RNA design rules from a massive open laboratory

Lee, Jeehyung; Kladwang, Wipapat; Lee, Minjae; Cantu, Daniel; Azizyan, Martin; Kim, Hanjoo; Limpaecher, Alex; Gaikwad, Snehal; Yoon, Sungroh; Treuille, Adrien; Das, Rhiju; Participants, Eterna

doi:10.1073/pnas.1313039111

Cited by 290 publications

(251 citation statements)

References 41 publications

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“…Examples have included riboswitches that are known from other techniques to form multiple structures, engineered sequences that failed to fold into target structures, and engineered switches explicitly designed to form multiple structures ( Fig. 6) Lee et al 2014;Reining et al 2013;Serganov et al 2004). For these cases, it is not possible to define a single secondary structure for the RNA, and a separate analysis method has been developed that models an ensemble of secondary structures and, importantly, estimates the associated increase in modeling uncertainty.…”

Section: Multiple States Of Rna As a Major Challengementioning

confidence: 99%

RNA structure through multidimensional chemical mapping

Tian

Das

2016

Quart. Rev. Biophys.

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Abstract. The discoveries of myriad non-coding RNA molecules, each transiting through multiple flexible states in cells or virions, present major challenges for structure determination. Advances in high-throughput chemical mapping give new routes for characterizing entire transcriptomes in vivo, but the resulting one-dimensional data generally remain too information-poor to allow accurate de novo structure determination. Multidimensional chemical mapping (MCM) methods seek to address this challenge. Mutate-and-map (M 2 ), RNA interaction groups by mutational profiling (RING-MaP and MaP-2D analysis) and multiplexed •OH cleavage analysis (MOHCA) measure how the chemical reactivities of every nucleotide in an RNA molecule change in response to modifications at every other nucleotide. A growing body of in vitro blind tests and compensatory mutation/rescue experiments indicate that MCM methods give consistently accurate secondary structures and global tertiary structures for ribozymes, ribosomal domains and ligand-bound riboswitch aptamers up to 200 nucleotides in length. Importantly, MCM analyses provide detailed information on structurally heterogeneous RNA states, such as ligand-free riboswitches that are functionally important but difficult to resolve with other approaches. The sequencing requirements of currently available MCM protocols scale at least quadratically with RNA length, precluding general application to transcriptomes or viral genomes at present. We propose a modify-cross-link-map (MXM) expansion to overcome this and other current limitations to resolving the in vivo 'RNA structurome'.

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Section: Multiple States Of Rna As a Major Challengementioning

confidence: 99%

RNA structure through multidimensional chemical mapping

Tian

Das

2016

Quart. Rev. Biophys.

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“…[33] enabled museum visitors to playfully interact with living cells. Commercial and academic cloud labs that enable remote users to design and run life-science experiments have been deployed for research [18,32,42] and education [19,20], e.g., Lee et al [32] enabled citizen science to help solve RNA structures, and Hossain et al [19,20] brought inquiry-based science learning with true experiments to classrooms and massive open online courses (MOOCs). Bioty is built on top of this cloud lab approach.…”

Section: Human-computer Interaction In the Life Sciencesmentioning

confidence: 99%

“…Future engineering applications such as for biological swarm control have been demonstrated [30], and applications for discovery research are in reach [9,32,20].…”

Section: Introductionmentioning

confidence: 99%

An interactive programming paradigm for realtime experimentation with remote living matter

Washington

Samuel-Gama

Goyal

et al. 2017

Preprint

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Life-science research is increasingly accelerated through instrumentation advancements -even supporting the real-time interaction with living matter in the cloud. This enables entirely new applications for research, education, and art. The creation of such applications is currently challenging and time consuming, even for experts, as it requires knowledge of biotechnology, hardware design, and software development in addition to continuous access to reliable and responsive biological materials. We therefore developed Bioty, a JavaScript-based web toolkit enabling rapid prototyping of versatile Human-Biology Interaction (HBI) applications utilizing swarms of motile, phototactic cells hosted on a remote cloud lab. We evaluated and demonstrated the utility of Bioty through user studies with both HBI novices and experts, who used Bioty to create applications such as interactive scientific experiments, biotic video games, and biological art. Our findings inform the design of development toolkits for programming the behavior of biological matter.

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“…RNA secondary structure, defined as the set of A-T, C-G, and G-U canonical pairs in an RNA structure, is a resolution that has proven useful for studying RNA. Secondary structures have been used to find functional RNA in genomes (Macke et al 2001;Klein and Eddy 2003;Torarinsson et al 2006;Uzilov et al 2006;Yao et al 2006;Nawrocki et al 2009;Gorodkin et al 2010;Gruber et al 2010;Fu et al 2015), to find regions of an RNA that are accessible for binding by siRNAs (Heale et al 2005;Lu and Mathews 2007;Tafer et al 2008), and for designing RNAs with desired structures or functions (Hofacker et al 1994;Zadeh et al 2010;Garcia-Martin et al 2013;Lee et al 2014). Secondary structure prediction can also be used to search for motifs of interest, such as binding sites for small molecules (Velagapudi et al 2014) or proteins (Re et al 2014).…”

Section: Introductionmentioning

confidence: 99%

Exact calculation of loop formation probability identifies folding motifs in RNA secondary structures

Sloma

Mathews

2016

RNA

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RNA secondary structure prediction is widely used to analyze RNA sequences. In an RNA partition function calculation, free energy nearest neighbor parameters are used in a dynamic programming algorithm to estimate statistical properties of the secondary structure ensemble. Previously, partition functions have largely been used to estimate the probability that a given pair of nucleotides form a base pair, the conditional stacking probability, the accessibility to binding of a continuous stretch of nucleotides, or a representative sample of RNA structures. Here it is demonstrated that an RNA partition function can also be used to calculate the exact probability of formation of hairpin loops, internal loops, bulge loops, or multibranch loops at a given position. This calculation can also be used to estimate the probability of formation of specific helices. Benchmarking on a set of RNA sequences with known secondary structures indicated that loops that were calculated to be more probable were more likely to be present in the known structure than less probable loops. Furthermore, highly probable loops are more likely to be in the known structure than the set of loops predicted in the lowest free energy structures.

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RNA design rules from a massive open laboratory

Cited by 290 publications

References 41 publications

RNA structure through multidimensional chemical mapping

RNA structure through multidimensional chemical mapping

An interactive programming paradigm for realtime experimentation with remote living matter

Exact calculation of loop formation probability identifies folding motifs in RNA secondary structures

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