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Selfstudy assignment answers lecture 8-9
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1. Genetic therapies can be developed thanks to thepossibilities offered by biotechnology. Use information from
the lectures, the paper by Lee et al (World J. Gastroenterol.
(2013) 19:8949-8962) and information on the web to answer
the following question. Genetic therapies are based on a
wide range of very diverse biotechnological molecules,
materials, methods and techniques. Describe for each of the
'tools' a-k below (on the next page).
1.1. the nature of the molecule (What type of molecule is it?
What is it made of?)
1.2. its intrinsic activity (What does it do?)
1.3. for what purpose it can be used in a therapeutic setting?
a. Ribozyme
1. TAre RNA molecules
2. They act as enzymes that can catalyze specific biochemical
reactions, such as the cleavage of RNA molecules
endonuclease
3. It can be used to target and degrade RNA for viral infections or
genetic diseases by preventing the translation of pathogenic
proteins. Degrade RNA
b. Aptamer
1. Short single-stranded DNA or RNA molecules
2. They bind to target molecules, such as proteins, small
molecules or cells high affinity binding to a target molecule
(does not bind hybridization)
3. They are used for targeted drug derlivery or as therapeutic
agents to block harmful protein interactions inhibit or activate
target, or block binding to another factor
c. Zinc Finger Nuclease (ZFN)
1. Proteins consisting of DNA binding zinc finger domain and a DNA-
cleaving nuclease domain
2. They create specific ds breaks in DNA, which after repair can lead
to gene disruption or correction endonuclease (DNA, ds break)
3. They are used for gene editing to correct genetic mutations
d. (ant)agonist
1. They are small molecules/ small compounds
2. Agonists activate receptors to produce a biological response,
while antagonists block receptors and prevent the response. High
affinity binding to target
3. Agonists and antagonists are widely used in treatments for
diseases such as hypertension (using beta-blockers), cancer
(using receptor-targeting antibodies), and various metabolic or
neurological disorders. Inhibit or activate or change conformation
of target
e. antisense oligonucleotide
, 1. short, synthetic strands of DNA or RNA that are complementary to
specific mRNA sequences.
2. antisense oligonucleotides bind to their target mRNA, blocking its
translation into protein or inducing its degradation. Binds to RNA
or DNA
3. Used to silence genes, RNA Degradation, splicing modulation,
translation inhibition
f. sense oligonucleotide
1. It binds to the template strand of DNA
2. It can block transcription
3. sense oligonucleotides can be employed in therapies designed to
enhance or restore gene expression
Antisense oligonucleotides do not block transcription but sense
oligonucleotides to block transcription.
The coding strand is from 5’-3’ and a template strand is from 3’-5’.
The antisense oligonucleotide binds to the coding strand (antisense)
and the sense oligonucleotide binds to the template strand (sense).
The splice modulators can bind to RNA but not to DNA since they are
not super strong binders. The antisense or sense oligonucleotides
are very strong binders and they invade the DNA double helix by
breaking it apart and then they bind to the coding or template
strand.
Why can the sense oligo only inhibit transcription at a high binding
strength?
- The binding needs to be so strong that RNA polymerase cannot
displace it. When the binding strength is low then the RNA
polymerase can remove the sense oligo and transcription wont be
inhibited anymore.
The antisense oligo is on the coding strand so the RNA polymerase
wont even be in contact with it and that’s why the binding strength
has to be so high in sense oligos but not in antisense oligos
g. TALEN (Transcription Activator-like Effector Nuclease)
1. engineered proteins made of DNA-binding domains (TALEs) fused
to a nuclease, similar to ZFNs.
2. They bind to specific DNA sequences and induce double-stranded
breaks, enabling targeted genome editing.
3. TALENs are used in gene editing applications for correcting
genetic mutations in inherited diseases
h. siRNA
1. siRNAs are short, double-stranded RNA molecules
2. They induce RNA interference (RNAi), a process that leads to the
degradation of specific mRNA molecules, preventing translation.
Binds RNA
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