of action have been noted, including acting as chaperones, stabilising and remodelling the RNA structure. Structural remodelling by PTB in particular will be discussed, and how this protein is able to facilitate recruitment of the ribosome to several IRESs by causing previously occluded sites to become more accessible.

Apoptosis↗