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Can RNA form base pairs?

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

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Can RNA form base pairs?

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  1. 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

  2. DNA vs RNA helices B-DNA A-RNA

  3. Uracil is missing this!

  4. Double stranded viral genomes • Members of the Reoviridae (eg, Rotaviruses)

  5. 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)

  6. Cap-dependent Cap-independent Stewart & Semler (1997) Sem Virol 8;242

  7. Cap-dependent Cap-independent

  8. What about ribosomal and transfer RNA?

  9. tRNA (cont.) tRNA cloverleaf

  10. 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

  11. Ribozyme structure

  12. 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

  13. Mechanism of RNAi

  14. 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

  15. 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

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