In this chapter, we present methods for denaturing and native gel electrophoresis of nucleic acids based on fluorescently labeled probes and automatic signal detection by a deoxyribonucleic acid sequencer. Specific examples are given for the determination of ribonucleic acid (RNA) fragmentation patterns, of (deoxy)ribozyme kinetics, and of direct or competitive gel-shift assays. These methods can replace widely used radioisotope-based protocols, for example, for secondary structure mapping of RNA and for the characterization of nucleic acid ligand interactions.
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