The Direction of DNA and RNA

In The Structure of DNA you paired A with T and G with C. College biology adds one more rule that trips almost everyone: every strand has a direction, and the two strands of a helix run opposite ways.

The numbers come from the sugar. Its carbons are numbered 1′ to 5′ ("one prime" to "five prime"). The base hangs on the 1′ carbon, the phosphate on the 5′ carbon, and the 3′ carbon carries an –OH group. In a strand, the phosphate of each nucleotide bonds to the 3′ carbon of the one before it. So one end of the strand has a free phosphate on a 5′ carbon (the 5′ end), and the other end has a free 3′ –OH (the 3′ end).

One nucleotide: the phosphate on the 5′ carbon, the base on the 1′ carbon, and the –OH on the 3′ carbon.

Key idea

The two strands of DNA are antiparallel: one runs 5′ → 3′ and its partner runs 3′ → 5′ beside it. New nucleotides are always added to the 3′ end, so strands grow 5′ → 3′. By convention, a sequence written alone is read 5′ → 3′, left to right.

Why it works

Why only the 3′ end? The enzymes that build DNA and RNA bond the 3′ –OH of the growing strand to the inner phosphate of an incoming nucleotide triphosphate. Breaking off the other two phosphates releases the energy for that bond. A 5′ end offers no –OH to attach to, so no polymerase can extend it. This one fact explains the lagging strand, primers and much of replication.

Base pairs and the 5′ and 3′ ends of both strands.

Worked examples

Worked example: Writing the partner beside the strand

A strand reads 5′-ATGCCA-3′. Write its partner directly underneath.

Pair each base: A→T, T→A, G→C, C→G, C→G, A→T.
That gives TACGGT under the strand, letter for letter.
The partner runs the other way, so its left end is 3′.

Answer: 3′-TACGGT-5′

Worked example: Writing the partner on its own

Write the same partner strand in the standard 5′ → 3′ order.

Start from 3′-TACGGT-5′.
Read it from its 5′ end, which is on the right: T, G, G, C, A, T.
This is called the reverse complement.

Answer: 5′-TGGCAT-3′

Common mistake

Writing the complement in the same 5′ → 3′ direction as the original: 5′-TACGGT-3′ for the partner of 5′-ATGCCA-3′. That strand runs the wrong way and would not pair. Check by lining the two up: the 5′ end of one must sit across from the 3′ end of the other.

RNA follows the same rules: it has 5′ and 3′ ends and is built 5′ → 3′. That is why mRNA is written 5′ → 3′, the direction a ribosome reads it.

The Direction of DNA and RNA

Worked examples

Practice

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Sources and further reading