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1. RNA as a Major-Groove Ligand: RNA–RNA and RNA–DNA Triplexes Formed by GAA and UUC or TTC Sequences

   https://doi.org/10.1021/acsomega.2c04358  

   Zhang, Jiahui ; Fakharzadeh, Ashkan ; Roland, Christopher ; Sagui, Celeste ( October 2022 , ACS Omega)
2. Efficient inhibition of RNA self-primed extension by addition of competing 3′-capture DNA-improved RNA synthesis by T7 RNA polymerase

   https://doi.org/10.1093/nar/gkz700  

   Gholamalipour, Yasaman ; Johnson, William C ; Martin, Craig T ( August 2019 , Nucleic Acids Research)

   Abstract In vitro synthesized RNA is used widely in studies of RNA biology, biotechnology and RNA therapeutics. However, in vitro synthesized RNA often contains impurities, such as RNAs with lengths shorter and longer than the expected runoff RNA. We have recently confirmed that longer RNA products are formed predominantly via cis self-primed extension, in which released runoff RNA folds back on itself to prime its own RNA-templated extension. In the current work, we demonstrate that addition of a DNA oligonucleotide (capture DNA) that is complementary to the 3′ end of the expected runoff RNA effectively prevents self-primed extension, even under conditions commonly used for high RNA yields. Moreover, the presence of this competing capture DNA during ‘high yield’ transcription, leads to an increase in the yield of expected runoff RNA by suppressing the formation of undesired longer RNA byproducts. 

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3. 3′ end additions by T7 RNA polymerase are RNA self-templated, distributive and diverse in character—RNA-Seq analyses

   https://doi.org/10.1093/nar/gky796  

   Gholamalipour, Yasaman ; Karunanayake Mudiyanselage, Aruni ; Martin, Craig T ( September 2018 , Nucleic Acids Research)
4. Comparison of RNA isolation methods on RNA-Seq: implications for differential expression and meta-analyses

   https://doi.org/10.1186/s12864-020-6673-2  

   Scholes, Amanda N. ; Lewis, Jeffrey A. ( December 2020 , BMC Genomics)
5. DEAH-RHA helicase•Znf cofactor systems in kinetoplastid RNA editing and evolutionarily distant RNA processes

   https://doi.org/10.14800/rd.1336  

   Cruz-Reyes, Jorge ; Mooers, Blaine HM ; Abu-Adas, Zakaria ; Kumar, Vikas ; Gulati, Shelly ( June 2016 , RNA & DISEASE)

   Multi-zinc finger proteins are an emerging class of cofactors in DEAH-RHA RNA helicases across highly divergent eukaryotic lineages. DEAH-RHA helicase•zinc finger cofactor partnerships predate the split of kinetoplastid protozoa, which include several human pathogens, from other eukaryotic lineages 100-400 Ma. Despite a long evolutionary history, the prototypical DEAH-RHA domains remain highly conserved. This short review focuses on a recently identified DEAH-RHA helicase•zinc finger cofactor system in kinetoplastid RNA editing, and its potential functional parallels with analogous systems in embryogenesis control in nematodes and antivirus protection in humans. 

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