1. 11 September, 2006 Chapter 6 DNA Structure

2. Overview The classical DNA structure is an antiparallel duplex of polynucleotides. The two strands of DNA have complementary sequence because of base pairing interactions. The major groove of a DNA duplex is carries accessible information about the sequence. DNA can exist in alternative structures. DNA molecules can melt and anneal. The linking number, composed of twist and writhe is a property of covalently closed circles. DNA in cells is negatively supercoiled. Topoisomerases cleave and rejoin strands to change the supercoiling state of DNA. RNA is usually single stranded, and form complex seconbdary and tertiary structures, including some that have enzymatic activity.

3. The DNA duplex

4. Bases, nucleosides, and nucleotides

5. Base pairing

6. Bases and Alternative Base Isoforms

7. Base Pairing

8. Major Groove Sequence Information

9. Alternative DNA Structures

10. DNA can melt and anneal.

11. DNA Tm Depends on %GC and [salt].

12. DNA renaturation kinetics depend on sequence complexity.

13. Linking number and DNA topology

14. DNA in most cells is negatively supercoiled. Nicked DNA spontaneously relaxes.

15. Topoisomerases enzymatically change the linking number.

17. Topoisomerases also disentangle DNA molecules.

18. Topoisomerase action

19. DNA topoisomers can be separated electrophoretically.

20. Ethidium causes DNA to underwind.

21. RNA Structures

22. Non-W/C base pairs

23. Some RNAs are enzymes.