DNA, the blueprint of life, is a complex molecule with a fascinating structure. Its double helix shape, formed by complementary base pairs, is key to its function in storing and transmitting genetic information.
DNA packaging is crucial for fitting the long molecule into cells. Nucleosomes, chromatin organization, and supercoiling all play important roles in compacting DNA while maintaining its accessibility for vital cellular processes.
DNA Structure
Double Helix and Base Pairing
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- DNA forms a double helix structure consisting of two intertwined strands
- Base pairing occurs between complementary nucleotides (adenine with thymine, guanine with cytosine)
- Hydrogen bonds form between complementary bases, stabilizing the double helix
- Two hydrogen bonds connect A-T pairs, while three hydrogen bonds connect G-C pairs
- Complementary strands run antiparallel, with one strand running 5' to 3' and the other 3' to 5'
- Base pair stacking contributes to the stability of the double helix through hydrophobic interactions
Structural Features of the Double Helix
- Major groove and minor groove form along the length of the double helix
- Major groove provides easier access for protein binding and interactions
- Minor groove offers a narrower space for specific protein recognition
- Phosphodiester bonds connect adjacent nucleotides within each strand
- Forms between the 3' hydroxyl group of one nucleotide and the 5' phosphate group of the next
- Creates the sugar-phosphate backbone of DNA
- Antiparallel strands result in asymmetric ends of the double helix
- 5' end has a terminal phosphate group
- 3' end has a terminal hydroxyl group
Chemical and Physical Properties
- DNA molecule carries a negative charge due to phosphate groups in the backbone
- Hydrophilic exterior and hydrophobic interior contribute to overall stability
- Base stacking interactions provide additional stability to the double helix
- Diameter of the DNA double helix measures approximately 2 nanometers
- One complete turn of the helix contains about 10.5 base pairs in B-DNA
- Rise per base pair in B-DNA is approximately 0.34 nanometers
DNA Packaging
Nucleosome Structure and Function
- Nucleosomes serve as the fundamental unit of DNA packaging in eukaryotic cells
- Each nucleosome consists of approximately 147 base pairs of DNA wrapped around a histone octamer
- Histone octamer contains two copies each of histones H2A, H2B, H3, and H4
- Linker DNA connects adjacent nucleosomes, ranging from 10 to 80 base pairs in length
- Histone H1 binds to the linker DNA, further compacting the chromatin structure
- Nucleosomes help regulate gene expression by controlling DNA accessibility
Chromatin Organization and Dynamics
- Chromatin represents the complex of DNA and proteins in the nucleus
- Primary structure of chromatin resembles a "beads on a string" appearance
- Higher-order chromatin structures include the 30 nm fiber and more compact forms
- Euchromatin refers to less condensed, transcriptionally active regions of chromatin
- Heterochromatin denotes highly condensed, transcriptionally inactive regions
- Chromatin remodeling enzymes can alter nucleosome positioning and DNA accessibility
- Histone modifications (methylation, acetylation, phosphorylation) influence chromatin structure and function
DNA Supercoiling and Topological Stress
- Supercoiling occurs when DNA is under- or overwound, creating torsional stress
- Negative supercoiling (underwinding) facilitates DNA strand separation for replication and transcription
- Positive supercoiling (overwinding) can inhibit DNA-dependent processes
- Topoisomerases regulate DNA supercoiling by introducing temporary breaks in the DNA
- Type I topoisomerases cut one strand of DNA to relieve supercoiling
- Type II topoisomerases cut both strands of DNA and pass another DNA segment through the break
DNA Conformations
B-DNA: The Most Common Form
- B-DNA represents the predominant conformation of DNA under physiological conditions
- Right-handed double helix with approximately 10.5 base pairs per turn
- Major groove measures 22 Å wide and 12 Å deep
- Minor groove measures 12 Å wide and 6 Å deep
- Base pairs are nearly perpendicular to the helical axis
- Hydration shell surrounds the DNA molecule, contributing to its stability
A-DNA: An Alternative Right-Handed Conformation
- A-DNA forms under dehydrating conditions or in some protein-DNA complexes
- Right-handed double helix with approximately 11 base pairs per turn
- Wider and shorter than B-DNA, with a more compact structure
- Major groove is narrower and deeper compared to B-DNA
- Minor groove is wider and shallower than in B-DNA
- Base pairs are tilted with respect to the helical axis
- Often observed in RNA-DNA hybrids and some protein-DNA interactions
Z-DNA: The Left-Handed Conformation
- Z-DNA forms a left-handed double helix, unlike B-DNA and A-DNA
- Occurs in sequences with alternating purine-pyrimidine bases (GC repeats)
- Zigzag pattern of the sugar-phosphate backbone gives it its name
- Approximately 12 base pairs per turn
- Narrower than B-DNA, with a more elongated structure
- Only one deep groove present, equivalent to the minor groove of B-DNA
- Formation of Z-DNA can be induced by high salt concentrations or negative supercoiling
- May play a role in gene regulation and genomic instability