IMAT Biology · Molecular Biology and Gene Expression

Nucleotides, the Double Helix and Base Pairing

DNA and RNA are chains of nucleotides; in DNA two antiparallel chains are held together by A-T and G-C base pairs, which makes every count on one strand predict the other.

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Why this matters

The papers ask Chargaff percentages (2011, 2013), counts of hydrogen and phosphodiester bonds (2013, 2017, 2018, 2023), a complementary strand (2024) and plain facts about the helix (2011, 2026). The 2023 paper also asked which base a DNA genome lacks and whether you can find the 5′ end from the letters alone.

Concept 1 of 5: Nucleotides: the building blocks of DNA and RNA

A nucleic acid is a long chain of the same kind of unit, the nucleotide. Every nucleotide has the same three parts; only the sugar and one of the bases differ between DNA and RNA. Learn the parts once and you can tell the two molecules apart from any list of components.

Definition

A nucleotide = a phosphate group + a pentose (five-carbon) sugar + a nitrogenous base.

A nucleoside is the sugar and base without the phosphate.
The base is attached to carbon 1′ of the sugar; the phosphate to carbon 5′.
Purines (adenine, guanine) have two rings; pyrimidines (cytosine, thymine, uracil) have one.
Nucleotides are joined by phosphodiester bonds (condensation reactions) between the phosphate on carbon 5′ of one sugar and carbon 3′ of the next. This makes the sugar-phosphate backbone.

Part	In DNA	In RNA
Sugar	deoxyribose (no -OH on carbon 2′)	ribose (-OH on carbon 2′)
Purine bases (two rings)	adenine, guanine	adenine, guanine
Pyrimidine bases (one ring)	cytosine, thymine	cytosine, uracil
Phosphate	one per nucleotide	one per nucleotide
Number of strands	usually two, as a double helix	usually one, which can fold back on itself

Thymine is found only in DNA and uracil only in RNA. Everything else in the first four rows is shared.

Practice this conceptself-check · 4 quick reps

DNA has no uracil, but DNA bases can still pair with uracil

Uracil is never part of DNA. But during transcription an adenine in the DNA template pairs with uracil in the new RNA. So 'DNA bases may form hydrogen bonds with uracil' is true, while 'DNA contains uracil' is false.

Concept 2 of 5: The DNA double helix: backbone outside, paired bases inside

Picture a twisted ladder. The two rails are sugar-phosphate backbones, and each rung is a pair of bases joined by hydrogen bonds. A purine always pairs with a pyrimidine, so every rung has the same length and the helix keeps the same width all along.

Definition

Double-stranded DNA is a double helix of two polynucleotide strands.

Complementary base pairing: A pairs with T by 2 hydrogen bonds; G pairs with C by 3 hydrogen bonds.
The strands are antiparallel: one runs 5′→3′, its partner 3′→5′.
The 5′ end of a strand has a free phosphate on carbon 5′; the 3′ end has a free -OH on carbon 3′.
The two strands are held together only by hydrogen bonds between bases. Phosphodiester bonds hold each strand together along its length.
Watson and Crick built the model in 1953, using Rosalind Franklin's X-ray crystallography images and Chargaff's base ratios.

Feature	Fact
Outside of the helix	the sugar-phosphate backbones, with negatively charged phosphates
Inside of the helix	the bases, stacked on each other and paired across the strands
A-T pair	2 hydrogen bonds
G-C pair	3 hydrogen bonds, so G-C rich DNA is harder to separate
Direction of the strands	antiparallel: 5′→3′ beside 3′→5′
Dimensions	about 2 nm wide, 0.34 nm per base pair, about 10 base pairs per turn

Practice this conceptself-check · 4 quick reps

Hydrogen bonds join the strands; phosphodiester bonds build each strand

Options often swap the two bonds. The bases of opposite strands are held by hydrogen bonds, which are weak and easy to break for copying. Each strand's own nucleotides are linked by covalent phosphodiester bonds, which stay intact when the helix opens.

Concept 3 of 5: Writing the complementary strand and reading 5′ to 3′

Base pairing means one strand fixes the other completely: replace each base by its partner. Because the strands are antiparallel, the partner strand runs the other way, so if you want to write it 5′→3′ like every other sequence, you must also reverse it.

Definition

To write the complementary strand of a DNA sequence:

Swap each base for its partner: A ↔ T, G ↔ C.
Label the ends: the complement of a 5′→3′ strand runs 3′→5′ underneath it.
To write it in the usual 5′→3′ form, read the complement backwards.
By convention sequences are written 5′→3′ unless labelled. The letters alone do not show which end is 5′: that end is defined by the free phosphate on carbon 5′, not by any base.

Worked example

One strand of DNA is 5′-ATGCCTAG-3′. Write the complementary strand (a) lined up beneath it and (b) in the 5′→3′ direction.

Practice this conceptself-check · 3 quick reps

Complement AND reverse to write the partner 5′→3′

Swapping the bases gives the partner strand running 3′→5′. Many options print those letters with 5′ and 3′ labels in the usual order, which is a different molecule. Reverse the complement before you compare it with options written 5′→3′.

A start codon does not mark the 5′ end

The 5′ end is a chemical feature (the free phosphate on carbon 5′). A sequence beginning with AUG or ATG tells you nothing about direction unless the ends are labelled or the 5′→3′ convention is stated.

Concept 4 of 5: Chargaff's rule: base percentages in double-stranded DNA

Every A in double-stranded DNA has a T opposite it, and every G a C. So across the whole molecule there are exactly as many A as T and as many G as C. Knowing one base's share fixes all four.

Definition

Chargaff's rule (for double-stranded DNA):

%A = %T and %G = %C.
So purines = pyrimidines = 50%: %A + %G = 50%.
Given one base, its partner has the same share, and the other two share what is left equally.
It does not hold for single-stranded DNA or RNA, which have no partner strand.

Chargaff's rule

\%A = \%T, \quad \%G = \%C, \quad \%A + \%G = 50\%

$\%A$ percentage of all bases that are adenine (and so on for T, G, C)

Worked example

In a sample of double-stranded DNA, 31% of the bases are adenine. Find the percentages of thymine, guanine and cytosine.

Practice this conceptself-check · 3 quick reps

Pair the right partners: G with C, A with T

Given guanine, the matching share belongs to cytosine, not thymine. To find thymine from guanine, double the guanine figure, subtract from 100%, then halve. Copying the guanine number as the answer is the commonest wrong option.

Chargaff's rule needs two strands

A single strand of DNA, or any RNA, can have any base ratio. The rule is a consequence of pairing, so it applies only to double-stranded DNA taken as a whole.

Concept 5 of 5: Counting nucleotides, hydrogen bonds and phosphodiester bonds

A stretch of double-stranded DNA is a list of base pairs. Each pair has two nucleotides, two sugars and two phosphates, and either 2 or 3 hydrogen bonds. Along each strand, neighbouring nucleotides are linked once, so a strand of n nucleotides has one link fewer than its number of nucleotides.

Definition

For a linear double-stranded fragment of N base pairs:

nucleotides = sugars = phosphates = 2N; purines = pyrimidines = N.
hydrogen bonds = 2 × (number of A-T pairs) + 3 × (number of G-C pairs).
phosphodiester bonds = 2(N − 1), because each strand of N nucleotides has N − 1 links.
A circular double-stranded molecule (a plasmid, a bacterial chromosome) has no ends, so 2N phosphodiester bonds.
To find the pairs from a count of one base: the number of A equals the number of A-T pairs, and the number of C equals the number of G-C pairs.

Bonds in a linear double-stranded fragment

n_{\text{H}} = 2\,n_{AT} + 3\,n_{GC}, \qquad n_{\text{PDE}} = 2(N - 1)

$n_{AT}, n_{GC}$ numbers of A-T and G-C base pairs
$N$ total base pairs, $N = n_{AT} + n_{GC}$
$n_{\text{PDE}}$ phosphodiester bonds in both strands together

Worked example

A linear double-stranded DNA fragment contains 60 nucleotides, 20% of which carry adenine. Find the numbers of base pairs, purines, hydrogen bonds and phosphodiester bonds.

Practice this conceptself-check · 4 quick reps

Count pairs, not nucleotides, before multiplying

If a fragment has 9 cytosines, it has 9 G-C pairs (9 C plus 9 G), not 18. Multiplying the nucleotide count by 3 double-counts every pair.

Phosphates are not phosphodiester bonds

Every nucleotide carries one phosphate, so phosphates = nucleotides. But a linear strand of n nucleotides has only n − 1 phosphodiester bonds, because the end nucleotide has no neighbour on one side.

Summary — formulas & gotchas at a glance

A revision cheat-sheet for the formulas and gotchas above. Click any concept name to jump back to its full explanation.

Formulas (2)

Chargaff's rule: base percentages in double-stranded DNA
Chargaff's rule
$\%A = \%T, \quad \%G = \%C, \quad \%A + \%G = 50\%$
Counting nucleotides, hydrogen bonds and phosphodiester bonds
Bonds in a linear double-stranded fragment
$n_{\text{H}} = 2\,n_{AT} + 3\,n_{GC}, \qquad n_{\text{PDE}} = 2(N - 1)$

Reference tables (2)

Nucleotides: the building blocks of DNA and RNA5 rows

Part	In DNA	In RNA
Sugar	deoxyribose (no -OH on carbon 2′)	ribose (-OH on carbon 2′)
Purine bases (two rings)	adenine, guanine	adenine, guanine
Pyrimidine bases (one ring)	cytosine, thymine	cytosine, uracil
Phosphate	one per nucleotide	one per nucleotide
Number of strands	usually two, as a double helix	usually one, which can fold back on itself

Thymine is found only in DNA and uracil only in RNA. Everything else in the first four rows is shared.

The DNA double helix: backbone outside, paired bases inside6 rows

Feature	Fact
Outside of the helix	the sugar-phosphate backbones, with negatively charged phosphates
Inside of the helix	the bases, stacked on each other and paired across the strands
A-T pair	2 hydrogen bonds
G-C pair	3 hydrogen bonds, so G-C rich DNA is harder to separate
Direction of the strands	antiparallel: 5′→3′ beside 3′→5′
Dimensions	about 2 nm wide, 0.34 nm per base pair, about 10 base pairs per turn

Watch out for (8)

DNA has no uracil, but DNA bases can still pair with uracil
→ Nucleotides: the building blocks of DNA and RNA
Hydrogen bonds join the strands; phosphodiester bonds build each strand
→ The DNA double helix: backbone outside, paired bases inside
Complement AND reverse to write the partner 5′→3′
→ Writing the complementary strand and reading 5′ to 3′
A start codon does not mark the 5′ end
→ Writing the complementary strand and reading 5′ to 3′
Pair the right partners: G with C, A with T
→ Chargaff's rule: base percentages in double-stranded DNA
Chargaff's rule needs two strands
→ Chargaff's rule: base percentages in double-stranded DNA
Count pairs, not nucleotides, before multiplying
→ Counting nucleotides, hydrogen bonds and phosphodiester bonds
Phosphates are not phosphodiester bonds
→ Counting nucleotides, hydrogen bonds and phosphodiester bonds

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