Structure, folding and flexibility of co-transcriptional RNA origami

McRae, Ewan K.S.; Rasmussen, H.H.; Liu, Jianfang; Bøggild, Andreas; Nguyen, Michael Hai; Vallina, Néstor Sampedro; Boesen, Thomas; Pedersen, Jan Skov; Ren, Gang; Geary, Cody; Andersen, Ellen Juul

doi:10.1038/s41565-023-01321-6

Cited by 30 publications

(46 citation statements)

References 88 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Where possible, we measured the deviation in TM-score, GDT_TS, INF, INF_WC, and lDDT between distinct experimentally captured conformations (red lines in Figure 2 ). More specifically, we compared the following structure pairs in targets with multiple conformations (see also Table 1 ): the point- mutations for the CPEB3 ribozyme 59 (R1107 vs R1108), the apo and holo structures of the aptamer Apta-FRET 60 (R1136), the young and mature conformations of 6HBC 61 (R1138), the four cryo-EM classes for the SL5 domain of the bat coronavirus HKU5 (R1156), and finally the RNA structures for the RsmZ-RsmA RNA-protein complexes with six vs. four proteins bound (R1189 vs R1190). In addition, for two cases, we measured the deviation between different models derived from the same experimental data (black lines in Figure 2 ), comparing distinct models built into the same cryo-EM density maps for the SL5 domains of SARS-CoV-2 (R1149) and BtCov-HKU5 (R1156).…”

Section: Resultsmentioning

confidence: 99%

“…The 'young' and 'mature' structures do not differ in their Watson-Crick-Franklin helices but, to interconvert, would require breaking of a kissing loop interaction, twisting of the two kissing elements about their helical axes, and then reformation of the kissing loop. 60 None of the CASP models produced models close to the 'young' structure. Other natural and designed RNA systems are known to display similar kinetic traps and topological isomers 65,66 , and it will be interesting to see if in future CASPs, such conformations can be blindly predicted.…”

Section: Topologically Accurate Casp15 Rna Models Miss Detailed Featu...mentioning

confidence: 99%

See 1 more Smart Citation

Assessment of three-dimensional RNA structure prediction in CASP15

Das

Kretsch

Simpkin

et al. 2023

Preprint

View full text Add to dashboard Cite

The prediction of RNA three-dimensional structures remains an unsolved problem. Here, we report double-blind assessments of RNA structure predictions in CASP15, the first CASP exercise in which RNA modeling was assessed. Forty two predictor groups submitted models for at least one of twelve RNA-containing targets. These models were evaluated by the RNA-Puzzles organizers and, separately, by a CASP-recruited team using metrics (GDT, lDDT) and approaches (Z-score rankings) initially developed for assessment of proteins and generalized here for RNA assessment. The two assessments independently ranked the same predictor groups as first (AIchemy_RNA2), second (Chen), and third (RNAPolis and GeneSilico, tied); predictions from deep learning approaches were significantly worse than these top ranked groups, who did not use deep learning. Further analyses based on direct comparison of predicted models to cryogenic electron microscopy (cryo-EM) maps and X-ray diffraction data support these rankings. With the exception of two RNA-protein complexes, models submitted by CASP15 groups correctly predicted the global topology of the RNA targets. Comparisons of CASP15 submissions to designed RNA nanostructures as well as molecular replacement trials highlight the potential utility of current RNA modeling approaches for RNA nanotechnology and structural biology, respectively. Nevertheless, challenges remain in modeling fine details such as non-canonical pairs, in ranking among submitted models, and in prediction of multiple structures resolved by cryo-EM or crystallography.

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Topologically Accurate Casp15 Rna Models Miss Detailed Featu...mentioning

confidence: 99%

Assessment of three-dimensional RNA structure prediction in CASP15

Das

Kretsch

Simpkin

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

“…Leveraging the algorithmic toolkit of nucleic acid nanotechnology [14][15][16], here we introduce a systematic method for expressing designer biomolecular condensates from synthetic RNA nanostructures. Our elementary motifs consist of star-shaped junctions, or nanostars, which fold co-transcriptionally and assemble thanks to programmable base-pairing interactions, forming liquid or gel-like condensates.…”

Section: Introductionmentioning

confidence: 99%

Co-transcriptional production of programmable RNA condensates and synthetic organelles

Fabrini,

Farag,

Nuccio

et al. 2023

Preprint

View full text Add to dashboard Cite

Condensation of RNA and proteins is central to cellular functions, and the ability to program it would be valuable in synthetic biology and synthetic cell science. Here we introduce a modular platform for engineering synthetic RNA condensates from tailor-made, branched RNA nanostructures that fold and assemble co-transcriptionally. Up to three orthogonal condensates can form simultaneously and selectively accumulate guest molecules. The RNA condensates can be expressed within synthetic cells to produce membrane-less organelles with controlled number, size, morphology and compositions, and that display the ability to selectively capture proteins. Thein situexpression of programmable RNA condensates could underpin spatial organisation of functionalities in both biological and synthetic cells.

show abstract

“…Nucleic acid nanotechnology facilitates the precise assembly of nucleic acid molecules into nanostructures with tailored sizes, shapes, and chemical compositions. − These programmable nanostructures, characterized by their controllable synthesis process and excellent biocompatibility, have found diverse applications in fields, such as cell protein translation, cell motion, and immune activation . Recently, single-stranded RNA (ssRNA) origamis have been extensively explored as a promising platform that can be transcribed from DNA templates and self-folded into defined structures both in vitro and in vivo . , These ssRNA origamis can be equipped with various “structure” or “sequence” modules to enrich specific biomedical functions, including drug delivery, gene editing, , regulation of molecular interactions, , and the facilitation of high-resolution structural characterization. , Though many endowed properties have been brought from external structural motifs and sequences to ssRNA origami, the versatility and the function of the intrinsic RNA molecular signature of RNA structures have not been fully utilized. The integration of functional modules at the “molecular” level holds significant potential for further expanding and diversifying the applications of ssRNA origami nanotechnology .…”

mentioning

confidence: 99%

“…13,14 These ssRNA origamis can be equipped with various "structure" or "sequence" modules to enrich specific biomedical functions, including drug delivery, 15 gene editing, 9,16 regulation of molecular interactions, 17,18 and the facilitation of high-resolution structural characterization. 18,19 Though many endowed properties have been brought from external structural motifs and sequences to ssRNA origami, the versatility and the function of the intrinsic RNA molecular signature of RNA structures have not been fully utilized. The integration of functional modules at the "molecular" level holds significant potential for further expanding and diversifying the applications of ssRNA origami nanotechnology.…”

mentioning

confidence: 99%

Single-Stranded RNA Origami-Based Epigenetic Immunomodulation

Dai

Chen

et al. 2023

Nano Lett.

View full text Add to dashboard Cite

The integration of functional modules at the molecular level into RNA nanostructures holds great potential for expanding their applications. However, the quantitative integration of nucleoside analogue molecules into RNA nanostructures and their impact on the structure and function of RNA nanostructures remain largely unexplored. Here, we report a transcription-based approach to controllably integrate multiple nucleoside analogues into a 2000 nucleotide (nt) single-stranded RNA (ssRNA) origami nanostructure. The resulting integrated ssRNA origami preserves the morphology and biostability of the original ssRNA origami. Moreover, the integration of nucleoside analogues introduced new biomedical functions to ssRNA origamis, including innate immune recognition and regulation after the precise integration of epigenetic nucleoside analogues and synergistic effects on tumor cell killing after integration of therapeutic nucleoside analogues. This study provides a promising approach for the quantitative integration of functional nucleoside analogues into RNA nanostructures at the molecular level, thereby offering valuable insights for the development of multifunctional ssRNA origamis.

show abstract

Structure, folding and flexibility of co-transcriptional RNA origami

Cited by 30 publications

References 88 publications

Assessment of three-dimensional RNA structure prediction in CASP15

Assessment of three-dimensional RNA structure prediction in CASP15

Co-transcriptional production of programmable RNA condensates and synthetic organelles

Single-Stranded RNA Origami-Based Epigenetic Immunomodulation

Contact Info

Product

Resources

About