Nucleic Acid Chemistry and Conformation
These notes are from the Spring 1995 Structural Biology class
given at Berkeley.
Note: These are incomplete and I have no intention of completing them.
Table of Contents
Methods of Studying Nucleic Acids and What We Have Learned From Them
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DNA Structure
- Generally double-stranded
- Helical
- Environmentally dependent structure
- Exquisitely dependent on sequence, which leads to base stacking
- Lots of types, but we will concnetrate on A, B, and Z
The structure of nucleic acids was first studied with fiber diffraction.
Methods and what we learn from them
NMR
- Base Pairing Schemes
- Base Pair Stability with change in conditions
- Sugar Puckers
- Glycosidic torsion angles
- Basic Helix Types
UV
Spectral properties are not additive: an ApG base step does not have the same spectrum as the A and G spectrums added together. Long DNA results in a smooth curve with a maximum at 260nm. The A260/A280 ratio is 1.8 for pure DNA, 2.0 for pure RNA. Base stacking results in a reduction in UV absorbance known as hypochromicity.
Circular Dichroism
Base stacking is a sequence-dependance phenomenon. A-like and B-like DNA have very different CD spectra.
Back to the Nucleic Acid Chemistry Table of Contents
Last revised: 1995 May 12 by
sev@byzantium.mckusick.com