DNA Secondary Structure
Describe the structure of duplex DNA
Composition
- 2 nucleotide chain running anti-parallel to one another
- 5' to 3' directionality
- 2 chains interact by the bases forming complementary base pairing (A-T and G-C)
- 1 helical turn (1 pitch) = 34 Å (3.4 nm)
- Width = 2 nm
- Distance btwn 2 bases (vertical) = 3.4 Å (0.34 nm)
Right-Handed Double Helix
Stacking on the bases
- perpendicular to the helical axis
- flat bases stack on top of each other
- electron cloud (pi-pi) interaction from the aromatic ring between the stacked bases contribute to the stability
- stacked bases attracted by induced dipole (van der Waals force) between the electron clouds
- base stacking also contribute to hydrophobic effect
- hydrophobic bases are buried by base stacking
Major and Minor Groove
- Why?: the geometry of the base pair / the angle of the glycosidic bonds is 120° (narrow angle) or 240° (wide angle)
- Minor groove: narrow angles on one edge of the base pairs
- Major groove: wide angles on the other edge
Major groove rich in info
- H-bond acceptor (A), H-bond donator (D), Methyl group (M), Non-polar hydrogen (H)
- Edge of A=T: ADAM signify AT base pair in the major groove
- Edge of G≡C: AADH stands for GC base pair
- Important: allow proteins to bind to specific DNA sequences without directly interacting with the bases and disrupting the
structure
Outline the essential features of Watson-Crick base pairing with reference to Chargaff's rules
Watson-Crick base pairing
Derives from: complementarity of shape and hydrogen bonding properties of the 4 bases
A=T H-bond btwn: C6 amino group (exocyclic) A + C4 carbonyl group T / N1 of A + N3 of T
G≡C H-bond btwn: C2 NH2 (exocyclic) on G + C2 carbonyl on C / N1 on G + N3 on C / C6 carbonyl on G + C4 NH2 (exocyclic) on C
Geometry
- 2 base pairs have exactly same geometry → distances btwn 2 sugar same → symmetry
- all 4 bases accommodated without distorting the DNA structure
- base pairs can stack on top of each other
- order of bases irregular but the overall DNA structure regular
Chargaff's Rule
- Showed: relative ratios of the 4 bases are not random
Describe the structure of duplex DNA
Composition
- 2 nucleotide chain running anti-parallel to one another
- 5' to 3' directionality
- 2 chains interact by the bases forming complementary base pairing (A-T and G-C)
- 1 helical turn (1 pitch) = 34 Å (3.4 nm)
- Width = 2 nm
- Distance btwn 2 bases (vertical) = 3.4 Å (0.34 nm)
Right-Handed Double Helix
Stacking on the bases
- perpendicular to the helical axis
- flat bases stack on top of each other
- electron cloud (pi-pi) interaction from the aromatic ring between the stacked bases contribute to the stability
- stacked bases attracted by induced dipole (van der Waals force) between the electron clouds
- base stacking also contribute to hydrophobic effect
- hydrophobic bases are buried by base stacking
Major and Minor Groove
- Why?: the geometry of the base pair / the angle of the glycosidic bonds is 120° (narrow angle) or 240° (wide angle)
- Minor groove: narrow angles on one edge of the base pairs
- Major groove: wide angles on the other edge
Major groove rich in info
- H-bond acceptor (A), H-bond donator (D), Methyl group (M), Non-polar hydrogen (H)
- Edge of A=T: ADAM signify AT base pair in the major groove
- Edge of G≡C: AADH stands for GC base pair
- Important: allow proteins to bind to specific DNA sequences without directly interacting with the bases and disrupting the
structure
Outline the essential features of Watson-Crick base pairing with reference to Chargaff's rules
Watson-Crick base pairing
Derives from: complementarity of shape and hydrogen bonding properties of the 4 bases
A=T H-bond btwn: C6 amino group (exocyclic) A + C4 carbonyl group T / N1 of A + N3 of T
G≡C H-bond btwn: C2 NH2 (exocyclic) on G + C2 carbonyl on C / N1 on G + N3 on C / C6 carbonyl on G + C4 NH2 (exocyclic) on C
Geometry
- 2 base pairs have exactly same geometry → distances btwn 2 sugar same → symmetry
- all 4 bases accommodated without distorting the DNA structure
- base pairs can stack on top of each other
- order of bases irregular but the overall DNA structure regular
Chargaff's Rule
- Showed: relative ratios of the 4 bases are not random
