Graphical exploratory data analysis of RNA secondary structure dynamics predicted by the massively parallel genetic algorithm

Shapiro, Bruce A.; Kasprzak, Wojciech K.; Grunewald, Calvin; Aman, Javed M.

doi:10.1016/j.jmgm.2006.04.004

Cited by 27 publications

(25 citation statements)

References 60 publications

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“…The program can simulate multi-pot assembly protocols and kinetic folding behaviors with possible differences in the starting states. An addition to StructureLab is used to visualize the folding and unfolding events (29). This approach is described in more detail in the Supporting Information.…”

Section: Resultsmentioning

confidence: 99%

Co-transcriptional production of RNA–DNA hybrids for simultaneous release of multiple split functionalities

Afonin

Desai

Viard

et al. 2013

Nucleic Acids Research

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Control over the simultaneous delivery of different functionalities and their synchronized intracellular activation can greatly benefit the fields of RNA and DNA biomedical nanotechnologies and allow for the production of nanoparticles and various switching devices with controllable functions. We present a system of multiple split functionalities embedded in the cognate pairs of RNA–DNA hybrids which are programmed to recognize each other, re-associate and form a DNA duplex while also releasing the split RNA fragments which upon association regain their original functions. Simultaneous activation of three different functionalities (RNAi, Förster resonance energy transfer and RNA aptamer) confirmed by multiple in vitro and cell culture experiments prove the concept. To automate the design process, a novel computational tool that differentiates between the thermodynamic stabilities of RNA–RNA, RNA–DNA and DNA–DNA duplexes was developed. Moreover, here we demonstrate that besides being easily produced by annealing synthetic RNAs and DNAs, the individual hybrids carrying longer RNAs can be produced by RNA polymerase II-dependent transcription of single-stranded DNA templates.

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Section: Resultsmentioning

confidence: 99%

Co-transcriptional production of RNA–DNA hybrids for simultaneous release of multiple split functionalities

Afonin

Desai

Viard

et al. 2013

Nucleic Acids Research

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“…The algorithm has been previously described (29,32). MPGAfold results were analyzed using the RNA/DNA structure analysis workbench StructureLab (30,31). Stem Trace (12), a component of StructureLab, was used to depict the results of 20 MPGAfold runs of the TCV 3Ј UTR population.…”

Section: Methodsmentioning

confidence: 99%

Structural Domains within the 3′ Untranslated Region of Turnip Crinkle Virus

McCormack

Yuan

Yingling

et al. 2008

J Virol

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159

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The genomes of positive-strand RNA viruses undergo conformational shifts that complicate efforts to equate structures with function. We have initiated a detailed analysis of secondary and tertiary elements within the 3 end of Turnip crinkle virus (TCV) that are required for viral accumulation in vivo. MPGAfold, a massively parallel genetic algorithm, suggested the presence of five hairpins (H4a, H4b, and previously identified hairpins H4, H5, and Pr) and one H-type pseudoknot (⌿ 3 ) within the 3-terminal 194 nucleotides (nt). In vivo compensatory mutagenesis analyses confirmed the existence of H4a, H4b, ⌿ 3 and a second pseudoknot (⌿ 2 ) previously identified in a TCV satellite RNA. In-line structure probing of the 194-nt fragment supported the coexistence of H4, H4a, H4b, ⌿ 3 and a pseudoknot that connects H5 and the 3 end (⌿ 1 ). Stepwise replacements of TCV elements with the comparable elements from Cardamine chlorotic fleck virus indicated that the complete 142-nt 3 end, and subsets containing ⌿ 3 , H4a, and H4b or ⌿ 3 , H4a, H4b, H5, and ⌿ 2 , form functional domains for virus accumulation in vivo. A new 3-D molecular modeling protocol (RNA2D3D) predicted that H4a, H4b, H5, ⌿ 3 , and ⌿ 2 are capable of simultaneous existence and bears some resemblance to a tRNA. The related Japanese iris necrotic ring virus does not have comparable domains. These results provide a framework for determining how interconnected elements participate in processes that require 3 untranslated region sequences such as translation and replication.Replication of plus-strand RNA viruses initially requires translation of the genomic RNA to produce the virus-encoded, RNA-dependent RNA polymerase (RdRp) and any auxiliary viral proteins necessary for transcription. In a process that is poorly defined but likely dictated by viral and/or cellular factors, translation is terminated and the genomic RNA becomes available for reiterative synthesis of complementary strands, a process that requires membrane association (1, 2, 26). For some viruses, subsequent viral plus-strand synthesis occurs in virus-specific membrane invaginations known as spherules, which contain a limited number of minus-sense genomes and whose formation is induced by specific viral proteins (1,15,26). Although the process of producing viral progeny has been extensively studied using many different viral systems, it remains poorly understood. For example, fundamental questions, such as the role that conformational shifts in RNA structure play in switching the template from translation to replication, the proteins required to enact such events, and if cis-acting core promoters, enhancers, and repressors are organized into functional, interacting modules, remain virtually unanswered.Recent reports that portions of RNA viral genomes undergo conformational shifts to execute different functions (10, 13, 21, 28) complicate efforts to assign biological roles to groups of cis-acting elements that may not structurally coexist. The ability of viral RNAs to assume multiple conformation...

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“…As a result alternative folding pathways can be explored. The analysis of MPGAfold results was performed with the help of our software workbench StructureLab (Shapiro and Kasprzak 1996;Kasprzak and Shapiro 1999;Shapiro et al 2006).…”

Section: Computational Analysis Of Rna Secondary Structure Comparisonsmentioning

confidence: 99%

The fraction of RNA that folds into the correct branched secondary structure determines hepatitis delta virus type 3 RNA editing levels

Linnstaedt

Kasprzak²,

Shapiro

et al. 2009

RNA

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RNA editing by the host RNA adenosine deaminase ADAR1 at the amber/W site of hepatitis delta virus RNA plays a central role in the viral replication cycle by affecting the balance between viral RNA synthesis and packaging. Previously, we found that HDV genotype III (HDV-3) RNA can form two secondary structures following transcription: an unbranched rod structure, which is characteristic of HDV, and a metastable branched structure that serves as the substrate for editing. The unstable nature of the branched editing substrate structure raised the possibility that structural dynamics of the RNA following transcription could determine the rate at which editing occurs. Here, editing and its control are examined in two HDV-3 isolates, from Peru and Ecuador. Analysis of editing in vitro by ADAR1 indicated that the branched structure formed by RNA derived from the Peruvian isolate is edited more efficiently than that from the Ecuadorian isolate. In contrast, in the context of replication, Peruvian RNA is edited less efficiently than RNA containing Ecuadorian sequences. Computational analyses of RNA folding using the massively parallel genetic algorithm (MPGAfold) indicated that the Peruvian RNA is less likely to form the branched structure required for editing than the Ecuadorian isolate. This difference was confirmed by in vitro transcription of these RNAs. Overall, our data indicate that HDV-3 controls RNA editing levels via (1) the fraction of the RNA that folds, during transcription, into the metastable branched structure required for editing and (2) the efficiency with which ADAR1 edits this branched substrate RNA.

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Graphical exploratory data analysis of RNA secondary structure dynamics predicted by the massively parallel genetic algorithm

Cited by 27 publications

References 60 publications

Co-transcriptional production of RNA–DNA hybrids for simultaneous release of multiple split functionalities

Co-transcriptional production of RNA–DNA hybrids for simultaneous release of multiple split functionalities

Structural Domains within the 3′ Untranslated Region of Turnip Crinkle Virus

The fraction of RNA that folds into the correct branched secondary structure determines hepatitis delta virus type 3 RNA editing levels

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