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Chapter
Viroids: Non-coding Circular RNAs Are Tiny Pathogens Provoking a Broad Response in Host Plants
More than 50 years ago, viroids were firstly described as the smallest RNA molecules capable to infect certain plants and to autonomously self-replicate in host plants. Viroids are covalently closed circular s...
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Article
Open AccessThe HHIP-AS1 lncRNA promotes tumorigenicity through stabilization of dynein complex 1 in human SHH-driven tumors
Most lncRNAs display species-specific expression patterns suggesting that animal models of cancer may only incompletely recapitulate the regulatory crosstalk between lncRNAs and oncogenic pathways in humans. A...
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Protocol
Fluorescence-Based Kinetic Measurements for RNA-Cleaving DNAzymes
Studying the catalytic behavior of biocatalysts under different conditions including temperature, buffer conditions, and cofactor concentrations is an important tool to understand their reaction mechanism. We ...
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Protocol
Predicting the Structure of a Viroid
Viroids are small non-coding RNAs that require a special sequence and structure to be replicated and transported by the host machinery. Many of these features can be predicted and later experimentally verified...
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Article
Time-resolved structural analysis of an RNA-cleaving DNA catalyst
The 10–23 DNAzyme is one of the most prominent catalytically active DNA sequences1,2. Its ability to cleave a wide range of RNA targets with high selectivity entails a substantial therapeutic and biotechnological...
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Protocol
Design of a DNAzyme
The efficiency of RNA-cleaving DNAzymes depends on a large extent on complex formation with their RNA targets. We describe available prediction tools that should help in the design of efficient DNAzymes and sh...
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Article
Inability of DNAzymes to cleave RNA in vivo is due to limited Mg \(^{2+}\) concentration in cells
Sequence specific cleavage of RNA can be achieved by hammerhead ribozymes as well as DNAzymes. They comprise a catalytic core sequence flanked by regions that form double strands with complementary RNA. While ...
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Article
Open AccessModelling the three-dimensional structure of the right-terminal domain of pospiviroids
Viroids, the smallest know plant pathogens, consist solely of a circular, single-stranded, non-coding RNA. Thus for all of their biological functions, like replication, processing, and transport, they have to ...
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Article
A 5′P degradation hot spot influences molecular farming of anticancerogenic nuclease TBN1 in tobacco cells
Tomato bifunctional nuclease 1 (TBN1) is a polyfunctional protein with anticancerogenic activity originally isolated as an overexpressed protein from viroid-infected tomato. Its molecular farming in plant cell...
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Article
Characterization of Potato spindle tuber viroid (PSTVd) incidence and new variants from ornamentals
We analyzed the spreading and persistence of PSTVd variants in several ornamentals in the territory of the Czech Republic. The pool of PSTVd variants detected in Solanum jasminoides, S. muricatum, Datura sp. and
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Article
Complete sequence of a cryptic virus from hemp (Cannabis sativa)
Hemp (Cannabis sativa) was found to be a useful propagation host for hop latent virus, a carlavirus. However, when virus preparations were analysed by electron microscopy, along with the expected filamentous part...
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Chapter
Methods for Predicting RNA Secondary Structure
The formation of RNA structure is a hierarchical process: the secondary structure builds up by thermodynamically favorable stacks of base pairs (helix formation) and unfavorable loops (non-Watson–Crick base pa...
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Chapter
Viroids: The Smallest Known Infectious Agents Cause Accumulation of Viroid-Specific Small RNAs
Viroids are plant-infectious, noncoding, unencapsidated, circular RNAs ranging in size from 250 to 400 nucleotides that are transcribed in a rolling-circle mechanism either in nuclei (Pospiviroidae) or in chlorop...
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Article
Open AccessLost in folding space? Comparing four variants of the thermodynamic model for RNA secondary structure prediction
Many bioinformatics tools for RNA secondary structure analysis are based on a thermodynamic model of RNA folding. They predict a single, "optimal" structure by free energy minimization, they enumerate near-opt...
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Article
Die Haushaltsrechtsreform des Bundes
Dieser Artikel beschreibt das wohl weitreichendste, gleichwohl aber von der Öffentlichkeit weitgehend unbemerkte Reformwerk der vergangenen Legislaturperiode. Die Haushaltsrechtsreform des Bundes wird in diese...
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Article
Open AccessConStruct: Improved construction of RNA consensus structures
Aligning homologous non-coding RNAs (ncRNAs) correctly in terms of sequence and structure is an unresolved problem, due to both mathematical complexity and imperfect scoring functions. High quality alignments,...
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Article
Open AccessAn enhanced RNA alignment benchmark for sequence alignment programs
The performance of alignment programs is traditionally tested on sets of protein sequences, of which a reference alignment is known. Conclusions drawn from such protein benchmarks do not necessarily hold for t...
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Chapter
A Computational Approach to Search for Non-Coding RNAs in Large Genomic Data
Over the last few years several specialized software tools have been developed, each allowing a certain class of RNAs insequencedatatobe found.Herewedescribeageneral tool that allows us to specify many differe...
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Article
Plant 7SL RNA and tRNATyr genes with inserted antisense sequences are efficiently expressed in an in vitro transcription system from Nicotiana tabacum cells
RNA polymerase III-driven cassettes for the expression of antisense RNAs and ribozymes have recently attracted much attention because (1) pol III genes are transcribed abundantly in all kinds of tissues and (2...
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Article
RNA structure and the regulation of gene expression
RNA secondary and tertiary structure is involved in post-transcriptional regulation of gene expression either by exposing specific sequences or throught the formation of specific structural motifs. An overview...
