DNA structure and replication
How DNA was identified as the genetic material, the double helix and base pairing, Chargaff's rules, semi-conservative replication, and PCR sums.
On this page
Every trait a breeder selects, every gene edited, every DNA marker used to identify a variety or a pathogen comes down to one molecule: deoxyribonucleic acid (DNA). Its structure, two strands wound into a double helix and held together by paired bases, explains both how genetic information is stored and how it is copied each time a cell divides.
DNA structure and replication are core topics in genetics, molecular biology and biotechnology courses, and the foundation for modern breeding tools.
How DNA was shown to be the genetic material
- 1869: Friedrich Miescher isolated "nuclein" from cell nuclei.
- 1928: Frederick Griffith found that a harmless strain of Streptococcus pneumoniae became deadly after mixing with heat-killed virulent bacteria: something had "transformed" it.
- 1944: O. T. Avery, C. M. MacLeod and M. McCarty showed that the transforming principle was DNA, not protein.
- 1952: A. D. Hershey and M. Chase showed, using radioactive labels, that a bacteriophage injects its DNA, not its protein coat, into bacteria.
- 1950: Erwin Chargaff found that in DNA the amount of adenine equals thymine, and guanine equals cytosine.
- 1952–53: X-ray diffraction images from Rosalind Franklin and Maurice Wilkins, with Chargaff's rules, allowed James Watson and Francis Crick to propose the double helix in 1953.
The structure of DNA
DNA is a polymer of nucleotides. Each nucleotide has three parts:
- a five-carbon sugar, deoxyribose;
- a phosphate group;
- one of four bases: the purines adenine (A) and guanine (G), with two rings, and the pyrimidines cytosine (C) and thymine (T), with one ring.
Nucleotides are linked by phosphodiester bonds between the 3′ carbon of one sugar and the 5′ carbon of the next, forming a sugar–phosphate backbone with a direction, from 5′ to 3′.
The Watson–Crick model:
- Two strands wind around each other in a right-handed double helix.
- The strands are antiparallel: one runs 5′ to 3′, the other 3′ to 5′.
- Bases pair inside: A with T by two hydrogen bonds, G with C by three. A purine always pairs with a pyrimidine, keeping the helix a constant width of about 2 nm.
- The common B form has about 10 base pairs per turn (about 10.5 in solution), a turn every 3.4 nm, so neighbouring base pairs are 0.34 nm apart.
- The helix has a major groove and a minor groove, where proteins read the sequence.
Because the strands are complementary, each can serve as a template for the other.
RNA differs
RNA has the sugar ribose, uses uracil (U) instead of thymine, and is usually single-stranded.
DNA in plant cells
In the nucleus, DNA wraps around histone proteins in nucleosomes (about 147 base pairs per histone octamer), which coil further into chromatin and chromosomes. Chloroplasts and mitochondria have their own small, usually circular genomes. Plant nuclear genome sizes vary hugely: about 135 million base pairs (Mb) in Arabidopsis, about 400 Mb in rice, about 2,300 Mb in maize, and about 16,000 Mb in bread wheat, most of it repetitive DNA.
Replication
Semi-conservative copying
Watson and Crick suggested that each strand serves as a template for a new partner. In 1958, M. Meselson and F. Stahl proved it: they grew bacteria on heavy nitrogen (15N), switched them to normal 14N, and separated DNA by density. After one generation, all DNA was of intermediate density; after two, half intermediate and half light. Each new double helix keeps one old and one new strand: replication is semi-conservative.
The replication fork
Replication starts at origins of replication: one in a bacterial chromosome, thousands in a plant chromosome. The main players:
- Helicase unwinds the double helix, and single-strand binding proteins keep the strands apart.
- Topoisomerases relieve the twisting ahead of the fork (DNA gyrase in bacteria).
- Primase makes a short RNA primer, because DNA polymerases cannot start a strand from scratch.
- DNA polymerase adds nucleotides to the 3′ end of the growing strand, so new DNA is always made 5′ to 3′. In E. coli, polymerase III does most of the copying and polymerase I replaces the primers with DNA; eukaryotes use polymerases α, δ and ε.
- Because the two template strands are antiparallel, the leading strand is made continuously toward the fork, while the lagging strand is made in short Okazaki fragments (discovered by Reiji and Tsuneko Okazaki in 1968) away from the fork.
- DNA ligase joins the fragments.
Accuracy
DNA polymerases proofread, removing wrongly paired bases with a 3′ to 5′ exonuclease activity, and mismatch repair corrects most remaining errors, bringing the error rate to about one in a billion or fewer per base copied.
Telomeres
Linear chromosomes lose a little DNA at their ends each round, because the final lagging-strand primer cannot be replaced. Repeated sequences called telomeres, maintained by the enzyme telomerase, protect the genes.
Three DNA calculations
Chargaff's rules. A DNA sample is 22 per cent guanine. Since G = C, cytosine is 22 per cent; A + T = 100 − 44 = 56 per cent, so A = T = 28 per cent.
Length of a genome. The haploid bread wheat genome has about 16 × 109 base pairs. At 0.34 nm per base pair: 16 × 109 × 0.34 nm = 5.4 × 109 nm = about 5.4 metres of DNA, packed into a nucleus a few micrometres across.
PCR. The polymerase chain reaction (invented by Kary Mullis in 1983) copies a DNA segment with a heat-stable polymerase, doubling the target each cycle. Starting from 1 copy, 30 cycles give 230 ≈ 1.07 × 109 copies. In practice efficiency is below 100 per cent: at 90 per cent efficiency, 30 cycles give 1.930 ≈ 2.3 × 108 copies.
Why it matters for agriculture
- DNA markers and sequencing identify varieties, track genes in breeding and diagnose pests and diseases.
- PCR-based tests detect pathogens, GMOs and food adulteration.
- Genetic engineering and genome editing rely on cutting, copying and joining DNA.
- Seed purity and variety protection use DNA fingerprints.
Key points
- DNA was proved to be the genetic material by Avery, MacLeod and McCarty (1944) and Hershey and Chase (1952).
- Watson and Crick (1953): antiparallel, right-handed double helix; A–T (two hydrogen bonds), G–C (three); about 10 bp and 3.4 nm per turn; 2 nm wide.
- Chargaff's rules: A = T and G = C.
- Replication is semi-conservative (Meselson and Stahl, 1958) and runs 5′ to 3′.
- Helicase, primase, DNA polymerase and ligase; leading strand continuous, lagging strand in Okazaki fragments.
- Proofreading and repair keep errors to about one in a billion bases.
What the exams ask
- School-leaving and entrance papers: the structure of a nucleotide, base pairing, the double helix, and differences between DNA and RNA.
- Degree and research-fellowship entrances: the experiments proving DNA is genetic material, Chargaff's rules, the Meselson–Stahl experiment, enzymes of replication, Okazaki fragments, and telomeres.
- Biotechnology examinations: PCR, sequencing, markers, and calculations from base composition and genome size.
Described in general terms: the kind of examination, not a past paper. Laisha never reproduces exam questions.
Questions people ask
Why is DNA copied in pieces on one strand?
DNA polymerase can only add nucleotides to a 3′ end. As the fork opens, one template allows continuous synthesis toward the fork, but the other must be copied backwards in short fragments that are later joined.
Why does G–C content matter?
G–C pairs have three hydrogen bonds and stack more strongly, so DNA rich in G and C needs higher temperatures to separate. This matters in PCR and in designing markers.
Do chloroplasts have their own DNA?
Yes, a small circular genome of roughly 120,000 to 160,000 base pairs in most plants, inherited usually through the mother, a relic of their origin as free-living cyanobacteria.
Sources
- Watson, J. D. and Crick, F. H. C. "Molecular structure of nucleic acids: a structure for deoxyribose nucleic acid." Nature 171, 737–738 (1953).
- Avery, O. T., MacLeod, C. M. and McCarty, M. "Studies on the chemical nature of the substance inducing transformation of pneumococcal types." Journal of Experimental Medicine 79, 137–158 (1944).
- Meselson, M. and Stahl, F. W. "The replication of DNA in Escherichia coli." Proceedings of the National Academy of Sciences 44, 671–682 (1958).
- Alberts, B. et al. Molecular Biology of the Cell, 7th edition. W. W. Norton, 2022.
- Watson, J. D. et al. Molecular Biology of the Gene, 7th edition. Pearson, 2014.
More in genetics and plant breeding
Discussion
Questions, corrections and notes from readers on this article. Every comment is checked before it appears: keep it on the topic, and do not share phone numbers, links or contact details.