8 - RNA-based Therapeutics

Question 1

RNA adaptations

Answer 1

RNA can adapt well-defined secondary and tertiary structures which are easily predictable

Question 2

hairpin vs stem-loop

Answer 2

hairpin has less base pairs unpaired

Question 3

mFold

Answer 3

predicts the secondary structure of RNA structures

Question 4

catalytic properties

Answer 4

folded RNA can have catalytic properties because tertiary structure can provide binding sites

Question 5

ribozyme structure

Answer 5

ribozymes fold so that the metal ion is close to 2’OH, therefore stabilizing the molecule

Question 6

antisense based therapy

Answer 6

• formiversen
• mipomersen
• eteplirsen

Question 7

formiversen

Answer 7

• antisense DNA that makes DNA-RNA complex
• ribonuclease H will then destroy RNA part
• treatment for AIDS

Question 8

mipomersen

Answer 8

• antisense DNA that makes DNA-RNA complex
• ribonuclease H will destroy RNA part
• treatment for bad cholesterol production

Question 9

eteplirsen

Answer 9

• recognizes exon 51 and skips it in the production mRNA
• frameshift introduces a stop codon
• treats mutation in dystrophan (Duchenne muscular dystrophy)

Question 10

RNA interference based therapy

Answer 10

• an easier way to destroy RNA, therefore it’s a more popular method than antisense based therapy
• only works on dsRNA

Question 11

RNA-induced silencing complex (RISC)

Answer 11

loads one strand inside and links the other through base pairing

Question 12

argonaute

Answer 12

protein with 4 domains that is the central component of RISC

Question 13

PAZ

Answer 13

AGO domain that recognizes the 3’ end

Question 14

PIWI

Answer 14

• AGO domain that is responsible for target cleavage

- structurally similar to RNase H

Question 15

RNA interference with RISC

Answer 15

• a virus injecting its genome of dsRNA will be destroyed by RISC
• production of dsRNA from microRNA will be destroyed by RISC
• dsRNA molecule made in lab will activate RISC to degrade specific RNA

Question 16

DICER

Answer 16

cuts up dsRNA into fragments

Question 17

examples of RNAi

Answer 17

• targeting vimentin gene
• Flavr Savr tomato
• patisiran

Question 18

vimentin gene

Answer 18

• vimentin inserted into a plasmid which is transcribed and hairpin is cut DICER
• strand pairs with vimentin
• one strand is recognized by RISC

Question 19

Flavr Savr tomato

Answer 19

• introduced mRNA gene that targeted polygalacturonase

- DICER cuts up introduced mRNA gene and RISC will degrade polygalacturonase

Question 20

polygalacturonase

Answer 20

breaks down oligosaccharides, resulting in softer fruit

Question 21

patisiran

Answer 21

• dsRNA is inserted with a lipid molecule that targets mutations of transthyretin (TTR) gene
• DICER cuts up RNA and RISC will degrade mutations of TTR gene
• first RNAi therapy
• treats hereditary transthyretin-mediated (hATTR) amyloidosis