Can RNA form base pairs?

• Yes, in many circumstances

• Some are strictly dsRNA molecules, others are folded back pieces of ssRNA with interactions between antiparallel and complementary residues

• Linked to the origin of life - folded RNA molecules can have enzymic function

• The issue is particularly relevant to new and exciting areas of biology

DNA vs RNA helices

B-DNA A-RNA

Uracil is missing this!

Double stranded viral genomes

• Members of the Reoviridae (eg, Rotaviruses)

Single stranded RNA viral genomes

• Generally have a double stranded (ie, fully base paired) intermediate (for example the Picornaviridae - eg, poliovirus, rhinovirus)

• When in single stranded form there is extensive internal base pairing to generate complex 3D structures that have certain functions (eg, Internal ribosomal entry in picornaviruses)

Cap-dependent

Cap-independent

Stewart & Semler (1997) Sem Virol 8;242

Cap-dependent

Cap-independent

What about ribosomal and transfer RNA?

tRNA (cont.)

tRNA cloverleaf

Ribozymes

• “Hammerhead” RNA structures that catalyse RNA and DNA degradation

• Tom Cech - Nobel prize for his discovery

• Wayne Gerlach et al (CSIRO) - “gene shears” or targeted ribozymes

• RNA base pairing is central to their formation and functioning

Ribozyme structure

RNA interference (RNAi)

• Very hot topic in molecular biology

• Also known as “post-transcriptional gene silencing”

• Discovered in plants, known to also operate in fungi, worms, insects and even mammalian cells (in a modified form - see later)

• Ancient origin - probably confers resistance to some viruses, may also have a role in development

Mechanism of RNAi

RNAi as a research tool

• Rapid generation of “loss-of-function” mutants

• Cannot introduce long dsRNA into mammalian cells as this induces antiviral response

• Short interfering RNA (siRNA) is very effective

• Can be added exogenously or synthesised endogenously

Web sites of interest/acknowledgments

• http://www.tulane.edu/~biochem/nolan/lectures/rna/frames/hambtx.htm and

http://www.tulane.edu/~biochem/nolan/lectures/rna/intro.htm

• http://www.ambion.com/techlib/append/RNAi_mechanism.html

• http://ntri.tamuk.edu/cell/ribosomes.html

• http://stat.tamu.edu/~dnguyen/SUP_review/TutorialFigures.pdf