sequencespecificity

Sequence specificity is the property of a molecular interaction or catalytic activity to discriminate among different sequences, such as nucleic acid sequences or amino acid motifs. In biology, many proteins exhibit sequence specificity by binding to particular DNA or RNA sequences or by recognizing specific sequence motifs within substrates. Examples include restriction endonucleases that cut DNA at defined sequences, transcription factors that bind promoter or enhancer motifs, and RNA-binding proteins that recognize particular RNA elements. Enzymes acting on nucleic acids often require a substrate containing a specific sequence to function.

Specificity arises from molecular contacts that distinguish bases or residues and from the three‑dimensional shape of the recognition site. Base‑specific hydrogen bonds, electrostatic interactions with the backbone, and shape readout contribute to selective binding. Some interactions tolerate mismatches (degeneracy), while others require an exact match. In practice, sequence specificity is described using consensus sequences, position‑weight matrices, or information‑theoretic measures that quantify how much each position contributes to recognition.

Measurement and implications: specificity is related to but distinct from affinity; a molecule may bind several sequences with different strengths. Off‑target binding is a major concern in gene editing and diagnostic applications. In computational biology, sequence specificity is modeled with motifs and PWM scanning; in synthetic biology, engineered DNA‑binding domains aim to improve specificity to reduce cross‑reactivity.

Common examples include enzymes or systems that recognize GAATTC (EcoRI), and programmable nucleases such as CRISPR‑Cas systems that require a guide RNA–adjacent PAM and a complementary seed sequence to target a locus.