Question

Identify/highlight all possible palindromic sequences. Which one of these two examples is most likely to form a hair loop - highlight the hair loop sequence?

Example 1: 5' - GCAACTGGATAGCCCTAGAAGGACTAGGGCTTTTCCAAGTCAA - 3'

Example 2: 5' - TATTTGCATTCCCTGCAGGGAATCGTTAAGGAGGGCAGTCTTAA - 3'

Answer 1

ANSWER- Palindromic sequences are those sequence which read the same in both forward (5'-3') and backward(3'-5') directions.

Example 1: 5' -GCAACTGGATAGCCCTAGAAGGACTAGGGCTTTTCCAAGTCAA-3'

3' -AGTTGACCTATCGGGATCTTCCTGATCCCGAAAAGGTTCAGTT-5'

In the above example, the reverse complement of the DNA sequence does read the same in the backward direction. Hence, there is no palindrome sequence.

Example 2. 5'-TATTTGCATTCCCTGCAGGGAATCGTTAAGGAGGGCAGTCTTAA-3'

3'- ATAAACGTAAGGGACGTCCCTTAGCAATTCCTCCCGTCAGAATT-5'

In the above example, the reverse complement of the DNA sequence does read the same in the backward direction. Hence, there is no palindrome sequence.

Answer 2. Example1. DNA sequence will form a hair loop structure.

Hairloop structure is formed two regions within the same sequence strand are complementary to each other when reading in opposite direction with an unpaired loop of sequence between them.

5' - GCAACTGGATAGCCCTAGAAGGACTAGGGCTTTTCCAAGTCAA - 3'

The region shaded in yellow - Complementary sequence

The region shaded in orange- Unpaired loop structure