Reverse complement converter

Original sequence

The input DNA sequence written in the standard 5' to 3' direction represents the sense strand or coding strand. This is how DNA sequences appear in scientific databases like GenBank and research publications.

The 5' and 3' ends refer to the carbon positions on the sugar backbone that determine the directional orientation of DNA.

Original: 5'-ATCGATCGATCG-3'

Reverse sequence

Reverse sequence is created by reversing the order of nucleotides from the original sequence. The last nucleotide becomes the first, and vice versa. This operation preserves the individual bases but changes their positional arrangement while maintaining the 5' to 3' directionality.

Think of it as reading the sequence backwards: if your original sequence spells "HELLO", the reverse would spell "OLLEH".

Original: 5'-ATCGATCGATCG-3'
Reverse:  5'-GCTAGCTAGCTA-3'

Complement sequence

Complement sequence is created by replacing each nucleotide with its Watson-Crick base pairing partner according to DNA's complementary base pairing rules:

• Adenine (A) pairs with Thymine (T)
• Guanine (G) pairs with Cytosine (C)

The complement sequence maintains the same 5' to 3' direction and nucleotide order as the original, showing which bases would hydrogen bond with each position in double-stranded DNA. This represents the theoretical pairing strand if DNA were synthesized in the same direction.

Original:   5'-ATCGATCGATCG-3'
Complement: 5'-TAGCTAGCTAGC-3'

Reverse complement sequence

Reverse complement sequence is created by combining both reverse and complement operations. This produces the actual antisense strand that pairs with your original sequence in natural double-stranded DNA.

Reverse complement is essential because DNA's antiparallel structure means the two strands run in opposite directions - when one strand reads 5' to 3', its partner reads 3' to 5'. This operation shows you exactly how your sequence appears on the opposite strand.

Original:           5'-ATCGATCGATCG-3'
Reverse Complement: 5'-CGATCGATCGAT-3'

Critical applications:

• PCR primer design - primers must be reverse complements of their target sites
• Gene finding - identifying open reading frames on both DNA strands
• Antisense oligonucleotide design - therapeutic molecules that bind to specific RNA sequences
• Restriction enzyme analysis - many enzymes recognize palindromic sequences on both strands

Original vs. reverse vs. complement vs. reverse complement

Here's how all four operations transform the same input sequence:

Original:           5'-ATCGATCGATCG-3'
Reverse:            5'-GCTAGCTAGCTA-3'
Complement:         5'-TAGCTAGCTAGC-3'
Reverse Complement: 5'-CGATCGATCGAT-3'

To understand why reverse complement is so important, here's how your original sequence appears in double-stranded DNA:

5'-ATCGATCGATCG-3'  ← Original sequence (sense strand)
3'-TAGCTAGCTAGC-5'  ← Natural complement (antisense strand)

Notice that the bottom strand, when read 5' to 3', becomes: 5'-CGATCGATCGAT-3' - exactly matching our reverse complement result.

FAQs

What is the reverse complement?

The reverse complement is a DNA sequence transformation that combines two operations: reversing the order of nucleotides and replacing each base with its complementary partner (A↔T, G↔C). For example, if your original sequence is 5'-ATCG-3', the reverse complement is 5'-CGAT-3'. This represents how your sequence appears on the opposite strand of the DNA double helix.

This transformation is essential for PCR primer design, gene annotation, and understanding DNA structure, since DNA naturally exists as antiparallel complementary strands running in opposite directions.

Is the reverse complement 5 to 3?

Yes, the reverse complement is always written in the 5' to 3' direction, following standard DNA notation conventions. When you perform this operation, you're reading the opposite DNA strand in its natural 5' to 3' orientation, since both DNA strands run antiparallel to each other.

For example, if the top strand reads 5'-ATCG-3', the bottom strand is 3'-TAGC-5'. The reverse complement flips this to the conventional 5' to 3' format: 5'-CGAT-3'.

Is cDNA the reverse complement of mRNA?

No, cDNA (complementary DNA) is the complement of mRNA, not the reverse complement. During reverse transcription, the enzyme reads mRNA in the 3' to 5' direction and synthesizes complementary DNA in the 5' to 3' direction using normal base-pairing rules (A pairs with U in RNA, but A pairs with T in DNA).

The confusion often arises because when researchers refer to "cDNA" in databases, they typically mean the double-stranded version where the coding strand matches the original mRNA sequence (except T replaces U). The actual synthesis process follows standard DNA replication, not reverse complement transformation.

Is antisense the same as reverse complement?

Antisense and reverse complement are related but not identical. The antisense strand of DNA is the reverse complement of the sense strand due to DNA's antiparallel structure. However, "antisense" has broader biological meaning - it refers to any nucleic acid (DNA or RNA) that can base-pair with a target sequence.

While reverse complement is purely a sequence transformation, antisense encompasses both the sequence relationship and biological function. For example, antisense oligonucleotides used in gene therapy are typically reverse complements of their target mRNA, but they're designed for specific therapeutic binding rather than just sequence manipulation.