DNA Base Pairing and Melting Temperature
Two duplex (ie. double stranded) DNA fragments are shown below. Under identical conditions (ie. ionic strength, buffer composition, temperature, etc.), which double-stranded fragment would denature at the lower temperature?
5' A-A-G-T-A-G-T-T-T-C-A 3'
3' T-T-C-A-T-C-A-A-A-G-T 5'
5' G-C-A-G-G-T-C-G-C-C-T 3'
3' C-G-T-C-C-A-G-C-G-G-A 5'
...dict which fragment would be more stable to thermal denaturation. How? Remember that A-T pairs have two Hydrogen bonds, while C-G pairs have three Hydrogen bonds. Therefore, denaturation of a DNA fragment with a higher percentage of C-G pairs would require more energy, compared to a DNA fragment with less C-G content.
So....compare the number of A-T and C-G pairs in each DNA fragment:
# A-T pairs: 8
# C-G pairs: 3
# A-T pairs: 3
# C-G pairs: 8 ...