Structural RNA Nanotechnology

Author: codygeary

Created: 2022-09-25 08:02pm

Edited: 2022-09-25 09:29pm

Keywords: STREAM, lab exercises, simulation, small classroom teaching, exploration, folding, origami, RNA

Description:

Lecture is based on the theory of cognitive contructivism, the learners construct their own mental framework of energetic barriers in folding by physical interaction with paper folding in class. The module uses the STREAM approach to take advantage of blended learning with both out-of-class activities to complete before lecture and in-class activities designed to help learners achieve higher levels of Bloom's taxonomy. Students are expected to reflect on their experiences during the in-class and out-of-class exercises, and the format encourages independent learning to giver students a deeper conceptual starting point for the lectures. The module consists of two 2h lectures that each have their own preparation and follow-up assignments, followed by a journal-club/workshop day. The format of each lecture is 1h of lecture followed by a 1h guided exercise. Technology is used in the form of Youtube videos, homemade tutorial guides and videos, Brightspace discussion forums, and finally learners design their own biomolecules using our lab's homebuilt software. A goal of this module design is to bring more active, social, and experiential learning into the pedagogy framework.

Intended Learning Outcomes:

Define structural rearrangement
Examine the concept of folding domains by assembling paper models
Develop an intuitive understanding of structural bifurcation
Explore how energy barriers interplay with folding pathways
Explain structural compaction
Design and prototype a RNA origami nanostructure

Resources	Tasks		Supports
Day 1 Preparation
Review Paper: RNA Nanotechnology	Read paper, short answer questions ↓	←	Brightspace links to paper
YouTube	Watch introductory video on Origami Follow tutorial on Miura-Ori Fold Photograph origami and discuss two prompt questions. ↓	←	Brightspace Discussion Forum Brightspace embedding of videos A4 Sheet of Paper
The Miura-Orig origami has the special property that it is overconstrained and cannot misfold, in folding it students discover generalizable folding properties (modularity, rigidity, compaction, etc).
Day 1 Lecture on RNA Folding and Design
Bistable Folding Example	Follow origami folding instructions as they appear between lecture slides. These intermediate folds are used as physical examples of folded states in a folding pathway. ↓	←	Square origami paper (provided by teacher)
Resource	Introduction to RNA folding energy landscapes. We use the example of a creased paper to show how structure increases the strength of an object. Next we fold the bird base shape, it is bistable. Students 'pop' the structure back and forth and see that there is an energy barrier to go through the unfolded state. By the end of the lecture instructions to finally fold the origami into a fully-flattened shape illustrate the concept of structural compaction. ↓	←	Lecture Slides
Physics-based simulation of paper origami compaction. The website has interactive controls and allows users to explore many different origami shapes and folds.	Visit the website and play with the paper crane folding model. Observe how compacting all folds simultaneously is different from following a step-wise folding pathway. ↓	←	Website: origamisimulator.org
A handout exercise that encodes the first four letters of their name into an RNA fold.	They follow the exercise and then each student will develop a complex strand path based on their personal encoding. After, if time permits, students can compare/contrast designs. The encoding step helps ensure everyone has a unique structure to share. Students count up the number of topological barriers in the structure based on a technique shown in lecture. Finally, they are asked to propose a 'best' design based on the discussion. ↓	←	Folding Exercise Handout (provided) Colored Crayons (provided)

Day 2 Preparation
RNA origami design tutorial	Visit the website and read through the tutorials that explain the ROAD design software and interface. Install and required software to do the exercise. ↓	←	Brightspace links Video tutorial
Paper on ROAD Design Software	Read the Nature Chemistry paper on RNA design in preparation to make your own related design. ↓	←	Brightspace link to paper
RNA design project	Read through the RNA design project and start to plan the project. ↓	←	Brightspace link

Day 2 Lecture: RNA nanotechnolgy applications
PPT slides also posted on Brightspace	RNA nanotechnology and applications. The lecture is designed to help students with their design projects by introducing a variety of techniques and modular RNA components that can be used to build a design. ↓	←	Lecture, 1h
Design workshop	Students have 1h in-class to continue work on their design projects. Teacher and teacher assistant are both available to offer technical support for design software and input preparation. ↓	←	Support, 1h

Day 3: RNA Design Workshop and Journal Club
Discussion and Summary	Students discuss the assigned paper on RNA design. ↓	←	Journal Club
Design workshop	Discussion on prototyping and ideation. Additional time for RNA design project is provided, and TA support is available for technical help.	←	Support