Genome Editing I

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Questions and Answers

What does TALEN stand for?

TAL Effector Nuclease

Transcription Activator-Like Effector Nuclease (correct)

Transcription-Activated Locus Editing Nuclease

TAL-Associated Ligand Enzyme

TALENs have a high potential for off-target effects compared to other genome editing techniques.

True

What is the primary function of TALENs in genomic engineering?

To make targeted double-strand breaks in DNA.

The RVD code in TALENs determines the _____ of nucleotide binding to the DNA.

specificity Signup and view all the answers

Match the following terms related to TALEN and their descriptions:

RVD = Repeat Variable Dipeptide Nuclease = Enzyme that cuts DNA Precision = Accuracy of targeting Off-target effects = Unintended modifications at similar sequences Signup and view all the answers

What does TALEN stand for?

Transcription Activator-Like Effector Nucleases Signup and view all the answers

TALENs can cause off-target effects similar to other genome editing techniques.

True Signup and view all the answers

What is the primary function of a TALEN?

To precisely edit specific DNA sequences. Signup and view all the answers

The precision in genomic engineering can be affected by off-target _____ in TALENs.

effects Signup and view all the answers

Match the following structural components of TALENs with their functions:

RVD = Recognizes specific DNA bases Nuclease domain = Induces double-strand breaks DNA binding domain = Binds to target DNA sequence Linker = Connects the RVD to the nuclease domain Signup and view all the answers

Which of the following describes the RVD code in TALENs?

It consists of amino acids that determine sequence specificity. Signup and view all the answers

Double-strand breaks created by TALENs are always repaired by homologous recombination.

False Signup and view all the answers

What are off-target effects?

Unintended mutations at unintended sites in the genome. Signup and view all the answers

Which RVDs are specifically associated with the nucleotide bases G, A, C, and T?

NK, NI, HD, NG/HG Signup and view all the answers

Genome editing results are always reversible.

False Signup and view all the answers

What is the main purpose of TALEN?

To induce double-strand breaks (DSBs) in DNA. Signup and view all the answers

TALEN is created by adding FokI or part of its ______.

catalytic domain Signup and view all the answers

Match the following terms with their descriptions:

TALEN = A type of nuclease that induces double-strand breaks RVD = Repeat variable diresidue responsible for nucleotide binding Off-target effects = Unintended modifications at unintended sites Genome editing = Permanent alteration of an organism's genetic material Signup and view all the answers

What can facilitate binding and cutting during genomic engineering?

Optimal arm proximity near target sites Signup and view all the answers

Off-target effects can potentially lead to deleterious effects in genomic engineering.

True Signup and view all the answers

What is a critical factor when aiming for precise targeting of gene loci?

Efficiency of binding and cutting Signup and view all the answers

The process of ______ is used to permanently alter genetic material.

genome editing Signup and view all the answers

Which of the following statements is correct regarding TALEN structure?

TALENs can bind to a specific nucleotide through RVD. Signup and view all the answers

Study Notes

Genome Editing I

Key topics include DNA damage, ZFN, TALEN, and CRISPR/Cas9.
Cas9 protein binds to CRISPR RNA and a target viral DNA.
Learning objectives cover types of DNA damage, DNA repair mechanisms (NER, BER, HR, NHEJ), genome editing methods (TALEN, Zn finger nuclease), and advantages/disadvantages of each.

Types of DNA Damage

Transitions are changes of nucleotide within the same base type (pyrimidine or purine).
Transversions involve changes from pyrimidine to purine or vice versa.
Insertions or deletions of one or two base pairs alter the gene reading frame.
Simple changes can affect only one base or lead to deleterious changes to proteins.
UV light can damage thymine bases, leading to thymine dimers.
UV light can also damage cytosine bases, leading to cytosine hydrate formation.
DNA strand breaks include single-strand breaks (SSB) and double-strand breaks (DSB).

DNA Repair Mechanisms

Multiple DNA repair mechanisms occur, including:
- Thymine dimer cleavage
- Base excision repair (BER)
- Nucleotide excision repair (NER)
- Homologous recombination (HR)
- Non-homologous end joining (NHEJ)

Genome Editing Tools

Zinc-finger nucleases (ZFNs) facilitate the formation of a double-strand break (DSB) at a specific locus.
- ZFNs can be constituted of several zinc finger proteins (ZFPs).
- FokI is the non-specific restriction enzyme that induces the DSB.
TALENs are transcription activator-like effector nucleases.
- TALEs consist of DNA-binding repeats, nuclear localization sequence, and transcriptional activation domain.
- Two highly variable residues (RVDs) allow recognition of single base pairs.
CRISPR/Cas9 is a gene editing tool.
CRISPR/Cas9-based systems use gRNA to target specific DNA sequences.
Exogenous DNA addition is possible through homology-directed repair (HDR) using vector-borne DNA. Homology arms need to be engineered into replacement DNA.

Off-Target Activity

Precise targeting of gene loci is important.
Genomic engineering at unintended sites can have deleterious effects.
Off-target effects can result from insufficient specificity of DNA binding or ambiguity of interdomain linker.
Off-target effects can include insertions and deletions.

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Description

Explore the fundamental concepts of genome editing, focusing on various DNA damage types and repair mechanisms. This quiz covers key methods like ZFN, TALEN, and CRISPR/Cas9, along with their advantages and disadvantages. Understand the intricacies of DNA transitions, transversions, and the effects of UV light on DNA.

Genome Editing I

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Podcast

Questions and Answers

What does TALEN stand for?

TALENs have a high potential for off-target effects compared to other genome editing techniques.

What is the primary function of TALENs in genomic engineering?

The RVD code in TALENs determines the _____ of nucleotide binding to the DNA.

Match the following terms related to TALEN and their descriptions:

What does TALEN stand for?

TALENs can cause off-target effects similar to other genome editing techniques.

What is the primary function of a TALEN?

The precision in genomic engineering can be affected by off-target _____ in TALENs.

Match the following structural components of TALENs with their functions:

Which of the following describes the RVD code in TALENs?

Double-strand breaks created by TALENs are always repaired by homologous recombination.

What are off-target effects?

Which RVDs are specifically associated with the nucleotide bases G, A, C, and T?

Genome editing results are always reversible.

What is the main purpose of TALEN?

TALEN is created by adding FokI or part of its ______.

Match the following terms with their descriptions:

What can facilitate binding and cutting during genomic engineering?

Off-target effects can potentially lead to deleterious effects in genomic engineering.

What is a critical factor when aiming for precise targeting of gene loci?

The process of ______ is used to permanently alter genetic material.

Which of the following statements is correct regarding TALEN structure?

Study Notes

Genome Editing I

Types of DNA Damage

DNA Repair Mechanisms

Genome Editing Tools

Off-Target Activity

Studying That Suits You

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