CHY 431 Structure and Mechanism in Biological Chemistry

Undergraduate Problem Set for Nucleic Acids and Genomics

Due not later than 2 February!

Select any seven problems and provide careful, detailed, well-worked out answers. Problem sets should be word processed. I prefer that they be sent to me electronically, but dead trees are acceptable.

1. (a) As we described in class with a cartoon, single stranded RNA often forms hairpin turns that allow it to base pair with itself. Here is the sequence of one such strand, reading from the 5' end: CUAGAUGGUAGGUACGGUUAUGGGAUAACUCUG. Suggest how this strand might form a hairpin. That is, which bases would pair, and which would be in the turn? More than one answer is possible. A graphic would be the best way to answer this.

(b) The RNAFold server will make a prediction of the folding of any segment of RNA or single-stranded DNA. Submit the sequence above to this server. Compare your prediction to that of the server and comment on any differences.

2. (a) Some naturally occurring polynucleotide sequences are palindromic; that is, they are self-complementary about an axis of symmetry. Such a sequence is:

---TCAAGTCCATGGACTTGG----
---AGTTCAGGTACCTGAACC----

Such sequences can form a double hairpin, or cruciform, conformation. (Think of the shape if you push toward the center on each end of this sequence, and one strand bulges upward while the other bulges downward.) Show how this sequence might form such a conformation, showing clearly the symmetry and self-pairing.

(b) Restriction endonucleases are enzymes that cleave both strands of DNA duplexes at specific sites. The recognition sites for these enzymes often are palindromic.

Here are two palindromic DNA sequences:

5'-G-A-A-T-T-C-3'
3'-C-T-T-A-A-G-5'

5'-G-A-T-A-T-C-3'
3'-C-T-A-T-A-G-5'

The palindromes can be found by carefully placing a two-fold symmetry axis between the strands, perpendicular to the page.