DNA

This step has some overlap with the previous days (Geerten's DNA part of this course), so we will move through it very quickly. I leave it in because others, outside the RU also use this material. And they don't have Geerten doing the other half...

We will analyze the A-T and G-C base-pairs, we will analyze the differences between the major and minor groove of normal B-DNA. The atom-nomenclature in the pictures is still the old one. But for now that seems not very relevant. It will be corrected one day.

Figure 14. The A-T base pair.

Figure 15. The G-C base pair.

Figure 16. A small stretch of bDNA.

The following list holds a series of questions with a high likelyhood of seeing them again at the amino acid and nucleic acid test...

• What are the three main components of each nucleotide?
• How many hydrogen bonds are there between the A and the T?
• Which groups are available on the A for hydrogen bonding?
• Which groups are available on the T for hydrogen bonding?
• How many hydrogen bonds are there between the G and the C?
• Which groups are available on the G for hydrogen bonding?
• Which groups are available on the C for hydrogen bonding?
• Why are the minor and major groove called minor and major?
• Which side of the A-T and C-G bases point into the major groove?
• Which side of the A-T and C-G bases point into the minor groove?
• Which differences are there between an A-T base pair and a C-G base pair in the major groove? And in the minor groove ?
• How many base pairs are there in one helical turn?

Helix in the major groove

The most common protein-DNA binding motif is the so-called 'helix in the major groove' motif.

Figure 17. Look at the helix in the major groove in the file CQT.pdb (available from the FILES list). This figure gives some hints already for answering the first question: "Which residues cause some specificity in this binding"? See the questions at the bottom of the page.

Find 10 classes of proteins that interact with DNA. For each, describe in 10-50 words the function. For one class you should find an example PDB file, load it is Yasara, analyze it, and be prepared for difficult questions from the assistant!

Question 14:

• Which residues cause some DNA - protein interaction specificity in the CQT file shown in figure 17?
• Which is the corresponding DNA motif?
• How often does that DNA motif occur in your own DNA? (Hint, a crude estimate is enough, you don't have to measure it).
• So why do we speak about specificity at all? Where does the specificity come from.