In a dideoxy DNA sequencing experiment, four separate reactions are carried out to provide the replicated material for DNA sequencing gels. Reaction products are usually run in gel lanes labeled A, T, C, and G.
Why is incorporation of a dideoxynucleotide during DNA sequencing identified as a 'replication-terminating' event?

Verified step by step guidance

1. Understand the structure of dideoxynucleotides (ddNTPs): Unlike regular deoxynucleotides (dNTPs), ddNTPs lack a hydroxyl group (-OH) at the 3' carbon of the sugar. This absence is critical for their role in terminating DNA replication.
2. Recall the mechanism of DNA synthesis: DNA polymerase adds nucleotides to the growing DNA strand by forming a phosphodiester bond between the 3' hydroxyl group of the last nucleotide and the 5' phosphate group of the incoming nucleotide.
3. Explain why ddNTPs terminate replication: When a ddNTP is incorporated into the growing DNA strand, the absence of the 3' hydroxyl group prevents the formation of the next phosphodiester bond. This halts further elongation of the DNA strand.
4. Relate this to the sequencing process: In dideoxy DNA sequencing, the incorporation of ddNTPs at random positions generates DNA fragments of varying lengths. Each fragment ends at the position where a ddNTP was incorporated.
5. Connect to gel electrophoresis: The DNA fragments are separated by size using gel electrophoresis, and the sequence of the original DNA template can be deduced by analyzing the positions of the fragments in the gel lanes labeled A, T, C, and G.

Key Concepts

Dideoxynucleotides

Dideoxynucleotides (ddNTPs) are modified nucleotides used in DNA sequencing that lack a hydroxyl group at the 3' carbon of the sugar. This structural modification prevents the addition of further nucleotides during DNA replication. When a ddNTP is incorporated into a growing DNA strand, it terminates the elongation process, leading to fragments of varying lengths that can be analyzed to determine the DNA sequence.

Chain Termination

Chain termination is a critical process in DNA sequencing where the incorporation of a dideoxynucleotide halts the synthesis of the DNA strand. This occurs because the absence of the 3' hydroxyl group prevents the formation of the phosphodiester bond necessary for adding additional nucleotides. As a result, each reaction produces DNA fragments that end at different points, allowing for the determination of the sequence based on fragment lengths.

Gel Electrophoresis

Gel electrophoresis is a laboratory technique used to separate DNA fragments based on their size. In the context of DNA sequencing, the terminated fragments generated from the incorporation of ddNTPs are loaded into a gel matrix and subjected to an electric field. Smaller fragments migrate faster than larger ones, allowing researchers to visualize and analyze the sequence of nucleotides by comparing the positions of the fragments in the gel lanes labeled A, T, C, and G.