DNA-Binding Motifs and Engineered Nucleases Quiz

DNA-Binding Motifs and Engineered Nucleases

• TF binding sites often contain inverted repeats, consisting of a nucleotide sequence and its reverse complement.
• Transcription Factors (TFs) are classified based on the presence of specific conserved motifs, including the helix-turn-helix, homeodomain, leucine zipper, basic helix-loop-helix, and zinc finger motifs.
• The helix-turn-helix (h-t-h) motif, consisting of about 20 amino acids, is used by many bacterial and eukaryotic regulatory proteins for DNA binding.
• The homeodomain motif, identified in fruit flies and made up of 60 amino acids, is found in TFs regulating body pattern development in various organisms, including humans.
• The basic leucine zipper motif, composed of 60-80 amino acids, features a hydrophobic surface, basic residues in the DNA-binding region, and is primarily used for dimerization.
• The basic helix-loop-helix (b-hlh) motif, containing ~50 amino acids, plays a role in DNA binding, dimer formation, and is often associated with development or cell cycle activity.
• TFs with b-hlh motifs, such as c-Myc and HIF-1, have been linked to cancer.
• Proteins with zinc finger motifs have diverse functions, including roles in DNA recognition, RNA packaging, and transcriptional activation.
• The zinc finger motif, consisting of ~30 amino acids, forms an elongated loop stabilized by Zn2+ ions and is found in eukaryotic and bacterial proteins.
• Single Zinc finger interactions are weak, and proteins with multiple zinc fingers have been designed for gene editing.
• Type I and II zinc finger motifs function differently, with Type II combining the Zn2+-binding motif with the helix-turn-helix motif.
• Engineered nucleases, such as zinc-finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs), are designed using zinc fingers joined to a FokI-derived DNA cleavage domain, and TALEs fused to FokI nucleases, respectively, for gene editing purposes.

DNA-Binding Motifs and Engineered Nucleases

• TF binding sites often contain inverted repeats, consisting of a nucleotide sequence and its reverse complement.
• Transcription Factors (TFs) are classified based on the presence of specific conserved motifs, including the helix-turn-helix, homeodomain, leucine zipper, basic helix-loop-helix, and zinc finger motifs.
• The helix-turn-helix (h-t-h) motif, consisting of about 20 amino acids, is used by many bacterial and eukaryotic regulatory proteins for DNA binding.
• The homeodomain motif, identified in fruit flies and made up of 60 amino acids, is found in TFs regulating body pattern development in various organisms, including humans.
• The basic leucine zipper motif, composed of 60-80 amino acids, features a hydrophobic surface, basic residues in the DNA-binding region, and is primarily used for dimerization.
• The basic helix-loop-helix (b-hlh) motif, containing ~50 amino acids, plays a role in DNA binding, dimer formation, and is often associated with development or cell cycle activity.
• TFs with b-hlh motifs, such as c-Myc and HIF-1, have been linked to cancer.
• Proteins with zinc finger motifs have diverse functions, including roles in DNA recognition, RNA packaging, and transcriptional activation.
• The zinc finger motif, consisting of ~30 amino acids, forms an elongated loop stabilized by Zn2+ ions and is found in eukaryotic and bacterial proteins.
• Single Zinc finger interactions are weak, and proteins with multiple zinc fingers have been designed for gene editing.
• Type I and II zinc finger motifs function differently, with Type II combining the Zn2+-binding motif with the helix-turn-helix motif.
• Engineered nucleases, such as zinc-finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs), are designed using zinc fingers joined to a FokI-derived DNA cleavage domain, and TALEs fused to FokI nucleases, respectively, for gene editing purposes.

Transcription Factor Binding Motifs and DNA Interaction

• TF binding sites typically contain inverted repeats, a nucleotide sequence followed by the reverse complementary sequence
• Recognition of DNA by TF typically occurs through certain amino acid side chains of an α helix known as the recognition helix
• TFs are classified based on the presence of specific conserved motifs such as the helix-turn-helix, homeodomain, leucine zipper, basic helix-loop-helix, and zinc finger motifs
• The helix-turn-helix (h-t-h) motif consists of about 20 amino acids and is used by many bacterial and eukaryotic regulatory proteins for DNA binding
• The homeodomain motif, identified in fruit fly, consists of 60 amino acids and is found in TFs regulating body pattern development in various organisms, including humans
• The basic leucine zipper motif, composed of 60-80 amino acids, contains a series of hydrophobic residues and is used for dimerization in DNA binding proteins
• The basic helix-loop-helix motif, made up of ~50 amino acids, contains two amphipathic α helices, one for DNA binding and the other for dimer formation, often involved in development or cell cycle activity
• The zinc finger motif, consisting of ~30 amino acids, is found in eukaryotic and bacterial proteins, with diverse functions including DNA recognition and transcriptional activation
• DNA-binding proteins with multiple zinc fingers have been designed for gene editing, as they strengthen binding to DNA
• Type I zinc finger motifs function as monomers and use one Zn2+ ion to stabilize the DNA binding domain, while type II motifs combine Zn2+-binding with the h-t-h motif and use two Zn2+ ions for DNA binding as dimers
• DNA binding proteins like zinc finger nucleases (ZFNs) and TALENs have been engineered for gene editing, using zinc fingers or TALEs fused to FokI nucleases to target and cleave specific DNA sequences
• TALENs consist of TALEs fused to FokI nucleases, targeting the nuclease complex to specific DNA sites using a minimum of 10-12 TALE modules for effective binding