Poster abstracts

Poster number 40 submitted by Sanjana Nallagatla

The use of RNA secondary and tertiary structure prediction software for remote undergraduate laboratory and research during pandemic distance learning

Sanjana Nallagatla (Adlai E. Stevenson High School), Joshua E. Sokoloski (Chemistry Department, Salisbury University)

Abstract:
The covid-19 pandemic has forced many undergraduate institutions to move their STEM instruction to online or remote modalities. Upper level, research based courses have a particular challenge to provide meaningful experiential learning opportunities for students. Here, we present a summary of free web-based RNA secondary and tertiary structure prediction software and how they can be used for both remote upper level courses and undergraduate/high school remote research. We evaluated several programs for their reliability and ease of use including Mfold 1, SPOT-RNA, RNAComposer, Vsfold5 4, and RNAfold 5. We also used these free web-based programs to analyze the structure of SARS-CoV-2 viral RNA as an example of upper level experiential learning during times of remote instruction. Using several structure prediction programs, we have found that a conserved coronavirus eight nucleotide sequence is involved in significant secondary and tertiary structure that differs from the structural context of the eight nucleotide sequence in other coronaviruses. In the MERS viral RNA, this octet is not significantly involved in secondary structures; however, when examining the secondary structure of SARS-CoV-2, this octet almost always forms a stem of 3 base pairs with a 5 nucleotide loop. In addition, the octet participates in a lot of hydrogen bonding when looking at the tertiary structure of SARS-CoV-2, but in MERS’s tertiary structure, the octet did not form any hydrogen bonds with the other nucleotides. These results show that the structural bioinformatics work of the past decade has allowed for meaningful research and teaching experiences to continue in a remote environment.

References:
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5.Vienna RNA webservices: rna.tbi.univie.ac.at/

Keywords: RNA Secondary Structure, SAR-CoV-2, RNA Folding