Every instruction in a living thing’s DNA is written with just four chemical letters, the same four in bacteria, oak trees and people.1PubMed Central. Efficient and sequence-independent replication of DNA containing a third base pair establishes a functional six-letter genetic alphabet Because there are so few, the rule that governs them is short: each letter has exactly one partner on the opposite strand. That means one strand always tells you exactly what the other says, which is what lets cells copy their genes. Scientists have also built working extra letters in the lab, showing the four natural ones are not the only possible chemistry.2PubMed Central. Efficient and sequence-independent replication of DNA containing a third base pair establishes a functional six-letter genetic alphabet
Meet the Four Letters A, T, G and C
Each letter stands for a small molecule called a base. A is adenine, T is thymine, G is guanine and C is cytosine. Every base hangs off a backbone of sugar and phosphate, and the order of the bases along that backbone spells out genetic information. One copy of the human genome in a single cell carries about 3 billion of these letters.
The letters come in two sizes. Adenine and guanine are purines, larger molecules built from two joined rings.3Pathwayz. What Are the Four DNA Letters and Their Pairing Rules? Cytosine and thymine are pyrimidines, smaller molecules with a single ring.4Pathwayz. What Are the Four DNA Letters and Their Pairing Rules? So every pair across the helix joins one big letter with one small one.
A DNA “word” is just a stretch of these letters, such as ATGGCT along one strand. A letter alone carries almost no meaning. Order is everything, much as the order of letters makes words in a sentence, and swapping or moving letters changes the message. Later, groups of three letters become instructions for building proteins. When an ancestry or medical test reports a result, it is telling you which letter sits at particular spots along the DNA.
It’s easy to mix up letters, genes and chromosomes. A letter is one base. A gene is a long stretch of letters with one job. A chromosome is a huge strand of DNA holding many genes.
The Pairing Rules A With T and G With C
In double-stranded DNA, the amount of G always equals the amount of C, and the amount of A equals the amount of T.5Journal of Biological Chemistry. Chargaff’s Rules: the Work of Erwin Chargaff Yet the overall mix of letters differs from one species to another.6Journal of Biological Chemistry. Chargaff’s Rules: the Work of Erwin Chargaff The partnership is A with T and G with C, often called Watson-Crick pairing after the scientists who described the double helix.7PubMed. True stabilization energies for the optimal planar hydrogen-bonded and stacked structures of guanine…cytosine, adenine…thymine, and their 9- and 1-methyl derivatives: complete basis set calculations at the MP2 and CCSD(T) levels and comparison with experiment
The two strands twist around each other, with the pairs forming the rungs of a twisted ladder. If one strand reads ATGC, the strand opposite reads TACG.
To work out a partner strand, go letter by letter: replace each A with T, each T with A, each G with C and each C with G. GGATCC becomes CCTAGG. You can check your work because every A on one strand should line up with a T on the other. In a real helix the partner strand runs in the opposite direction, so a textbook may write it reversed. Homework usually asks only for the letter-by-letter swap, so follow what the question asks.
The equal-amounts rule also solves percentage problems. If a sample is 30% A, it must also be 30% T, which together make 60%. The remaining 40% is shared equally between G and C, so each is 20%. This shortcut only works for double-stranded DNA. A single strand has no partner, so its A and T amounts need not match.
Why A Fits T and G Fits C
Partners are held together by hydrogen bonds, weak attractions between atoms on facing bases. A and T form two of these weak links between letters, while G and C form three.8PubMed Central. Prebiotic competition and evolution in self-replicating polynucleotides can explain the properties of DNA/RNA in modern living systems That is why a G–C pair holds about twice as tightly as an A–T pair, roughly 29 versus 15 units of binding energy in calculations.9PubMed. True stabilization energies for the optimal planar hydrogen-bonded and stacked structures of guanine…cytosine, adenine…thymine, and their 9- and 1-methyl derivatives: complete basis set calculations at the MP2 and CCSD(T) levels and comparison with experiment Pairing big with small also keeps the ladder’s width even all the way along.
Mismatches don’t work. Two big letters would push the strands apart and bulge the ladder outward. Two small ones would leave a gap too wide for the weak links to reach across. A mismatch such as A with C cannot line up its weak links properly, so it forms a poor, unstable pair. Cells have repair machinery that notices misfit pairs and fixes them.
The weak links between letters are only part of the glue. Flat bases also stack on top of each other like coins.10NPTEL. Physical Properties of DNA Bases avoid water, so tucking them inside the helix with the backbone outside makes DNA more stable.11NPTEL. Physical Properties of DNA Each stacked step is weak on its own, but millions of them add up to a sturdy structure.12NPTEL. Physical Properties of DNA
The weakness of the links is a feature. The strands must come apart to be read or copied, and weak links let the cell do this without wrecking the letters. Meanwhile the strong bonds of the sugar-phosphate backbone stay intact, so the order of the letters is preserved while the strands are separated.
How Pairing Lets DNA Copy Itself
When a cell divides, its DNA unzips and new letters are added opposite each old one by the pairing rule. Each new double helix therefore has one old strand and one new strand.
In order, the process goes like this. First the helix is unwound and the two strands are pulled apart, exposing the letters. Next, free letters pair with the exposed letters following the A–T and G–C rule. A copying enzyme then joins the new letters into a continuous new strand. Proofreading follows as the enzyme snips out a wrong letter it just added. Together, choosing the matching letter and proofreading make copying enzymes extremely accurate.13PubMed. The fidelity of human DNA polymerase gamma with and without exonucleolytic proofreading and the p55 accessory subunit
A wrong letter that escapes proofreading gets copied as if it were correct. The next copy pairs faithfully with the error, so one slip becomes a permanent letter change. That is what a mutation is, in pairing terms.
Damage can break pairing too. Ultraviolet light can fuse neighbouring T letters into a joined pair.14Journal of Photochemistry and Photobiology A: Chemistry. Reaction mechanism of thymine dimer formation in DNA induced by UV light The fused letters put a kink in the strand and lose their proper bonds with the opposite strand.15Journal of Photochemistry and Photobiology A: Chemistry. Reaction mechanism of thymine dimer formation in DNA induced by UV light Copying stalls at the damage, which is one reason sunlight harms skin cells.
Why G and C Make DNA Stickier
The share of G and C letters in a stretch of DNA is called its GC content. More G–C pairs mean more three-link pairs, so a higher temperature is needed to pull the strands apart.16National Institute of Justice. DNA Amplification | GC Content Percentage A stretch low in G and C comes apart at a lower temperature. The share is a useful guide, but two stretches with the same amount can still differ, because letter order also affects stability.17National Institute of Justice. DNA Amplification | GC Content Percentage
Very GC-rich DNA is awkward to copy. A single strand rich in G and C can pair with itself and fold back into a hairpin instead of staying straight.18PubMed. PCR-amplification of GC-rich regions: ‘slowdown PCR’ These hairpins can block the copying enzyme in a lab reaction, so such regions are often harder to copy than ordinary DNA.
You meet this in DNA tests, which copy short regions using small matching pieces called primers. Primers work best with about 40–60% G and C. With too little, they fall off, and with too much, they stick in the wrong places.
U, the Letter That Replaces T in RNA
When a gene is read, the cell makes RNA, which uses uracil (U) where DNA uses T. So in RNA, A pairs with U instead of T. U is a single-ring letter like T and C.19Pathwayz. What Are the Four DNA Letters and Their Pairing Rules?
This creates a homework trap. When asked for an RNA copy of a DNA strand, pair each A with U, not T. T never appears in an RNA answer, so check that you haven’t written one. The G–C rule is the same in both, so only the A partner changes.
DNA keeps U out for a reason. Cytosine can lose part of its structure and turn into uracil, which happens fairly often in cells.20PubMed Central. Keeping Uracil Out of DNA: Physiological Role, Structure and Catalytic Mechanism of dUTPases If not fixed, a G–C pair would turn into an A–T pair, a permanent mutation.21PubMed Central. Keeping Uracil Out of DNA: Physiological Role, Structure and Catalytic Mechanism of dUTPases Because of this, cells run a repair system that cuts U out of DNA.22PubMed Central. Keeping Uracil Out of DNA: Physiological Role, Structure and Catalytic Mechanism of dUTPases Since DNA normally uses T, any U found there stands out as damage. If U were a normal DNA letter, the cell could not tell damage from the genuine letter.
Pairing loosens when codes are read. When proteins are built, the third letter of each three-letter instruction can pair more loosely.23PubMed Central. The wobble hypothesis revisited: uridine-5-oxyacetic acid is critical for reading of G-ending codons A U in that spot can pair with G as well as A, and chemical tweaks to U let some reader molecules handle even more letters.24PubMed Central. The wobble hypothesis revisited: uridine-5-oxyacetic acid is critical for reading of G-ending codons
Exceptions, Modified Letters and Extra Letters
An A–T or G–C pair can briefly flip into another shape, called a Hoogsteen pair, in which the bigger letter rotates half a turn.25PubMed Central. Widespread Transient Hoogsteen Base-Pairs in Canonical Duplex DNA with Variable Energetics These flips are rare and short-lived but happen throughout ordinary DNA.26PubMed Central. Transient Hoogsteen Base Pairs in Canonical Duplex DNA They show up more where the normal pair is weaker, and appear where proteins grab DNA or where it is damaged.27PubMed Central. Widespread Transient Hoogsteen Base-Pairs in Canonical Duplex DNA with Variable Energetics
Cells can also attach a small chemical tag, a methyl group, to C without changing which letter it is.28PubMed Central. Epigenetics of Modified DNA Bases: 5-Methylcytosine and Beyond Over 4% of all C letters in human DNA are tagged, and more than 80% of C letters sitting next to G.29PubMed Central. Epigenetics of Modified DNA Bases: 5-Methylcytosine and Beyond Tagging helps switch genes off, and active gene switches are usually left untagged.30PubMed Central. Epigenetics of Modified DNA Bases: 5-Methylcytosine and Beyond A tagged C is still a C and still pairs with G, because the tag doesn’t change its pairing face.
In the lab, scientists have designed an artificial pair of letters that cells’ copying enzymes accept.31PubMed Central. Discovery, Characterization, and Optimization of an Unnatural Base Pair for Expansion of the Genetic Alphabet DNA with this third pair copies with over 99.9% accuracy, creating a working six-letter alphabet.32PubMed Central. Efficient and sequence-independent replication of DNA containing a third base pair establishes a functional six-letter genetic alphabet Such DNA can be copied and read into RNA alongside A–T and G–C.33PubMed Central. Unnatural base pair systems toward the expansion of the genetic alphabet in the central dogma Extra letters can also mark damaged spots so they can be found and read.34PubMed Central. Identification of DNA lesions using a third base pair for amplification and nanopore sequencing