DNA STRUCTURE

DNA is composed of polynucleotide chains

Structure: twisting around each other in the form of a double helix.

DNA STRUCTURE (1)

Schematic model

Space-filling model

Nucleoside & Nucleotide, the fundamental building block of DNA

phosphoester bond glycosidic bond

Phosphodiester linkages: repeating, sugar-phosphate backbone of the polynucleotide chain

DNA polarity: is defined by the asymmetry of the nucleotides and the way they are joined.

Bases in DNA

adenine

purines
guanine

N9

cytosine

pyrimidines
thymine
N1

Each bases has its preferred tautomeric form (Related to Ch 9)

DNA STRUCTURE (2)

The two strands of the double helix are held together by base pairing in an antiparallel orientation, Which is a
stereochemical consequence of the way that adenine and thymine,and guanine and cytosine, pair with each other. (Related to replication

DNA STRUCTURE (3)

and transcription)

The Two Chains of the Double Helix Have Complementary Sequences

DNA STRUCTURE (4)

Watson-Crick Base Pairing

Example: If sequence 5-ATGTC-3 on one chain, the opposite chain must have the complementary sequence 3TACAG-5 (Related to replication and transcription)

The strictness of the rules for Waston-Crick pairing derives from the complementarity both of shape and of hydrogen bonding properties between adenine and thymine and between guanine and cytosine.

A:C incompatibility

Hydrogen Bonding Is Important for the Specificity of Base Pairing

The hydrogen bonds between complementary bases contribute to the thermodynamic stability of the helix (why?) and the specificity of base pairing Stacking interactions between bases significantly contribute to the stability of DNA double helix

DNA STRUCTURE (5)

The double helix has Minor and Major grooves (What & Why)
It is a simple consequence of the geometry of the base pair.

DNA STRUCTURE (5)

(See the Structural Tutorial of this chapter for details)

The Major groove is rich in chemical information

DNA STRUCTURE (6)

(What are the biological relevance?)

The edges of each base pair are exposed in the major and minor grooves, creating a pattern of hydrogen bond donors and acceptors and of van der Waals surfaces that identifies the base pair.

A: H-bond acceptors

D: H-bond donors

H: non-polar hydrogens

M: methyl groups

The double helix exists in multiple conformations.

The B form (10 bp/turn), which is observed at high humidity, most closely corresponds to the average structure of DNA under physiological conditions
A form (11 bp/turn), which observed under the condition of low humidity, presents in certain DNA/protein complexes. RNA double helix adopts a similar conformation.

DNA STRUCTURE (7)

DNA STRUCTURE (8)

DNA strands can separate (denature) and reassociate (anneal)

Key terms to understand 1. Denaturation 2. Hybridization 3. Annealing/renature 4. Absorbance 5. Hyperchromicity 6. Tm (melting point)