凝膠遷移滯後實驗（electrophoretic mobility shift assays，EMSA）是近年發展起來的研究核酸與蛋白質相互作用簡單、快速、敏感的方法。目前已經成為轉錄因子研究的經典方法。
其基本原理是蛋白質可以與末端標記的核酸探針結合，電泳時這種複合物比無蛋白結合的探針在凝膠中泳動的速度慢，即表現為相對滯後（如下圖所示）。該方法可用於檢測DNA結合蛋白、RNA結合蛋白，並可通過加入特異性的抗體（supershift）來檢測特定的蛋白質，並可進行未知蛋白的鑑定。
簡單說明以下EMSA技術的優缺點，基本原理和實驗方法。
Electrophoretic mobility shift assay (EMSA)
Introduction
Advantage：
can separate different types of complexes, such as monomer and dimer => better than filter binding
easier to see the complex than footprint assay
Disadvantage: do not know where the binding site is.
Rationale
DNA-protein complex will have a smaller mobility than that of free DNA on native gel
gel electrophoresis and molecular sieve
cage effect - difference between footprint and EMSA
Data interpretation
nonspecific binding
smearing between DNA and complex bands
Methods
Lable DNA
Mix DNA and protein to form complex
Add nonspecific competitor
Separate complex with free probe on a native gel