Antioligonucleotides

Question 1

Base mod what are they and what do they do to increase affinity

Answer 1

2-amino-A-U
Add an amino group to A increases stability by 2-3degrees
G-AP (g-clamp)
Add 4 hydrogen bonds 
15degrees for 1 mod

Question 2

Backbone mod what are they

Answer 2

1st gen phosphorothioate

PNA peotide nucleic acid

Question 3

Phosphorothioate what do they do to increase affinity and cause nuclease resisitance

Answer 3

Removes Dnas -ve charge so that it can enter dna much more easily

Question 4

PNA what do they do to increase affinity and cause nuclease resisitance

Answer 4

Lack of charge - good for getting inti cells more easily
Can attach Arg (charge) to help it dissolve
11 bonds between bases (same distance as nirmal base pairing)

Question 5

Suger mod what are they

Answer 5

2nd gen 2’-methoxy

LNA

Question 6

2’-methoxy what do they do to increase affinity and cause nuclease resisitance

Answer 6

Forced into N type

Increase duplex

Question 7

LNA what do they do to increase affinity and cause nuclease resisitance

Answer 7

Locked in N tyoe because of cross linking

Question 8

What is a gapmer and what does it help with

Answer 8

Gapmer is a unmoded gap between the suger and backbone mods which allows suceptibility for the RNase H digestion
But keeps resistance and affinity

Question 9

What are the small molecules that are attached that can increase the affinity and soecificity

Answer 9

Minor groove binders Netropsin
Intercalators pyrene
Edge binders spermine

Question 10

Small molecules

What happens when you attach non nucleic acid groups

Answer 10

Increase stability of helix

Question 11

Intercalators what are they and what do they do

Answer 11

Flat aromatic molecules
Uses base stacking
Slightly unwinds helix - increasing size of helix by 1 bp

Question 12

Edge binders what do they do to increase affinity

Answer 12

Charged molecules which bid to -ve backbone

Neutralising the overal charge

Question 13

Cross linking agents what do they do to increase affinity

Answer 13

Psoralen
Intercalates back onto DNA and under uv light crosslinks 2 Ts
TpA step

Question 14

Cleavage agents what do they do to increase affinity

Answer 14

Edta : fe
Nicks backbone, chelates
Fe3+ reacts with the backbone and breaks it

Question 15

Delivery methods

Answer 15

Peptide / cholesterol (covalent)
- attach something hydrophobic Arg Lys
Peptides non covalent
Peptide lipid conjugates
Cationic polymers
Lyposomes in the presence of dna
Lyposomes for cell specific delivery

Question 16

Drugs used

Answer 16

Vitravene 1st gen
Alicaforsen 1st gen
Mipomersen 2nd gen
Clusterin 2nd gen

Question 17

Vitravene what is it
What does it target
Admin

Answer 17

21-mer phosphorothioate oligo
Targets CMV mRNA encoding CMV polymeristation 
Inflammation of eyes
CMV causes retinitis in aids patients 
Iv adminin eyes discontinued

Question 18

Alicaforsen what is it
What does it target
Admin

Answer 18

20- mer phosphorothioate oligo
Targets 3’ untranslated regions of 1CAM-1 mRNA
1CAM-1 is a glycoprotein involved in cell trafficing in irritable bowl pathophysiology
Ulcerative colitis (passed phase 3 )
Admin iv

Question 19

Mipomersen what is it
What does it contain
What does it target
Admin

Answer 19

20- mer phosophorothioate
Gapmer containing 2’- ome (N - type sugar pucker, decreasing degradation) mod and methyl-c (decreasing inflammation)
Targets coding region of apolipoprotein B mRNA (increasing in choleasterol)
Mutations on apolipoprotein B causes hypercholesterolemia
Iv

Question 20

Clusterin what is it
What does it contain
What does it inhibit
What canit be used for

Answer 20

21- mer phosphorothioate containing 2’-OMe mod gapmer
CAGCA—–TCAT can be cut by RNase H
Inhibits production of clusterin
- which acts as cell survival protein and is over expressed in response to cancer treatment
In combo with anticancer by increasung apoptosis
Binds to inital site in exon 2 if human CLU
Still at phase 2

Question 21

What are the ways to increase affinity
Specificity
Resisitance in these ON

Answer 21

Base mod
Backbone mod
Configuration
Sugar mod
3' mod