Y-form DNA binding

Definition

Target type: molecularfunction

Binding to a DNA segment shaped like a Y. This shape occurs when DNA contains a region of paired double-stranded DNA on one end and a region of unpaired DNA strands on the opposite end. [GOC:elh, PMID:16781730]

Y-form DNA is a non-canonical DNA structure characterized by a three-stranded helical arrangement, where two strands are parallel and the third strand is antiparallel. This structure is formed when a polypurine: polypyrimidine sequence in double-stranded DNA undergoes a structural transition under certain conditions, such as high pH, elevated temperature, or the presence of specific cations. Y-form DNA binding proteins recognize and bind to this unique structure, playing a crucial role in various cellular processes. The molecular function of Y-form DNA binding proteins can be described as follows:

1. **Recognition and Binding:** Y-form DNA binding proteins possess specific structural features that enable them to recognize and bind to the three-stranded helical arrangement of Y-form DNA. This recognition involves specific interactions between amino acid residues in the protein and the exposed bases and sugar-phosphate backbone of the Y-form DNA structure.

2. **Stabilization and Modulation of Y-form DNA:** Once bound, Y-form DNA binding proteins can stabilize the Y-form DNA structure, preventing its transition back to the canonical double-stranded conformation. This stabilization can be achieved through various mechanisms, including electrostatic interactions, hydrogen bonding, and hydrophobic interactions.

3. **Regulation of DNA Replication and Transcription:** Y-form DNA binding proteins can influence DNA replication and transcription by modulating the accessibility of DNA to other proteins involved in these processes. For instance, they may block the progression of DNA polymerase or RNA polymerase, or they may recruit other proteins involved in DNA repair or recombination.

4. **Involvement in DNA Repair and Recombination:** Y-form DNA can arise during DNA replication or repair processes. Y-form DNA binding proteins may participate in the recognition and repair of DNA damage, or they may facilitate the exchange of genetic information during recombination.

5. **Regulation of Gene Expression:** Y-form DNA binding proteins have been implicated in the regulation of gene expression. They may act as transcription factors, either activating or repressing the expression of specific genes, or they may indirectly modulate gene expression by influencing the activity of other regulatory proteins.

The precise function of Y-form DNA binding proteins is dependent on the specific protein and its cellular context. However, their ability to bind and stabilize Y-form DNA provides them with a unique role in maintaining genome integrity and regulating cellular processes. '
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Proteins (3)

Compounds (5)