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At least 1,225 records · Page 68Linked to original sources
PubMed1979

[Secondary structure of RNA secreted by Ehrlich ascites carcinoma cells].

The RNA, secreted by the cells of Ehrlich ascite carcinoma stimulates the inoculability and growth of the tumour. It contains double-helical regions, is resistable to the effects of pancreatic RNAse, has a melting point at 74 degrees and is eluted from the hydroxylapatite column by 0,25 M phosphate buffer. During its interaction with ethidium bromide the RNA increases the fluorescence of the dye. The amount of double-helical regions in the RNA makes up to 60%. These double-helical regions are formed in the carcinoma-secreted RNA due to RNA self-supercoiling. This was demonstrated by fluorescence studies of the RNA-ethidium bromide complex under various RNA denaturation and renaturation conditions.

Animals↗
PubMed1976

Use of cross-linking in studying the structure of RNA tumour viruses.

Treatment of intact avian myeloblastosis virus (AMV) with dimethyl suberimidate dihydrochloride (DMS), a cross-linking agent specific for amino groups, was found to result in progressive cross-linking among viral proteins, as revealed by polyacrylamide gel electrophoresis (PAGE) in the presence of sodium dodecyl sulphate (SDS). Free viral proteins were not cross-linked. The cross-linked protein complex with an apparent molecular weight of 50,000 daltons was studied in detail.

Avian Leukosis Virus↗
PubMed1999

Structural studies of symmetric DNA undecamers containing non-symmetrical sheared (PuGAPu):(PyGAPy) motifs.

Interstrand purine-purine stacks originate from tandem sheared purine.purine pairing and represent one of the most important motifs in both DNA and RNA structures. Several RNA and DNA structures, solved recently in both solution and the solid state, contain these special motifs, which greatly increase the structural diversity of nucleic acid molecules. The direct evidence for the sheared purine-purine pairing at neutral pH in solution remains, however, elusive. In this manuscript, we have used high resolution NMR methods to study a series of symmetrical DNA duplexes containing two non-symmetrical 5'-(PuGAPu)/(PyGAPy)-3' motifs. Many strong- and medium-strength NOEs across the G.A base pair were detected in the H2O-NOESY spectra collected at a relatively low temperature (-5 degrees C). These NOEs, especially those from A-6NH2 to G-H1', G-H4', and G-2NH2, clearly define the proposed side-by-side sheared G.A pairing nature. Another interesting feature is the strong NOEs exhibited by the unpaired G-imino proton in the G.A pair to its own G-2NH2, which implies that G-2NH2 is involved in H-bonding with a base in the minor groove edge. The finding that non-symmetrical (PuGAPu):(PyGAPy) motif also form similarly stable structures loosens the requirement for a more restricted (PyGAPu)2 motif in forming the interstrand purine-purine stacks.

Base Pairing↗
PubMed2004

A genomic selection strategy to identify accessible and dimerization blocking targets in the 5'-UTR of HIV-1 RNA.

Defining target sites for antisense oligonucleotides in highly structured RNA is a non-trivial exercise that has received much attention. Here we describe a novel and simple method to generate a library composed of all 20mer oligoribonucleotides that are sense- and antisense to any given sequence or genome and apply the method to the highly structured HIV-1 leader RNA. Oligoribonucleotides that interact strongly with folded HIV-1 RNA and potentially inhibit its dimerization were identified through iterative rounds of affinity selection by native gel electrophoresis. We identified five distinct regions in the HIV-1 RNA that were particularly prone to antisense annealing and a structural comparison between these sites suggested that the 3'-end of the antisense RNA preferentially interacts with single-stranded loops in the target RNA, whereas the 5'-end binds within double-stranded regions. The selected RNA species and corresponding DNA oligonucleotides were assayed for HIV-1 RNA binding, ability to block reverse transcription and/or potential to interfere with dimerization. All the selected oligonucleotides bound rapidly and strongly to the HIV-1 leader RNA in vitro and one oligonucleotide was capable of disrupting RNA dimers efficiently. The library selection methodology we describe here is rapid, inexpensive and generally applicable to any other RNA or RNP complex. The length of the oligonucleotide in the library is similar to antisense molecules generally applied in vivo and therefore likely to define targets relevant for HIV-1 therapy.

5' Untranslated Regions↗
PubMed2000

RNA motifs mediating in vivo site-specific nonhomologous recombination in (+) RNA virus enforce in vitro nonhomologous crossovers with HIV-1 reverse transcriptase.

There are several lines of evidence that both RNA viruses and retroviruses recombine according to a copy choice mechanism. Using the brome mosaic virus (BMV)-based system, we recognized elements in the RNA structure that enhance nonhomologous crossovers within or near the local heteroduplex formed by recombining molecules. The same structural motifs were employed in vitro to test the ability of human immunodeficiency virus reverse transcriptase (HIV-RT) to switch templates during DNA synthesis. We demonstrated that a specific combination of the local double-stranded region with short homologous sequences and a hairpin structure allows template switching by HIV-RT. In contrast to BMV replicase, HIV-RT does not mediate the detectable level of recombination using only the heteroduplex structure, though local hybridization between RNA molecules efficiently pauses primer extension. Moreover, the presented data suggest that a proper arrangement of identified structural motifs can ensure site specificity of RNA-RNA recombination. These results indicate that HIV-RT utilizes the same or a very similar mechanism as BMV replicase to change nonhomologous RNA templates in a site-specific manner.

Base Sequence↗
PubMed2004

The human T-cell lymphotropic virus type-I dimerization initiation site forms a hairpin loop, unlike previously characterized retroviral dimerization motifs.

The formation of genomic RNA dimers during the retroviral life cycle is essential for optimal viral replication and infectivity. The sequences and RNA structures responsible for this interaction are located in the untranslated 5' leader RNA, along with other cis-acting signals. Dimer formation occurs by specific interaction between identical structural motifs. It is believed that an initial kissing hairpin forms following self-recognition by autocomplementary RNA loops, leading to formation of an extended stable duplex. The dimerization initiation site (DIS) of the deltaretrovirus human T-cell lymphotropic virus type-I (HTLV-I) has been previously localized to a 14-nucleotide sequence predicted to contain an RNA stem loop. Biochemical probing of the monomeric RNA structure using RNAse T1, RNAse V1, RNAse U2, lead acetate, and dimethyl sulfate has led to the generation of the first structural map of the HTLV-I DIS. A comprehensive data set of individual nucleotide modifications reveals that the structural motif responsible for HTLV-I RNA dimerization forms a trinucleotide RNA loop, unlike any previously characterized retroviral dimerization motif. Molecular modeling demonstrates that this can be formed by an unusual C:synG base pair closing the loop. Comparative phylogeny indicates that such a motif may also exist in other deltaretroviruses.

5' Untranslated Regions↗
PubMed1983

Molecular biology of rotaviruses. V. Terminal structure of viral RNA species.

The terminal structure of rotavirus genomic ds RNA and in vitro transcribed mRNA was investigated using S1 nuclease digestion and 3' terminal sequence analysis. S1 nuclease analysis indicated that viral mRNA was not a truncated copy of the genome RNA at its 5' end. The 3' terminal sequence analysis of genomic plus strands and mRNA showed that they were coterminal indicating that in vitro transcribed mRNA is a full length copy of the genomic template. The sequence analysis performed on isolated viral RNA species plus strands revealed a completely conserved 3' terminal octanucleotide 5'-AUGUGACC-3' present in both UK tissue culture adapted bovine rotavirus and a human rotavirus isolate. Sequencing of isolated genomic minus strands again revealed a completely conserved 3' terminal sequence of approximately the same length as that seen for the viral plus strands.

Base Sequence↗