DNA Reverse Complement Practice for Both Strands

Write the bases that pair with 5′–AGTC–3′ directly underneath it and you get TCAG. Read that same complementary DNA strand from its 5′ end and you get GACT. The direction matters when you search for a pattern. It can be missing from the printed sequence and still appear on the other strand.

Pair the bases, then find the 5′ end

In double-stranded DNA, A pairs with T and C pairs with G. The two strands are antiparallel, meaning they run in opposite directions. If the given strand runs 5′ to 3′ from left to right, its aligned partner runs 3′ to 5′. See the strand diagram in the NHGRI gene-finding guide.

Given strand       5′–AGTC–3′
Aligned partner    3′–TCAG–5′

The partner's 5′ end is on the right. Read from there to get 5′–GACT–3′, the reverse complement of AGTC. If you got TCAG, you paired the bases correctly and still need to read from the right. If you got CTGA, you reversed the given letters and still need to pair the bases. Biopython shows the two operations side by side.

Keep the end labels attached to the letters as you work. If the given strand starts at 3′ on the left, the partner you write underneath already starts at 5′ on the left. You can report it in that order.

Search both strands from one printed sequence

Look for an exact match to 5′–AACG–3′ in the fragment below. Call the printed strand the reference (+) and its partner the − strand. For either strand, count positions from 1 at the left end of the reference and include both endpoints in your answer.

Reference (+)    5′–TTA CGTT CGTAA–3′
Partner (−)      3′–AAT GCAA GCATT–5′

There’s no AACG in the top row. The middle block of the bottom row reads GCAA from left to right. Read those same four bases from right to left, in the partner's 5′→3′ direction, and they spell AACG. The block covers reference positions 4–7 (−). If you write the whole partner as 5′–TTACGAACGTAA–3′ and count from its own 5′ end, the match is at 6–9. Both counts point to the same four base pairs.

You can get the reference positions without writing the bottom row. Slide a four-base window along the reference one position at a time. Check each window for AACG to find a + match and for CGTT, the reverse complement of AACG, to find a − match. A CGTT window on the reference has AACG directly across from it when you read the partner 5′ to 3′.

The + and − labels here refer to the printed reference. Coding and template describe what each strand does for a particular gene during transcription. Practice identifying the coding and template strands.

Try these on paper

1. Write the aligned partner of 5′–CGTAA–3′ and label its ends. Then write that partner 5′ to 3′.
2. The given strand is 3′–TACGGC–5′. Write its partner 5′ to 3′. Where would you start to read the given strand itself 5′ to 3′?
3. AGGA reads the same backward. Does its reverse complement also match the original?
4. Search 5′–TCAACGATCGTTAG–3′ for 5′–AACG–3′ on either strand. Give the reference positions and strand for each match.
5. Search 5′–CGAATTCG–3′ for 5′–GAATTC–3′ on either strand. How many strands have a match, and how many distinct spans does that cover?

Answer key

1. 5′–TTACG–3′. The aligned partner is 3′–GCATT–5′. Start reading at the 5′ end on the right.
2. 5′–ATGCCG–3′. The partner's 5′ end is already on the left. The given strand's 5′ end is on the right, so its sequence in that direction is 5′–CGGCAT–3′. The reverse complement of CGGCAT is ATGCCG.
3. AGGA reverses to AGGA, and its reverse complement is TCCT.
4. 3–6 (+) and 9–12 (−). The reference contains AACG at 3–6 and CGTT at 9–12.
5. 2–7 on both strands, one span. The aligned partner of 5′–GAATTC–3′ is 3′–CTTAAG–5′. Read it from the right and you get GAATTC again. A sequence that equals its reverse complement is a reverse-complement palindrome.

Retry the step you missed tomorrow

Cover the right column and answer from memory. For the first prompt, write the end labels too.

Front	Back
The aligned partner reads 3′–GCATT–5′. What do you report 5′ to 3′?	5′–TTACG–3′. Start at the 5′ end on the right.
A reference window reads 5′–CGTT–3′. Which strand has 5′–AACG–3′ at that span?	The − strand. AACG is the reverse complement of CGTT.

Try the same steps with fresh sequences in the DNA reverse complement flashcards. Practice labeling the paired strands, correcting reversal errors, and finding exact matches on either strand.

You’ll use the same direction check in the PCR primer practice worksheet.

This worksheet was drafted with AI assistance. Example answers were checked against Biopython 1.88.