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Nitrogenous bases pair with each other using hydrogen bonds. Learn how base pairs keep DNA together and how they help RNA take on useful shapes. Afterwards, you can test your knowledge with a quiz.


Base pairs keep the double strand of DNA together. If we think of DNA as a twisted ladder, each rung is a pair of nitrogenous bases, such as adenine and thymine or guanine and cytosine. Remember that there are four bases in DNA, and their sequence spells out the information DNA carries.

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You can think of genes as the words or sentences they spell. The pairs are stuck together, not with real covalent bonds, but with a weak attraction we call a hydrogen bond.

Types of Base Pairs

Each nitrogenous base has a partner. In DNA, adenine and thymine pair up, and so do guanine and cytosine.

Adenine-Thymine base pair.

Dotted lines show hydrogen bonds. R is where the base attaches to the backbone of DNA.

Adenine-thymine base pair

In the related molecule RNA, thymine is replaced by its close relative uracil, so the pairs are adenine-uracil and guanine-cytosine.

Guanine-Cytosine base pair. Dotted lines show hydrogen bonds. R is where the base attaches to the backbone of DNA.

guanine-cytosine base pair

Structure of Base Pairs

The bases’ ability to pair up comes from their nitrogen atoms (they are called nitrogenous bases, after all!) Each nitrogen (shown above as a letter N) has a pair of electrons that makes it slightly negative, so it can be attracted to the slightly positive hydrogen atoms on its partner (shown as a letter H). We call this a hydrogen bond, and it’s drawn as a dashed line in the illustrations above.Each base has a place where it attaches to the sugar-phosphate backbone of DNA or RNA. In our ladder analogy, the two backbones are the two vertical parts of the ladder. The hydrogen bonds occur between the base on one strand and its partner on the other strand.As you see in the illustration, guanine-cytosine pairs are connected by three hydrogen bonds, and adenine-thymine pairs are connected by two.

Adenine-uracil bonds, not shown, are also connected by two.

Function of Base Pairs

The attraction we call a hydrogen bond isn’t a real chemical bond; it’s like when a sock sticks to your pants after you take them out of the dryer. You can easily take the sock off – it’s not permanently attached – but an electrical attraction keeps the sock there temporarily.Since the hydrogen bonds are so weak, they can be easily broken when it’s time to make a copy of DNA. Enzymes break the bonds, ‘unzipping’ the double helix into two separate strands.

base pairs allow DNA to replicate
DNA replication

Because each base pairs with a certain partner, the enzymes that build the new (daughter) strand can easily read the old (parent) strand and use it as a guide.

For example, if the parent strand has an A, the daughter strand needs a T to match up with it. This is the key feature that allows DNA to be replicated.RNA doesn’t always exist in a double strand.

Sometimes it’s just a single strand, and that means it can fold back on itself. The bases pair to each other, creating hairpin shapes, like in the illustration below. The specially shaped RNA can then act like an enzyme to do other important jobs in the cell. The illustration here shows a transfer RNA, which helps to build proteins.

tRNA showing base pairs
TRNA showing base pairs


Base pairs occur when nitrogenous bases make hydrogen bonds with each other. Each base has a specific partner: guanine with cytosine, adenine with thymine (in DNA) or adenine with uracil (in RNA).The hydrogen bonds are weak, allowing DNA to ‘unzip’. This lets enzymes replicate the DNA.In addition to keeping DNA together in a double strand, another function of base pairing is to allow RNA to take on complex shapes, which lets it do other jobs in the cell, such as building proteins.

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