Lecture 1
Introduction to RNA structure	
	Primary structure
		definition
		bases & ribose-phosphate backbone
		modified nucleosides
		5' and 3' ends
		comparison with protein primary structure
			only 4 basic possibilities rather than 20
			much less chemical diversity even among these 4 choices
	Secondary structure
		definition
		grey areas
			pseudoknot helices
			lone bps
			non-canonical bps regions
			loop bps (e.g. GnrA)
		representations
			traditional train-tracks
			mountains
			circle & arcs
			lists (bp & helix)
			in alignments
		parts of a secondary structure
			nomenclature - Pn, Jn, Ln
			hairpin, aka stem-loop
			long-range helix
			irregularities
				bulges
				mispairs
			loops
				terminal loops
					tetraloop
					triloops
					others
				internal loops
					symmetric loops
					asymmetric loops
			junctions
				w/ or w/o loops
				tri-junctions
				cruciforms
			pseudoknots
				simple
				complex
			terminal helix
			5' or 3' tails
		features of compared secondary structures
			conserved sequences (usually in joining regions or functional helices)
				show P w/ CRI-V, and logo
			conserved sequence length
			helices with variable length
			connections with variable length
			additional helical elements
			additional 5' or 3' length
			core structure/sequence
		comparison with protein secondary structure
			largely sequence independent
			defined by sidechain interactions, not backbone structure
		3D info in secondary structures
			helices
			motifs of known structure
		Usefulness of a secondary structure
	Tertiary & quarterary structure (BRIEF - subject of later talks)
		definition
		tertiary interactions
			GNRA/minor groove interaction
			GAAA/receptor interaction
			helical stacks
			3-way junction
			cruciform
			simple pseudoknot
		local 3D structure
		global structure
			hierarchical structure
			analogous replacements
		comparison with protein tertiary structure
			helical stacks ~ protein domains