Table of Contents
Overview: What Makes DNA Special?
Deoxyribonucleic acid (DNA) is the molecule in almost all living organisms that stores hereditary (genetic) information. In this chapter, the focus is on its structure—how DNA is built at the molecular level and how this structure makes it suitable as a stable, copyable information carrier.
Higher-level concepts like “nucleic acids as carriers of genetic information” and how information in DNA becomes proteins (gene expression, genetic code) are covered in other chapters. Here we concentrate on the physical and chemical architecture of DNA.
Chemical Building Blocks of DNA
Nucleotides: The Basic Units
DNA is a polynucleotide: a long chain made of many repeating units called nucleotides.
Each DNA nucleotide has three components:
- A phosphate group (phosphoric acid residue)
- A sugar: 2-deoxyribose
- A nitrogenous base (a “base” for short)
The general structure can be represented as:
- Sugar–phosphate backbone (repeating pattern)
- Bases projecting from the sugar, like letters attached to a string
The Sugar: 2-Deoxyribose
The sugar in DNA is a 5-carbon (pentose) sugar called 2-deoxyribose.
- “Deoxy” means that at the 2′-carbon (C2′) there is a hydrogen instead of a hydroxyl group (–OH) as in ribose (RNA’s sugar).
- This missing OH group makes DNA more chemically stable than RNA.
Carbons in the sugar are numbered 1′ to 5′:
- C1′: attached to the base
- C3′: carries a hydroxyl group (–OH) that can form bonds with the next nucleotide
- C5′: linked to the phosphate group
The Phosphate Group
The phosphate group:
- Connects the 5′ carbon of one sugar to the 3′ carbon of the next sugar,
- Gives DNA its negative charge (due to ionized phosphate groups),
- Forms part of the sugar–phosphate “backbone” that is on the outside of the helix.
The Nitrogenous Bases
There are four different bases in DNA:
- Purines (two-ring structures)
- Adenine (A)
- Guanine (G)
- Pyrimidines (one-ring structures)
- Cytosine (C)
- Thymine (T)
The base type defines the nucleotide:
- A nucleotide with adenine is a deoxyadenosine monophosphate (dAMP), and similarly for others (dGMP, dCMP, dTMP).
These bases store information through their sequence along the DNA strand.
Nucleosides vs. Nucleotides
Two related terms are important:
- Nucleoside = base + sugar (no phosphate)
- e.g., deoxyadenosine (adenine + deoxyribose)
- Nucleotide = base + sugar + phosphate
- e.g., deoxyadenosine monophosphate (dAMP)
DNA strands are made of nucleotides linked together; nucleosides are intermediates and naming units in biochemistry.
How Nucleotides Join: The Sugar–Phosphate Backbone
Phosphodiester Bonds
Neighboring nucleotides in a single DNA strand are joined via phosphodiester bonds:
- The phosphate group of one nucleotide forms covalent bonds with:
- The 3′-OH group of one sugar
- The 5′-OH group of the next sugar
This creates a repeating structure:
$$
\text{(sugar)}\;-\;\text{phosphate}\;-\;\text{(sugar)}\;-\;\text{phosphate}\;-\;\dots
$$
with bases sticking out from the sugars.
This is called the sugar–phosphate backbone:
- Strong covalent bonds protect the linear order of bases,
- The backbone is the same regardless of the base; only the bases vary.
Directionality: 5′ to 3′
Because the backbone is asymmetric (5′ end vs. 3′ end), each strand has a direction:
- The 5′ end usually has a free phosphate group at the 5′ carbon.
- The 3′ end usually has a free hydroxyl group at the 3′ carbon.
DNA sequences are conventionally written from 5′ to 3′, for example:
- 5′–A T G C C A–3′
This directionality is crucial for DNA replication and transcription, but here it primarily defines the structural orientation of the polymer.
Double-Stranded Structure: The Double Helix
Two Strands Running Antiparallel
In cells, DNA usually exists as a double-stranded molecule: two polynucleotide strands wound around each other.
Key features:
- The strands run in opposite directions (antiparallel):
- One strand is 5′ → 3′
- The other is 3′ → 5′
- The sugar–phosphate backbones are on the outside.
- The bases point inward and pair with bases of the opposite strand.
The general structural model is a right-handed double helix, often called B-DNA (the most common form in cells under normal conditions).
Complementary Base Pairing
Bases from opposite strands pair in a very specific way through hydrogen bonds:
- Adenine (A) pairs with Thymine (T)
- Guanine (G) pairs with Cytosine (C)
Thus:
- A–T pair: typically 2 hydrogen bonds
- G–C pair: typically 3 hydrogen bonds
These pairs are called complementary base pairs.
Rules:
- Purine always pairs with pyrimidine.
- A DNA strand’s sequence determines the complementary strand uniquely.
If one strand is:
- 5′–A G C T T A–3′
The complementary strand is:
- 3′–T C G A A T–5′
Chargaff’s Rules
In double-stranded DNA:
- The amount of A ≈ amount of T
- The amount of G ≈ amount of C
So:
$$
\%A \approx \%T,\quad \%G \approx \%C
$$
Total base composition varies by species, but these relationships hold for typical double-stranded DNA. This reflects the complementary base-pairing structure.
Stability of the Double Helix
Several interactions stabilize the helix:
- Hydrogen bonds between complementary bases
- Many weak bonds together create strong overall stability.
- Base stacking interactions
- Bases are flat, aromatic rings.
- They stack like coins, interacting via hydrophobic interactions and van der Waals forces.
- Hydrophilic backbone facing outward
- Sugar–phosphate backbone is polar and interacts well with water and ions.
- Bases are relatively hydrophobic and are shielded inside.
Regions rich in G–C pairs:
- Have more hydrogen bonds per base pair (3 vs. 2),
- Tend to be more thermally stable than A–T-rich regions.
Helix Geometry: Major and Minor Grooves
The double helix is not perfectly symmetrical. The way the base pairs attach to the sugars creates two grooves:
- A major groove
- A minor groove
These grooves:
- Run along the helix,
- Expose edges of the bases to the outside.
Many proteins that interact with DNA (like transcription factors and other DNA-binding proteins) “read” the sequence by fitting into these grooves, especially the major groove, where more chemical information (patterns of hydrogen bond donors/acceptors) is accessible.
Different Structural Forms of DNA
While B-DNA is the standard structure in most cellular conditions, DNA can adopt alternative conformations:
- B-DNA
- Right-handed helix
- ~10 base pairs per turn
- Most common in cells
- A-DNA
- Right-handed, shorter and wider than B-DNA
- Occurs under conditions with lower water content
- DNA–RNA hybrids and double-stranded RNA often resemble A-form
- Z-DNA
- Left-handed helix
- Zig-zag sugar–phosphate backbone
- Forms in certain sequences (often alternating purine–pyrimidine, e.g., CGCGCG) and conditions
These forms can influence how proteins recognize and interact with DNA.
DNA Topology: Linear, Circular, and Supercoiled DNA
Linear vs. Circular DNA
Depending on the organism and genetic element, DNA molecules can differ in overall shape:
- Linear DNA:
- Typical for eukaryotic chromosomes.
- Circular DNA:
- Typical for bacterial chromosomes, plasmids, and many organelle genomes (e.g., mitochondria, chloroplasts).
Supercoiling
Long DNA molecules rarely exist as simple, relaxed helices; they are often supercoiled:
- Supercoiling = additional twisting of the double helix upon itself, like an over- or underwound telephone cord.
- Enzymes called topoisomerases manage supercoiling (introducing or removing twists).
Supercoiling:
- Compacts DNA so it can fit inside cells,
- Influences accessibility of DNA for replication and transcription (more or less tightly wound).
DNA as a Stable Yet Copyable Information Carrier
Although detailed mechanisms of replication and expression are covered elsewhere, certain structural features are directly related to DNA’s role as a hereditary material:
- Complementary strands:
- Each strand contains all information needed to reconstruct its partner.
- Enables semi-conservative replication (each new DNA molecule has one old and one new strand).
- Specific base pairing:
- Guarantees accurate copying of information (A with T, G with C).
- Stable covalent backbone:
- Protects the order of bases from random breakage.
- Double-stranded nature:
- Provides a template and a backup for sequence information.
These properties arise directly from the structural organization discussed in this chapter.
Summary of Key Structural Features
- DNA is a double-stranded polynucleotide with a sugar–phosphate backbone and four kinds of bases: A, T, G, C.
- Nucleotides are linked by 3′–5′ phosphodiester bonds, giving each strand a defined 5′ → 3′ direction.
- Two antiparallel strands form a right-handed double helix (B-DNA) stabilized by complementary base pairing (A–T, G–C), hydrogen bonds, and base stacking.
- The double helix has major and minor grooves where proteins can bind and recognize sequences.
- DNA can be linear or circular and often exists in supercoiled forms.
- The specific, complementary, and stable structure of DNA underlies its ability to store and faithfully transmit genetic information.