DNA Structure: The Double Helix and Nucleotides
DNA (deoxyribonucleic acid) is a double helix made of two strands of nucleotides, each containing a sugar, a phosphate group and one of four bases (adenine, thymine, cytosine and guanine), with the strands held together by complementary base pairing. In brief: adenine always pairs with thymine (A–T) through two hydrogen bonds, and cytosine always pairs with guanine (C–G) through three. The sugar-phosphate backbone is on the outside, and the base pairs are stacked inside like the steps of a twisted ladder. The sequence of bases carries the genetic information.
The structure of DNA explains how genetic information is stored, copied and passed on. This guide explains the parts of a nucleotide, how nucleotides join into strands, the rules of complementary base pairing, the features of the double helix, works through base-counting examples and corrects common mistakes.
What is a nucleotide?
Nucleotides are the monomers of nucleic acids. Each DNA nucleotide has three components.
- A phosphate group (PO₄³⁻), which carries a negative charge.
- A deoxyribose sugar, a five-carbon sugar. The carbons are numbered 1′ to 5′ (read “one prime”). The “deoxy” means that it has one less oxygen than ribose, the sugar in RNA.
- A nitrogenous base: one of four types. Adenine (A) and guanine (G) are purines, with a double-ring structure. Cytosine (C) and thymine (T) are pyrimidines, with a single ring.
The base is attached to the 1′ carbon of the sugar, and the phosphate is attached to the 5′ carbon.
How is a DNA strand built?
Nucleotides are linked in a chain by phosphodiester bonds, which are covalent bonds between the phosphate of one nucleotide and the 3′ carbon of the sugar of the next. This forms the sugar-phosphate backbone, a strong, repeating structure. The bases stick out from the backbone and are the part that carries the information.
A strand has direction. One end has a free phosphate on the 5′ carbon (the 5′ end), and the other end has a free hydroxyl on the 3′ carbon (the 3′ end). The two strands in the double helix run in opposite directions, which is called antiparallel.
What is complementary base pairing?
The bases on one strand pair with bases on the other by hydrogen bonds. The pairing is specific, because of the shape and the arrangement of hydrogen-bond donors and acceptors, and because a purine always pairs with a pyrimidine, so the width of the double helix is constant (about 2 nanometers).
- Adenine (A) pairs with thymine (T) by two hydrogen bonds.
- Cytosine (C) pairs with guanine (G) by three hydrogen bonds.
A DNA region with more C–G pairs is more stable and needs more heat to separate the strands (it has a higher melting temperature). Complementary base pairing makes it possible to copy DNA accurately, because each strand can serve as a template for a new strand. It also allows the information in DNA to be transcribed into RNA.
What is the double helix?
The two antiparallel strands coil around each other to form a right-handed double helix. One full turn is about 3.4 nanometers long and contains about 10 base pairs, so the distance between the base pairs is about 0.34 nanometers. The backbones are on the outside, which allows the charged phosphates to interact with water, and the bases are on the inside, stacked on each other and held together by hydrogen bonds, and by hydrophobic interactions between the stacked bases. The helix has a wider major groove and a narrower minor groove, where proteins can bind to recognize particular sequences.
A human cell contains about 3.2 billion base pairs in a haploid set of chromosomes. If the DNA of one diploid cell were stretched out, it would be about 2 meters long (6.4 billion base pairs × 0.34 nm ≈ 2.2 m), but it fits in a nucleus about 6 micrometers across, by being tightly coiled.
DNA and RNA compared
| Feature | DNA | RNA |
|---|---|---|
| Sugar | Deoxyribose | Ribose |
| Bases | A, T, C, G | A, U, C, G |
| Strands | Two (double helix) | Usually one |
| Stability | Very stable | Less stable |
| Main role | Stores genetic information | Protein synthesis and regulation |
| Location in eukaryotes | Mainly nucleus (also mitochondria, chloroplasts) | Nucleus and cytoplasm |
Worked example: base pairing and Chargaff’s rules
Example 1: writing the complementary strand
One strand of DNA reads 5′-ATGCCGTT-3′. Find the complementary strand.
- Pair each base in order: A with T, T with A, G with C, C with G, C with G, G with C, T with A, T with A.
- Because the strands are antiparallel, the new strand is written underneath in the opposite direction: 3′-TACGGCAA-5′.
- To write it in the usual 5′ to 3′ direction, read it from right to left: 5′-AACGGCAT-3′.
The two forms describe the same strand. The key rule is that the complementary strand runs in the opposite direction, so its 3′ end faces the 5′ end of the original strand. A reliable check is that the new strand has the same number of bases, and that every column pairs A–T or C–G.
Example 2: Chargaff’s rules
Erwin Chargaff found in the late 1940s that in DNA, the amount of A equals the amount of T, and the amount of C equals the amount of G. Suppose a sample of double-stranded DNA is 30 percent adenine. What are the percentages of the other bases?
- A = 30 percent, so T = 30 percent.
- A + T = 60 percent, leaving 40 percent for C + G.
- C = G, so each is 20 percent.
The totals add to 30 + 30 + 20 + 20 = 100 percent. The proportion of A + T versus G + C varies between species, but the A = T and C = G rule applies to every double-stranded DNA.
How is DNA packaged in cells?
In eukaryotes, DNA is wrapped around histone proteins to form beadlike units called nucleosomes. These are coiled further into chromatin fibers, which are condensed during cell division into visible chromosomes. In prokaryotes, the circular DNA is supercoiled and organized in the nucleoid. Mitochondria and chloroplasts have their own circular DNA.
How was the structure discovered?
Friedrich Miescher isolated DNA in 1869. In 1944 Oswald Avery, Colin MacLeod and Maclyn McCarty showed that DNA is the genetic material. Alfred Hershey and Martha Chase confirmed this in 1952 using bacteriophages. Rosalind Franklin and Raymond Gosling produced X-ray diffraction images of DNA, including “Photo 51”, in 1952, and Maurice Wilkins also worked on X-ray studies. James Watson and Francis Crick proposed the double-helix model in Nature in April 1953, and Watson, Crick and Wilkins received the Nobel Prize in Physiology or Medicine in 1962. Franklin had died in 1958, and the Nobel Prize is not given posthumously. The contribution of her data is now widely recognized.
Which mistakes are common?
Mistake 1: Pairing A with G or C with T
A pairs with T, and C pairs with G. Purines pair with pyrimidines.
Mistake 2: Using uracil in DNA
Uracil is found in RNA. In DNA, thymine pairs with adenine.
Mistake 3: Forgetting that strands are antiparallel
The two strands run in opposite directions: one 5′ to 3′ and the other 3′ to 5′.
Mistake 4: Saying that hydrogen bonds hold the backbone together
The backbone is held by covalent phosphodiester bonds. Hydrogen bonds link the bases between strands.