What is the Reverse Complement?
In molecular biology, the reverse complement of a DNA or RNA sequence is essential for understanding how nucleic acids interact. DNA is double-stranded, with each strand running in opposite directions (5' to 3' and 3' to 5'). The reverse complement gives you the sequence of the complementary strand read in the same direction as the original.
How Complementary Base Pairing Works
In DNA, adenine (A) pairs with thymine (T), and guanine (G) pairs with cytosine (C). In RNA, thymine is replaced by uracil (U), so adenine pairs with uracil. This tool handles both DNA and RNA sequences, automatically applying the correct base pairing rules.
DNA Base Pairs
- A (Adenine) ↔ T (Thymine)
- G (Guanine) ↔ C (Cytosine)
RNA Base Pairs
- A (Adenine) ↔ U (Uracil)
- G (Guanine) ↔ C (Cytosine)
When to Use Each Option
Reverse Complement
Use this for primer design, finding binding sites on the opposite strand, or understanding how a sequence would appear on the complementary strand when read in the 5' to 3' direction.
Complement Only
Use this to see what the complementary strand looks like without reversing. This shows base-by-base pairing in the same position.
Reverse Only
Use this to simply reverse the sequence without complementing. Useful for checking palindromic sequences or reading a sequence backwards.
Common Applications
- PCR Primer Design: Forward and reverse primers must be complementary to opposite strands
- Restriction Site Analysis: Many restriction enzymes recognize palindromic sequences
- Probe Design: Hybridization probes need to be complementary to target sequences
- Sequence Annotation: Understanding features on both strands of genomic DNA
- CRISPR Guide RNA Design: Finding target sites and PAM sequences
Command Line Equivalent
For those familiar with the command line, you can achieve the same result for DNA using: echo "ATGC" | tr ACGTacgt TGCAtgca | rev. However, this web tool provides a more accessible interface for those who prefer not to use the terminal.
Tips for Using This Tool
- Whitespace and line breaks are automatically removed from your input
- Both uppercase and lowercase letters are accepted and preserved
- Invalid characters will trigger an error - ensure your sequence only contains valid bases
- Long sequences are formatted with 60 characters per line for readability