DNA Double Helix Structure
The DNA double helix is the molecular basis of heredity. Its structure — discovered by Watson and Crick in 1953 using X-ray diffraction data from Franklin and Wilkins — explains how genetic information is stored, copied, and expressed. The 13 structures shown are central to AP Biology Units 3 and 6 (Gene Expression and Genetics).
Sugar-Phosphate Backbone
The outer rails of the twisted-ladder structure — alternating deoxyribose sugars and phosphate groups linked by covalent phosphodiester bonds. Two antiparallel backbones spiral around each other; the backbones are hydrophilic and face the aqueous environment.
Deoxyribose Sugar
A 5-carbon pentose sugar at the core of each nucleotide. Deoxyribose lacks the 2′-hydroxyl group present in ribose (RNA's sugar), making DNA more chemically stable. Each sugar connects to one phosphate group and one nitrogenous base.
Phosphate Group
A negatively charged phosphate ion (\(\ce{PO4^3-}\)) that bridges adjacent sugars via phosphodiester bonds. The negative charge gives the DNA backbone its overall negative charge, enabling binding to positively charged histone proteins and migration toward the positive pole in gel electrophoresis.
Nitrogenous Base
A nitrogen-containing ring compound that projects inward from each sugar toward the helix axis. Bases pair with complementary bases on the opposite strand via hydrogen bonds. Purines (A, G) have two fused rings; pyrimidines (T, C) have one ring. Base stacking between adjacent pairs contributes significantly to helix stability.
Adenine (A)
A purine base that pairs with Thymine via 2 hydrogen bonds (A=T). Adenine is found in both DNA and RNA (where it pairs with Uracil). It is also the core of ATP and NAD⁺, making it central to energy metabolism.
Thymine (T)
A pyrimidine base found only in DNA (not RNA). Thymine pairs with Adenine via 2 hydrogen bonds. RNA uses Uracil (U) in place of Thymine. The methyl group on Thymine that distinguishes it from Uracil provides an additional level of DNA stability.
Guanine (G)
A purine base that pairs with Cytosine via 3 hydrogen bonds (G≡C). The extra hydrogen bond makes G-C-rich DNA regions more resistant to thermal denaturation. Guanine is present in both DNA and RNA.
Cytosine (C)
A pyrimidine base that pairs with Guanine via 3 hydrogen bonds. Cytosine can be methylated (5-methylcytosine) at CpG dinucleotides — a key epigenetic modification that typically silences gene expression without altering the DNA sequence.
Hydrogen Bonds
Noncovalent attractions between complementary bases: 2 for A-T pairs, 3 for G-C pairs. Individually weak, but collectively the thousands of hydrogen bonds along a DNA molecule provide stability while still allowing strand separation by helicase during replication and by RNA polymerase during transcription.
Major Groove
The wider (~22 Å) gap that spirals along the outside of the helix. The major groove exposes the edges of base pairs, enabling transcription factors, repressors, and other regulatory proteins to recognize specific DNA sequences without unwinding the helix — the structural basis of gene regulation.
Minor Groove
The narrower (~12 Å) gap alternating with the major groove. Less accessible for sequence-specific protein binding, but targeted by certain antibiotics and DNA-staining dyes (e.g., Hoechst 33258). Some structural proteins bind in the minor groove.
3′ End
The strand terminus bearing a free 3′ hydroxyl (-OH) group on the deoxyribose. DNA polymerase adds new nucleotides exclusively to the 3′-OH, meaning synthesis always proceeds 5′→3′. The 3′ end is the growing tip of the new strand during replication.
5′ End
The strand terminus bearing a free 5′ phosphate group. DNA and RNA sequences are written 5′→3′ by convention. In mRNA, the 5′ end receives the 5′ cap that stabilizes the transcript and facilitates ribosome binding during translation.