The following four DNA oligos are mixed in equimolar concentration, heated to 95°C, and slowly annealed in a microcentrifuge tube.

5’ GCG GGA ATT TA 3’
5’ GCC TAC TCC CGC 3’
5’ CGA TGG GTA GGC 3’
5’ TAA ATC CAT CG 3’

Which of the following secondary structures will predominantly be present?

Correct option is D

Explanation:

• When these four oligos are mixed, they can form two DNA duplexes through complementary base pairing. Specifically, they can form a Holliday junction, a four-stranded intermediate that occurs during genetic recombination.
• The Holliday junction structure is typical in processes like crossing over during meiosis or DNA repair.
• Holliday junctions can form when two DNA duplexes are exchanged, which is what happens here in the sequence combinations, leading to the formation of a four-stranded structure.

Why the other options are incorrect:

• Option 1: This option suggests the formation of two B-form double-stranded DNA molecules, which is not the most likely outcome given the sequences provided. These oligos are more likely to form a complex, not just separate B-form double strands.
• Option 2:Stem-loop structures form when a single strand of DNA folds back onto itself, but the sequences provided are designed to pair with other sequences, making the formation of stem-loops unlikely.
• Option 3:Z-form DNA requires specific sequences, typically alternating purines and pyrimidines, which the given sequences do not meet. Additionally, Z-DNA forms under specific conditions, which are not suggested by this setup.

Information Booster:

1. Holliday Junction Formation:

   • A Holliday junction is a four-stranded DNA structure that typically forms during genetic recombination, such as in crossing-over during meiosis or during DNA repair.
   • The provided sequences can anneal with each other in a way that leads to the formation of a four-stranded structure, which is characteristic of a Holliday junction.

2. Structure of the Sequences:

   • The given sequences can pair to form two DNA duplexes. The Holliday junction involves the exchange of strands between two duplexes, which results in a four-stranded intermediate.

3. Annealing Process:

   • The sequences are heated to 95°C and then slowly annealed. This heat-denaturation followed by slow cooling promotes the formation of double-stranded DNA structures or more complex forms, like the Holliday junction.

4. Base Pairing:

   • The complementary nature of the sequences facilitates annealing into a four-stranded structure. These sequences are designed to interact with each other, leading to the formation of a Holliday junction, which is common in recombination processes.