Evaluating Capillary Electrophoresis Systems: Sequencing Difficult DNA Templates

For many researchers, examining difficult DNA template sequencing is an essential part of evaluating a capillary electrophoresis system. Template regions that present increased average sequencing complexity are not uncommon. Most difficult templates contain a feature such as a GC-rich region or a hairpin loop that may inhibit the activity of DNA polymerase. Long homopolymer strings can also reduce the effectiveness of certain sequencing chemistries. Difficult templates can add time and cost to sequencing projects, while researchers troubleshoot the problem with strategies such as experimenting with different reaction conditions, opposite strand sequencing, or extra manual trimming and editing. Ideally, a capillary electrophoresis system should read through difficult templates with little or no modification to protocol.