RNAaffiniteitschapering

RNA affinity refers to the strength of interaction between an RNA molecule and a binding partner, such as a protein, another RNA, or a small molecule. Affinity is commonly quantified by the equilibrium dissociation constant (Kd); lower values indicate tighter binding. Relative affinities span from high (low nanomolar to picomolar Kd) to moderate and low (micromolar to millimolar). The kinetics of binding are described by kon and koff, with Kd = koff / kon.

RNA affinity is influenced by sequence and structure. Primary sequence dictates binding motifs, while secondary and tertiary structures such as hairpins, loops, pseudoknots, and G-quadruplexes create binding interfaces. Chemical modifications, including methylation (e.g., m6A) and pseudouridine, can modulate recognition and stability. Environmental conditions, particularly ionic strength and Mg2+ concentration, pH, and temperature, also affect binding.

Measurement approaches include electrophoretic mobility shift assays (EMSAs), filter binding assays, surface plasmon resonance (SPR), bio-layer interferometry, isothermal titration calorimetry (ITC), and various fluorescence-based methods. RNA affinity is deliberately engineered in applications such as RNA aptamers, selected by SELEX to bind targets with high affinity and specificity. Aptamers and related RNA regulators are used in research, diagnostics, and potential therapeutics, while riboswitches illustrate natural mechanisms by which RNA affinity for ligands governs gene expression. A key consideration is that high affinity does not automatically guarantee specificity, so analyses often combine affinity with selectivity assessments.