Part 2: DNA Structure and Chemistry
The Blueprint of Life
DNA (deoxyribonucleic acid) is the molecular basis of heredityβa polymer of extraordinary elegance that encodes the instructions for building and operating all known living organisms. Understanding its structure reveals how genetic information is stored, replicated, and transmitted across generations.
This section explores DNA from its basic chemical building blocks to its complex three-dimensional organization, covering the fundamental principles that make DNA uniquely suited to serve as the universal information molecule of life.
Historical Discovery
Friedrich Miescher
Isolated "nuclein" from white blood cells in pus-soaked bandages, marking the first identification of DNA as a distinct substance.
Frederick Griffith
Discovered bacterial transformation, demonstrating that genetic material could be transferred between organisms.
Avery, MacLeod, McCarty
Proved that DNA (not protein) was the "transforming principle" and the carrier of genetic information.
Erwin Chargaff
Discovered base pairing rules: A=T and G=C in equal proportions (Chargaff's rules).
Rosalind Franklin
Produced Photo 51, the critical X-ray diffraction image showing DNA's helical structure.
Watson & Crick
Proposed the double helix model, winning the 1962 Nobel Prize. Their famous paper in Nature began: "We wish to suggest a structure for the salt of deoxyribose nucleic acid (D.N.A.)."
Chapter Topics
2.1 Nucleotide Structure
The building blocks: purines, pyrimidines, sugars, and phosphates
2.2 The Double Helix
Watson-Crick model, base pairing rules, antiparallel strands
2.3 DNA Conformations
A-DNA, B-DNA, Z-DNA and their biological significance
2.4 DNA Topology
Supercoiling, linking number, topoisomerases
2.5 Chromatin Structure
Nucleosomes, histones, higher-order packaging
DNA Chemical Components
DNA is a polymer composed of repeating units called nucleotides. Each nucleotide consists of three components:
1. Nitrogenous Base
The information-carrying component
Purines: Adenine (A), Guanine (G)
Pyrimidines: Cytosine (C), Thymine (T)
2. Deoxyribose Sugar
5-carbon pentose sugar
β’ Missing 2'-OH group
β’ More stable than ribose
β’ Connects base to backbone
3. Phosphate Group
Links nucleotides together
β’ Creates 5'β3' polarity
β’ Negative charge
β’ Phosphodiester bonds
The Phosphodiester Bond
Nucleotides are linked via phosphodiester bonds between the 5' phosphate of one nucleotide and the 3' hydroxyl of the next. This creates the sugar-phosphate backbone with inherent directionality (5'β3'), which is crucial for replication and transcription.
The Four DNA Bases
Purines (Two-Ring Structure)
Adenine (A)
6-aminopurine
- β’ Pairs with Thymine (2 H-bonds)
- β’ Amino group at C6 position
- β’ Found in ATP, NAD+, FAD
Guanine (G)
2-amino-6-oxopurine
- β’ Pairs with Cytosine (3 H-bonds)
- β’ Amino at C2, carbonyl at C6
- β’ Found in GTP, cGMP
Pyrimidines (One-Ring Structure)
Cytosine (C)
4-amino-2-oxopyrimidine
- β’ Pairs with Guanine (3 H-bonds)
- β’ Can be methylated (5-mC)
- β’ Prone to deamination β Uracil
Thymine (T)
5-methyl-2,4-dioxopyrimidine
- β’ Pairs with Adenine (2 H-bonds)
- β’ Methylated C5 (vs. Uracil in RNA)
- β’ DNA-specific base
DNA Structure Overview
Key Dimensions (B-DNA)
| Helix diameter | 2.0 nm (20 Γ ) |
| Rise per base pair | 0.34 nm (3.4 Γ ) |
| Base pairs per turn | 10.5 |
| Helical pitch | 3.4 nm (34 Γ ) |
| Major groove width | ~22 Γ |
| Minor groove width | ~12 Γ |
Base Pairing Rules
Adenine-Thymine pair
Guanine-Cytosine pair
Chargaff's Rules:
β’ [A] = [T] and [G] = [C]
β’ [Purines] = [Pyrimidines]
β’ A+T/G+C ratio varies by species
Watson-Crick Base Pairing
The specific base pairing (A-T and G-C) is determined by the geometry of hydrogen bond donors and acceptors on the bases. A purine always pairs with a pyrimidine, maintaining the constant helix diameter. The three hydrogen bonds in G-C pairs make them stronger than A-T pairs, affecting DNA melting temperature and stability.
Forces Stabilizing DNA Structure
1. Hydrogen Bonds
Between complementary bases (A-T: 2 bonds, G-C: 3 bonds). Each bond contributes ~2-3 kcal/mol. While individually weak, the cumulative effect of millions of base pairs provides significant stability.
2. Base Stacking (Ο-Ο Interactions)
The primary stabilizing force. Aromatic rings of adjacent bases stack atop each other, creating van der Waals interactions and hydrophobic effects. Contributes more to stability than hydrogen bonding. Each stack contributes ~5-10 kcal/mol.
3. Hydrophobic Effect
The hydrophobic bases are buried in the interior of the helix, away from water. The hydrophilic sugar-phosphate backbone faces the aqueous environment. This arrangement is thermodynamically favorable.
4. Ionic Interactions
Cations (MgΒ²βΊ, KβΊ, NaβΊ, polyamines) neutralize the negative charges of the phosphate backbone, reducing electrostatic repulsion between the two strands. DNA is a polyanion with one negative charge per nucleotide.
DNA Conformational Forms
| Property | A-DNA | B-DNA | Z-DNA |
|---|---|---|---|
| Helix sense | Right-handed | Right-handed | Left-handed |
| Diameter | 26 Γ | 20 Γ | 18 Γ |
| Rise per bp | 2.6 Γ | 3.4 Γ | 3.7 Γ |
| Base pairs per turn | 11 | 10.5 | 12 |
| Helical pitch | 28 Γ | 34 Γ | 45 Γ |
| Major groove | Narrow, deep | Wide, deep | Flat |
| Minor groove | Wide, shallow | Narrow, deep | Narrow, deep |
| Conditions | Low humidity, RNA-DNA | Physiological | High salt, GC-rich |
A-DNA
Found in dsRNA and RNA-DNA hybrids. Compact, dehydrated form.
B-DNA
Most common form in cells. Watson-Crick model represents B-DNA.
Z-DNA
Left-handed helix. May regulate transcription at promoter regions.
DNA Melting and Stability
DNA melting (denaturation) is the separation of the two strands when heated. The melting temperature (Tm)is the temperature at which 50% of the DNA is double-stranded.
Melting Temperature Calculation
For short oligonucleotides (<20 bp):
This rule works well for simple estimation of primer Tm
Factors Increasing Tm
- β’ Higher G-C content (3 H-bonds)
- β’ Longer DNA length
- β’ Higher salt concentration
- β’ Presence of MgΒ²βΊ
- β’ Circular vs. linear DNA
Factors Decreasing Tm
- β’ Lower G-C content
- β’ Denaturants (urea, formamide)
- β’ Mismatches in sequence
- β’ Organic solvents
- β’ Low ionic strength
DNA Topology: Supercoiling
DNA in cells is not a simple linear moleculeβit is supercoiled, meaning the double helix is itself twisted into a higher-order structure.
The Linking Number Equation
Linking Number
Number of times strands wrap
Twist
Helical winding of strands
Writhe
Superhelical coiling
Negative Supercoiling
Underwound DNA (Lk < Lkβ). Common in most organisms. Facilitates strand separation for replication and transcription. Created by DNA gyrase.
Positive Supercoiling
Overwound DNA (Lk > Lkβ). Found in some extremophiles. Generated ahead of replication forks. Removed by topoisomerases.
Chromatin: DNA Packaging
The human genome contains ~3.2 billion base pairs, stretching ~2 meters if fully extended. To fit into a nucleus ~6 ΞΌm in diameter, DNA must be compacted ~10,000-fold. This is achieved through hierarchical packaging into chromatin.
Nucleosome (11 nm fiber)
147 bp of DNA wrapped 1.65 turns around histone octamer (H2A, H2B, H3, H4 Γ 2)
Chromatin Fiber (30 nm)
Nucleosomes fold into higher-order structure, stabilized by H1 linker histone
Chromatin Loops (300 nm)
30 nm fiber forms loops attached to protein scaffold
Metaphase Chromosome (1400 nm)
Maximum compaction during cell division; visible under light microscope
Compaction Ratio
Relaxed DNA β Metaphase chromosome: ~10,000Γ compaction
Interphase nucleus: ~1,000Γ compaction (allows transcription)
Key Equations and Values
Molecular Weight of DNA
Average MW per nucleotide ~330 daltons
Length of DNA
Each base pair rises 0.34 nm (3.4 Γ ) along the helix
Number of Helical Turns
B-DNA has 10.5 bp per turn
Human Genome Size
Per diploid cell (23 chromosome pairs)
Learning Objectives
After completing Part 2, you should be able to:
- βDescribe the chemical structure of nucleotides and nucleic acids
- βExplain Watson-Crick base pairing and Chargaff's rules
- βCompare different DNA conformations (A, B, Z forms)
- βCalculate DNA length, molecular weight, and helical turns
- βIdentify forces that stabilize the double helix
- βUnderstand DNA topology and supercoiling
- βExplain the linking number equation (Lk = Tw + Wr)
- βDescribe the role of topoisomerases
- βOutline chromatin organization and nucleosome structure
- βCalculate DNA melting temperature
Clinical Relevance
Topoisomerase Inhibitors
Anticancer drugs (doxorubicin, etoposide, topotecan) and antibiotics (ciprofloxacin) target topoisomerases, blocking DNA replication in rapidly dividing cells or bacteria.
DNA Repair Disorders
Defects in DNA structure recognition lead to diseases like Xeroderma Pigmentosum and Werner Syndrome. Understanding DNA chemistry is key to developing treatments.
Epigenetics
DNA methylation and histone modifications alter chromatin structure without changing the sequence, affecting gene expression in development and disease.
PCR and Diagnostics
Understanding DNA melting and annealing is essential for PCR primer design, used in genetic testing, pathogen detection, and forensics.