Learning Objective: Describe the structural organization of DNA—including supercoiling, nucleosome formation, chromatin structure, and higher-order packaging—and explain how these organizational levels regulate gene accessibility and function.
Organization of DNA
Large eukaryotic and prokaryotic DNA molecules must be compacted to fit inside the cell while remaining accessible for replication, transcription, and repair. DNA organization involves multiple hierarchical levels, beginning with supercoiling and progressing to chromatin and chromosome formation.
Supercoiling
Mitochondrial DNA and most prokaryotic genomes exist as closed circular DNA. These molecules may be relaxed or supercoiled depending on torsional strain.
Types of Supercoiling
Negatively supercoiled DNA
Forms when DNA is underwound. This is the predominant and biologically active form because it facilitates strand separation needed for replication and transcription.
Positively supercoiled DNA
Formed when DNA is overwound. Less favorable for biological reactions.
Topoisomerases
Topoisomerases regulate the amount of supercoiling by creating reversible breaks in DNA:
Topoisomerase I
Cuts one strand to relieve supercoils.
Topoisomerase II (e.g., DNA gyrase in E. coli):
Cuts both strands, introducing negative supercoils.
Clinical relevance:
Activity
Nucleosomes and Chromatin
Eukaryotic nuclear DNA is packaged with proteins to form chromatin, whose fundamental unit is the nucleosome.
Histones
Histones are small, positively charged proteins rich in lysine and arginine, which facilitate strong interactions with negatively charged DNA.
Nucleosome Structure
- A histone octamer contains: 2 × (H2A, H2B, H3, H4)
- ~147 bp of DNA wraps around this octamer to form a 10-nm fiber (“beads on a string”).
- Histone H1, bound to linker DNA, promotes compaction into a 30-nm fiber (solenoid).
Higher-Order Packaging
- 30-nm fibers form looped domains attached to scaffolding proteins.
- Further coiling forms chromosome arms visible during mitosis.
Euchromatin vs Heterochromatin
Euchromatin
- Lightly packed, transcriptionally active.
- Open configuration allows transcription factors and polymerases to access DNA.
Heterochromatin
- Densely packed, transcriptionally silent.
- Found in centromeres, telomeres, and other silent genomic regions (e.g., Barr body).
Mnemonic: “EUchromatin = Expressed” “HETEROchromatin = Highly condensed”
Activity
Chromosomes During the Cell Cycle
- Interphase: mixture of euchromatin and heterochromatin; nucleoli visible.
- Mitosis: DNA becomes maximally condensed; metaphase chromosomes are used for karyotyping to detect:
- aneuploidy
- translocations
- deletions
- duplications
- inversions
