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Illumina dye sequencing is a technique used to determine the series of base pairs in DNA. It was developed by Solexa and is based on reversible dye-terminators that enable the identification of single bases as they are introduced into growing DNA strands. It is often employed to sequence difficult regions, such as homopolymers and repetitive sequences. As well, it can be used for whole-genome and region sequencing, transcriptome analysis, small RNA discovery, methylation profiling, and genome-wide protein-nucleic acid interaction analysis.

Procedure

 * 1) DNA molecules are attached to primers on a slide and amplified so that local colonies are formed.
 * 2) The four types (A, C, T, G) of reversible terminate bases are added, each fluorescently labeled with a different color and attached with a blocking group.
 * 3) The four bases compete for the binding site and non-incorporated molecules are washed away.
 * 4) After each synthesis a laser is applied resulting in the removal of the 3’ terminal blocking group and the probe generating a detectable color that is associated with each base allowing for the next cycle.
 * 5) Process repeated until DNA molecule sequenced.

Materials

 * Local colonies of DNA molecules
 * The four bases with blocking groups and different fluorescent labels
 * DNA polymerase
 * Detecting system

Benefits over other techniques
This technique offers a number of advantages over traditional sequencing methods. For instance, due to the automated nature of illumina dye sequencing it is possible to sequence multiple strands at once and gain actual sequencing data quickly. Whereas, Sanger sequencing can only characterize one template at a time and sequences have to be separated using polyacrylamide-urea gel, which is time consuming. Additionally, it only uses DNA polymerase as opposed to multiple, expensive enzymes required for other sequencing techniques (i.e. Pyrosequencing).