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DNA Base Pairing and Melting Temperature

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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?

Fragment A:

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'

Fragment B:

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'

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Solution Preview

Key concept: Understanding the structure and stability of base pairs in nucleic acids.

When heated, DNA "denatures" because the thermal energy of molecular motion overcomes the stabilizing forces (including Hydrogen bonds between bases), which favour the double helix. (DNA denaturation is the process by which the two complementary strands unwind and separate. DNA denaturation is sometimes called "melting").

By studying the composition of the above double-stranded DNA fragments, we can ...

Solution Summary

The solution provides a description of how to compare the melting temperature (also called denaturation temperature) of two or more duplex (double stranded) DNA sequences. Hint: when answering the question, take into account the number of hydrogen bonds between different base pairs

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