1. Spectroscopy of Biopolymers
Introduction to Biopolymers (II)
Nucleic Acids

2. Structure of nucleic acid

3. 去氧核醣核酸 DNA

4. 磷酸
去氧核醣核酸 DNA
五碳醣 鹼基 核 甘 酸 核 甘
鹼基間氫鍵
主 鏈

5. 去氧核醣核酸 DNA T A C G

6. Torsion Angles in nucleic Acids
The structure of nucleic acids are defined by the torsion angles along the phosphoribose backbone (a to z), the torsion angles within the sugar ring( n0 to n4) and the rotation of the nucleobase relative to the sugar (c). Rotation about c places the base either extended from the ribose (anti) or sitting above the ring (syn)

7. Sugar conformation of nucleic acids

9. 去氧核醣核酸 DNA

14. A-Form RNA or DNA Most RNA and RNA-DNA duplex in this form
Shorter, wider helix than B.
Deep, narrow major groove not easily accessible to proteins
Wide, shallow minor groove accessible to proteins, but lower information content than major groove.
Favored conformation at low water concentrations
Base pairs tilted to helix axis and displaced from axis
Sugar pucker C3'-endo (in RNA 2'-OH inhibits C2'-endo conformation)

15. B-Form DNA Most common DNA conformation in vivo
Narrower, more elongated helix than A.
Wide major groove easily accessible to proteins
Narrow minor groove
Favored conformation at high water concentrations (hydration of minor groove seems to favor B-form)
Base pairs nearly perpendicular to helix axis
Sugar pucker C2'-endo
Look at this spacefilling view of B-form DNA.

16. Helix has left-handed sense
Can be formed in vivo, given proper sequence and superhelical tension, but function remains obscure.
Narrower, more elongated helix than A or B.
Major "groove" not really groove
Narrow minor groove
Conformation favored by high salt concentrations, some base substitutions, but requires alternating purine-pyrimidine sequence.
N2-amino of G H-bonds to 5' PO: explains slow exchange of proton, need for G purine.
Base pairs nearly perpendicular to helix axis

17. Z-form DNA GpC repeat, not single base-pair
P-P distances: vary for GpC and CpG
GpC stack: good base overlap
CpG: less overlap.
Zigzag backbone due to C sugar conformation compensating for G glycosidic bond conformation
Conformations:
G; syn, C2'-endo
C; anti, C3'-endo