Capillary Electrophoresis (CE) provides researchers with the ability to separate and analyze very small amounts of DNA. CE offers important advantages over other available methods because of the speed and reproducibility of analysis. Further, the high sensitivity of detection and the ability to increase sample throughput with parallel analysis has led to the creation of a full range of techniques for the analysis of DNA molecules, from modified DNA-adducts and single strand oligonucleotides through to PCR-amplified DNA fragments and whole chromosomes. Capillary Electrophoresis of Nucleic Acids provides these analytical protocols, which can be used for detection and analysis of mutations and modifications to precise DNA loci through to entire genomes of organisms. Volume I broadly addresses instrumentation, signal detection and the capillary environment, as well as the integration of mass spectrometry and CE for the analysis of small oligonucleotides and modified nucleotides. It opens with a description of the basic CE instrumentation and discusses DNA sequencing by CE and the methods for the manufacture of microchip devices. Also covered are issues regarding the choices of separation media, and the fast separations of large DNA molecules and chromosomes using pulsed-field capillary electrophoresis. The book closes by offering choices for the analysis of small therapeutic oligonucleotides, nucleosides, ribonucleotides and DNA metabolism product by CE as well as those products arising from environmental and cellular damage through disease.