Be able to describe the structure of:

• DNA in general
• nucleic acids
• the phosphodiester linkages between nucleic acids

Understand the importance of chemistry and conditions

Understand the concept of base stacking and how it contributes to structure

Describe the B-form (BR - it's the major form) of the double helix

• major/minor groove
• antiparallel nature
• Watson Crick base pairing
• handedness
• residues per turn

Define:

• repeats
• hairpins
• denaturation/melting

Understand the difference between primary and secondary structures in DNA and RNA (this is review!)

Describe the degrees of freedom of DNA

• twisting
• bending
• compression

Understand and calculate degree of supercoiling

• linking number (including handedness)
• twist and writhe

Topoisomerases

• Understand what they do
• Know the difference between the types

Assays/techniques to be familiar with:

• Hyperchromatic shift assay
• Hybridization
• Gel electrophoresis