1. PROPERTIES OF DNA I PRIMARY SEQUENCE A. Base Pairing
B. Nucleotide Conformations
C. Types of DNA
D. Supercoiling
E. Restriction nucleases
F. DNA Sequencing

3. Lactam
(keto)
Lactim
(enol)
TAUTOMERIC FORMS

4. Conformational Rules
Nucleotides are flexible and can be twisted about their C-O-P bonds
There are 7 torsion angles in a nucleotide
One torsion angle joins base to sugar
The deoxyribose ring is “puckered” and not flat
Puckering influences position of PO4 on the 3’ and 5’ position of the ring

5. CONFORMATION OF SUGAR-PHOSPHATE
Nucleotides in DNA have 7 torsion angles that
govern orientation of nucleotide chain.
Favorable
Unfavorable
Z-DNA

6. Torsion Angles in a Nucleotide
Rotation at  hindered
C-O-P bonds flexible
C-C, C-O, P-O flexible

7. Conformations of the Deoxyribose Ring
No Tilt
Tilts Bases
C2’-endo 5’
C3’-endo
C3’-endo is found in A-DNA
C2’-endo is found in B-DNA
Note 3’ and 5’ PO4 group in C2’endogives bases an
arrangement more perpendicular to the helix axis

8. TYPES OF DNA 1. 3 types: A, B, and Z 2. Not in equilibrium
3. Transition depends on humidity, temperature
and DNA binding proteins

9. B-DNA (Watson-Crick) 90% humidity
1. Two Antiparallel polynucleotide strands
2. Sugar phosphates on periphery
(Minimize charge repulsion)
3. Helix approximately 20 Angstroms in diameter
base pairs per turn, ~36 degrees per base pair
5. Bases flat, perpendicular to axis
6. Major and minor grooves readily apparent

10. Major
Minor

11. A DNA: What distinguishes A DNA from B DNA?
A DNA is wider and flatter: 11 base-pairs per turn instead
of The helix diameter is 26 angstroms instead
of 20. The major groove is narrow and subdued.
Is base-pairing the same?
Yes.
But the bases join around the axis and not through
the axis and are tilted 20 degrees.
Why is A DNA important to know?
A DNA is seen in single-stranded RNA molecules that fold back on themselves. A DNA is also seen in DNA-RNA hybrids. Low humidity causes it to form from B DNA

12. Z-DNA
1. Left handed helix
Angstron diameter
3. No major groove
base pairs per turn
5. Repeating units is a dinucleotide dRY or dYR:
d(GC)
d(CG)
d(AC)
d(GT)
6. Formation also depends on high salt to block charge
repulsion

13. Z-DNA
Transition region
CGCGCG
Negative twisted DNA

14. DNA Dialogue What forces hold a typical DNA molecule together?
ANS: Hydrogen bonds between bases either through or
or around the axis and base stacking
What is base stacking?
Stacking implies vertical interactions between bases as
they sit on top of one another
What sort of interactions?
Mainly van der Waal forces created by hydrophobic
interactions
Are the forces of interaction the same for all bases?
No. Stacking interactions between G and C give rise to
greater stacking energy than A to T

15. What does this do to the DNA?
Ans: The greater the GC content of DNA the greater
the stability, thermal stability in particular
What do you mean by thermal stability?
Two ways to view thermal stability. It could be the heat
energy required to separate or melt the strands
What else besides heat?
Thermal could reflect the strength of bonding of the two
DNA strands to one another though a combination
of both H-bonding and base stacking
How is thermal stability measured?
Next slide

16. A260 Melting Point of DNA Temperature oC Tm (melting temperature)
Lower G + C
Higher G + C
A260
Temperature oC 50 70
Tm (melting temperature) 90
Hyperchromicity

17. Examples: DNA-Protein Interactions
Rule: The interaction of proteins with nucleic acids is an
important biological property governing nucleic acid
function in replication and transcription
Examples:
1. Endo and Exonucleases, kinases, ligases
2. Histones
3. Transcription Repressor proteins
4. Transcription Enhancer proteins
5. Topoisomerases
6. Single strand DNA binding proteins
7. DNA-RNA polymerases

18. Rule: In DNA-RNA-Protein interactions there must
exist a structural harmony between the nucleic acid and
the protein at points of contact
Transcription Factors
1. Helix-turn-helix protein (HTH)
a. Bind to operators
b. Typically dimeric
c. Repress transcription of specific genes
2. Zinc finger protein
a. Eukaryotic
b. Cysteine and Histidine rich
1. Typically cys2-his2

19. Zinc Fingers (continued)
c. Designed to recognize asymmetric
base sequences
3. Leucine Zippers
a. Leucine repeats every 7th residue
b. Dimerizes as a coil-coil, -leucine are teeth
c. Basic region adjacent to zipper binds to DNA
d. Differ from other transcription factors
by engaging DNA at basic end of protein
e. Typical is the AP1 transcription factor
composed of c-jun and c-fos leucine zippers,
related to v-jun and v-fos, known
heterodimeric oncogenes

20. Y shape is a typical feature of zippers bZIP Zinc Finger
Project into
DNA grooves
Y shape is a typical
feature of zippers
bZIP
Zinc Finger
DNA must have an
inverted repeat to
accommodate bZIP
Leucine Zipper