Antioligonucleotides Flashcards
Base mod what are they and what do they do to increase affinity
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
Backbone mod what are they
1st gen phosphorothioate
PNA peotide nucleic acid
Phosphorothioate what do they do to increase affinity and cause nuclease resisitance
Removes Dnas -ve charge so that it can enter dna much more easily
PNA what do they do to increase affinity and cause nuclease resisitance
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)
Suger mod what are they
2nd gen 2’-methoxy
LNA
2’-methoxy what do they do to increase affinity and cause nuclease resisitance
Forced into N type
Increase duplex
LNA what do they do to increase affinity and cause nuclease resisitance
Locked in N tyoe because of cross linking
What is a gapmer and what does it help with
Gapmer is a unmoded gap between the suger and backbone mods which allows suceptibility for the RNase H digestion
But keeps resistance and affinity
What are the small molecules that are attached that can increase the affinity and soecificity
Minor groove binders Netropsin
Intercalators pyrene
Edge binders spermine
Small molecules
What happens when you attach non nucleic acid groups
Increase stability of helix
Intercalators what are they and what do they do
Flat aromatic molecules
Uses base stacking
Slightly unwinds helix - increasing size of helix by 1 bp
Edge binders what do they do to increase affinity
Charged molecules which bid to -ve backbone
Neutralising the overal charge
Cross linking agents what do they do to increase affinity
Psoralen
Intercalates back onto DNA and under uv light crosslinks 2 Ts
TpA step
Cleavage agents what do they do to increase affinity
Edta : fe
Nicks backbone, chelates
Fe3+ reacts with the backbone and breaks it
Delivery methods
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
Drugs used
Vitravene 1st gen
Alicaforsen 1st gen
Mipomersen 2nd gen
Clusterin 2nd gen
Vitravene what is it
What does it target
Admin
21-mer phosphorothioate oligo Targets CMV mRNA encoding CMV polymeristation Inflammation of eyes CMV causes retinitis in aids patients Iv adminin eyes discontinued
Alicaforsen what is it
What does it target
Admin
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
Mipomersen what is it
What does it contain
What does it target
Admin
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
Clusterin what is it
What does it contain
What does it inhibit
What canit be used for
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
What are the ways to increase affinity
Specificity
Resisitance in these ON
Base mod Backbone mod Configuration Sugar mod 3' mod
