Towards SINEUP-based therapeutics: Design of an in vitro synthesized SINEUP RNA

Valentini, Paola; Pierattini, Bianca; Zacco, Elsa; Mangoni, Damiano; Espinoza, Stefano; Webster, Natalie A.; Andrews, Byron; Carninci, Piero; Tartaglia, Gian Gaetano; Pandolfini, Luca; Gustincich, Stefano

doi:10.1016/j.omtn.2022.01.021

Cited by 5 publications

(4 citation statements)

References 81 publications

(145 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Modified nucleotides (2′O methyl-ATP, N6 methyl-ATP, and pseudo-UTP) are introduced to increase the activity and stability of therapeutic SINEUPs. Structural studies using circular dichroism spectroscopy identified common core structures that govern the activity of miniSINEUPs with different modifications in solution that could further simplify their design and manufacturing (Valentini et al, 2022).…”

Section: Sineupsmentioning

confidence: 99%

Natural antisense transcripts as drug targets

Khorkova

Stahl

Joji

et al. 2022

Front. Mol. Biosci.

View full text Add to dashboard Cite

The recent discovery of vast non-coding RNA-based regulatory networks that can be easily modulated by nucleic acid-based drugs has opened numerous new therapeutic possibilities. Long non-coding RNA, and natural antisense transcripts (NATs) in particular, play a significant role in networks that involve a wide variety of disease-relevant biological mechanisms such as transcription, splicing, translation, mRNA degradation and others. Currently, significant efforts are dedicated to harnessing these newly emerging NAT-mediated biological mechanisms for therapeutic purposes. This review will highlight the recent clinical and pre-clinical developments in this field and survey the advances in nucleic acid-based drug technologies that make these developments possible.

show abstract

Section: Sineupsmentioning

confidence: 99%

Natural antisense transcripts as drug targets

Khorkova

Stahl

Joji

et al. 2022

Front. Mol. Biosci.

View full text Add to dashboard Cite

show abstract

“…Detection speed with real-time IVT monitoring using light-up aptamer and fluorescent dye pair is at least 100 times faster than conventional polyacrylamide gel electrophoresis (PAGE) method ( Valentini et al, 2022 ), whereas PAGE method shows RNA bands that can provide purity information of RNA transcripts. Although the light-up aptamer-based method cannot provide quality information of IVT, eventually the purity of RNA products can be checked during compulsory HPLC purification process ( Karikó et al, 2011 ) and/or by other endpoint analytical methods for applications in cells and in vivo .…”

Section: Introductionmentioning

confidence: 99%

“…If transcribed RNAs will not be used for further applications after real-time IVT monitoring using light-up aptamer and dye pair, in other words, if IVT is only monitored to check transcription activity itself for IVT optimization, introduction of ribozyme domain would be unnecessary ( Valentini et al, 2022 ). For example, effects of IVT components have been investigated using Broccoli aptamer-based ( Kartje et al, 2021 ) or iSpinach aptamer ( Autour et al, 2016 )-based monitoring of transcription activity in a real-time (STAR) system ( Valentini et al, 2022 ). An approach based on contact quenching of fluorophores linked to quenchers such as dinitroaniline and fluorophore-binding aptamer has also been used for real-time IVT monitoring ( Sunbul and Jäschke, 2013 ).…”

Section: Introductionmentioning

confidence: 99%

“…For examples, raman spectroscopy is likely to be applied for RNA manufacturing also by measuring NTP consumption ( Matuszczyk et al, 2023 ). Circular dichroism (CD) that sensitively probes the chirality of nucleic acids would be useful to analyze nucleotide modifications and functional structure of RNA ( Valentini et al, 2022 ) during IVT and the database is currently available as a public repository ( Zhang et al, 2023 ). Time-resolved infrared spectroscopy would also be an option to analyze RNA folding that affects the function of RNA such as aptamer ( Brauns and Dyer, 2005 ).…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Real-time monitoring strategies for optimization of in vitro transcription and quality control of RNA

Lee,

Song,

Kim

et al. 2023

Front. Mol. Biosci.

View full text Add to dashboard Cite

RNA-based therapeutics and vaccines are opening up new avenues for modern medicine. To produce these useful RNA-based reagents, in vitro transcription (IVT) is an important reaction that primarily determines the yield and quality of the product. Therefore, IVT condition should be well optimized to achieve high yield and purity of transcribed RNAs. To this end, real-time monitoring of RNA production during IVT, which allows for fine tuning of the condition, would be required. Currently, light-up RNA aptamer and fluorescent dye pairs are considered as useful strategies to monitor IVT in real time. Fluorophore-labeled antisense probe-based methods can also be used for real-time IVT monitoring. In addition, a high-performance liquid chromatography (HPLC)-based method that can monitor IVT reagent consumption has been developed as a powerful tool to monitor IVT reaction in near real-time. This mini-review briefly introduces some strategies and examples for real-time IVT monitoring and discusses pros and cons of IVT monitoring methods.

show abstract