New functionality of RNAComposer: application to shape the axis of miR160 precursor structure

Antczak, Maciej; Popenda, Mariusz; Żok, Tomasz; Sarzyñska, Joanna; Ratajczak, Tomasz; Tomczyk, Katarzyna; Adamiak, Ryszard W.; Szachniuk, Marta

doi:10.18388/abp.2016_1329

Cited by 149 publications

(149 citation statements)

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“…In some cases, the generated 3D structures did not correlate with long-distance interactions or relative positioning of the helixes deduced from the provided experimental data (i.e., Puzzle 8). This prompted us to develop new functionality of the RNAComposer system (Antczak et al 2016) that allows the user to introduce a particular, user-defined 3D element for the structure assembly. This functionality was subsequently utilized in solving Puzzles 13 and 14.…”

Section: Adamiak Groupmentioning

confidence: 99%

“…New functionality of RNAComposer was implemented (Antczak et al 2016), and user-defined 3D structure elements for the internal loop (7-UGACUGGCGAACAG-20; 33-CGGGGAG-39 and the single strand: 7-UGACUGGCGAACAG-20) were introduced. Those structural elements were identified in RNA FRABASE (Popenda et al 2008(Popenda et al , 2010) using our own scripts.…”

Section: Puzzle 13mentioning

confidence: 99%

“…In order to force preservation of those contacts in the resultant 3D model with the lowest radius of gyration, the three-way junction 4-UGAC-7; 20-GCGG-23; 55-CA-56 was manually adjusted in PyMol. This 3D motif was used as a user-defined element during 3D model assembly (Antczak et al 2016). 3D models predicted by RNAComposer are characterized by very good local agreement with the reference structure in regard to the E-loop motif and 10 nt apical loop, and are therefore ranked within the top five 3D models within the MCQ category ) and all INF-based categories (Supplemental Fig.…”

Section: Puzzle 14mentioning

confidence: 99%

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RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme

Miao

Adamiak

Antczak

et al. 2017

RNA

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185

209

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RNA-Puzzles is a collective experiment in blind 3D RNA structure prediction. We report here a third round of RNA-Puzzles. Five puzzles, 4, 8, 12, 13, 14, all structures of riboswitch aptamers and puzzle 7, a ribozyme structure, are included in this round of the experiment. The riboswitch structures include biological binding sites for small molecules (S-adenosyl methionine, cyclic diadenosine monophosphate, 5-amino 4-imidazole carboxamide riboside 5 ′ -triphosphate, glutamine) and proteins (YbxF), and one set describes large conformational changes between ligand-free and ligand-bound states. The Varkud satellite ribozyme is the most recently solved structure of a known large ribozyme. All puzzles have established biological functions and require structural understanding to appreciate their molecular mechanisms. Through the use of fast-track experimental data, including multidimensional chemical mapping, and accurate prediction of RNA secondary structure, a large portion of the contacts in 3D have been predicted correctly leading to similar topologies for the top ranking predictions. Template-based and homologyderived predictions could predict structures to particularly high accuracies. However, achieving biological insights from de novo prediction of RNA 3D structures still depends on the size and complexity of the RNA. Blind computational predictions of RNA structures already appear to provide useful structural information in many cases. Similar to the previous RNA-Puzzles Round II experiment, the prediction of non-Watson-Crick interactions and the observed high atomic clash scores reveal a notable need for an algorithm of improvement. All prediction models and assessment results are available at http://ahsoka.ustrasbg.fr/rnapuzzles/.

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Section: Adamiak Groupmentioning

confidence: 99%

Section: Puzzle 13mentioning

confidence: 99%

Section: Puzzle 14mentioning

confidence: 99%

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RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme

Miao

Adamiak

Antczak

et al. 2017

RNA

Self Cite

185

209

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“…RNAComposer was used for prediction of RNA 3D structural models (http://rnacompo ser.cs.put.poznan.pl/). This is a fully automated RNA structure modeling server that predicts RNA 3D structures based on sequence and secondary structure [61][62][63].…”

Section: Rna Structure Predictionmentioning

confidence: 99%

“…5). Models were generated using RNAComposer, which is an advanced tool for modeling atomic-resolution 3D models of RNAs based on their sequence and secondary structures [61,62]. Predicted structural models correspond well with the NMIA reactivity changes observed in the linking sequence.…”

Section: Models Of Pal1-pal2 Interactions In Monomer and Dimermentioning

confidence: 99%

Retroviral-like determinants and functions required for dimerization of Ty1 retrotransposon RNA

et al. 2019

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During replication of long terminal repeat (LTR)-retrotransposons, their proteins and genome (g) RNA assemble into virus-like particles (VLPs) that are not infectious but functionally related to retroviral virions. Both virions and VLPs contain gRNA in a dimeric form, but contrary to retroviruses, little is known about how gRNA dimerization and packaging occurs in LTR-retrotransposons. The LTR-retrotransposon Ty1 from Saccharomyces cerevisiae is an informative model for studying LTR-retrotransposon and retrovirus replication. Using structural, mutational and functional analyses, we explored dimerization of Ty1 genomic RNA. We provide direct evidence that interactions of self-complementary PAL1 and PAL2 palindromic sequences localized within the 5′UTR are essential for Ty1 gRNA dimer formation. Mutations disrupting PAL1-PAL2 complementarity restricted RNA dimerization in vitro and Ty1 mobility in vivo. Although dimer formation and mobility of these mutants was inhibited, our work suggests that Ty1 RNA can dimerize via alternative contact points. In contrast to previous studies, we cannot confirm a role for PAL3, tRNAiMet as well as recently proposed initial kissing-loop interactions in dimer formation. Our data also supports the critical role of Ty1 Gag in RNA dimerization. Mature Ty1 Gag binds in the proximity of sequences involved in RNA dimerization and tRNAiMet annealing, but the 5′ pseudoknot in Ty1 RNA may constitute a preferred Gag-binding site. Taken together, these results expand our understanding of genome dimerization and packaging strategies utilized by LTR-retroelements.

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A Non‐G‐Quadruplex DNA Aptamer Targeting NCL for Diagnosis and Therapy in Bladder Cancer

Liu

Pei

et al. 2023

Adv Healthcare Materials

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Bladder cancer (BC) is a highly aggressive malignant tumor affecting the urinary system, characterized by metastasis and a poor prognosis that often leads to limited therapeutic success. This study aims to develop a novel DNA aptamer for the diagnosis and treatment of BC using a tissue‐based systematic evolution of ligands by an exponential enrichment (SELEX) process. By using SELEX, this work successfully generates a new aptamer named TB‐5, which demonstrates a remarkable and specific affinity for nucleolin (NCL) in BC tissues and displays marked biocompatibility both in vitro and in vivo. Additionally, this work shows that NCL is a reliable tissue‐specific biomarker in BC. Moreover, according to circular dichroism spectroscopy, TB‐5 forms a non‐G‐quadruplex structure, distinguishing it from the current NCL–targeting aptamer AS1411, and exhibits a distinct binding region on NCL compared to AS1411. Notably, this study further reveals that TB‐5 activates NCL function by promoting autophagy and suppressing the migration and invasion of BC cells, which occurs by disrupting mRNA transcription processes. These findings highlight the critical role of NCL in the pathological examination of BC and warrant more comprehensive investigations on anti‐NCL aptamers in BC imaging and treatment.

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New functionality of RNAComposer: application to shape the axis of miR160 precursor structure

Cited by 149 publications

References 74 publications

RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme

RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme

Retroviral-like determinants and functions required for dimerization of Ty1 retrotransposon RNA

A Non‐G‐Quadruplex DNA Aptamer Targeting NCL for Diagnosis and Therapy in Bladder Cancer

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