Learning Objective: Explain the structural organization of nucleic acids—including phosphodiester bonding, polarity, base-pair complementarity, DNA helical forms, Chargaff’s rules, and the principles of denaturation, renaturation, and hybridization.
Nucleic Acid Structure
Nucleic acids are polymers of nucleotides linked by 3′ → 5′ phosphodiester bonds, where the phosphate of one nucleotide connects the 3′ carbon of its sugar to the 5′ carbon of the next nucleotide. This creates chains with inherent polarity:
- 5′ end: usually contains a phosphate (p-)
- 3′ end: usually contains a hydroxyl (-OH)
Sequences are always written 5′ → 3′, for example:
- 5′–TCAG–3′ (standard notation)
- If reversed, ends must be labeled: 3′–GACT–5′
- Phosphate notation possible: pTpCpApG
- DNA may include “d”: dTdCdAdG
In eukaryotes:
- DNA = double-stranded (dsDNA)
- RNA = single-stranded (ssRNA)
Viral genomes may contain ssDNA or dsRNA.
Activity
Key Features of Double-Stranded DNA
1. Antiparallel Strands
One strand runs 5′ → 3′, the other 3′ → 5′.
2. Complementary Base Pairing
- A–T (2 hydrogen bonds)
- G–C (3 hydrogen bonds, stronger pairing)
3. Chargaff’s Rules
In dsDNA (and dsRNA):
- %A = %T (or %U)
- %G = %C
- Total purines (%A + %G) = total pyrimidines (%C + %T)
Example: If a DNA sample has 10% G → 10% C → remaining 80% split as 40% A & 40% T.
4. DNA Helical Forms
- B-DNA (Watson–Crick DNA): most common; right-handed; 10 bp per turn; bases stacked inside; sugar-phosphate backbone outside; major and minor grooves allow protein binding.
- Z-DNA: left-handed; occurs in GC-rich regions; may have regulatory roles.
Activity
Pharmacology Bridge
- Daunorubicin and doxorubicin intercalate between bases → inhibit topoisomerase II → block replication (used in leukemias).
- Cisplatin crosslinks DNA → structural distortion → apoptosis (used in bladder & lung cancer).
Activity
DNA Denaturation & Renaturation
Denaturation (“Melting”)
Disrupts:
- Hydrogen bonds
- Base stacking
Caused by:
- Heat
- Alkaline pH
- Chemicals (formamide, urea)
Covalent bonds remain intact; the strands simply separate.
Renaturation (Annealing)
If denaturing conditions are reversed slowly (e.g., cooling), complementary ssDNA reanneal to form dsDNA.
Hybridization
Used in Southern blotting and PCR:
A known DNA probe binds complementary target sequences during renaturation.
