Sequential Chip Protocols

Sequential chromatin immunoprecipitation, known as SeqChIP, is a biological test intended to define the ways in which two proteins interact within one region of a deoxyribonucleic acid (DNA) strand. Researchers engage a specific set of ordered tasks to reveal three possible relationships between proteins under assessment. As with most science tests, it beings with cleaning and ends with conclusion. According to Harvard researchers, technological advances in SeqChIP analysis may allow scientists to more broadly study biological phenomena.

Prepare

• SeqChIP experiments contain careful preparation in order to sanitize and clean the magnetic beads for experiment. Researchers must wash the beads multiple times and clean them in "block" solution. The beads are then suspended for drying and re-washed. Generally, scientists leave a day prior to the final washing before moving forward to the linking stage. Given the nature of varying DNA strands for assessment, this stage of preparation also varies in complexity. However, one scientific truth remains: the cleaner the test, the cleaner the result.

Crosslink

• Scientists select DNA protein complexes, or areas in the strand, for enhancement with an antibody. In effect, biologists juxtapose proteins in order to observe their interaction. Once observed, cross-link needs to be confirmed in reverse order. Do the proteins still relate when the sequence is reversed? SeqChIP scientists believe that the co-existence of both proteins when assessed in the opposite direction provide compelling evidence of complete co-occupancy, and permit unambiguous differentiation of partial occupancy and no co-occupancy.

Purify

• Polymerase Chain Reaction, or "PCR," is a DNA-amplification process that checks the quality, or purity, of DNA. PCR is conducted in three stages. First, PCR melts the strands apart by raising temperature. Then, researchers bring the two template strands back together with PCR primers. Finally, biologists incubate the DNA so that polymerase primers cause cells under examination to cluster. From there, researchers move to the examination of the clusters.

Assess

• Analysis examines the DNA strands for the presence or absence of "occupancy," an interactive relationship between proteins. Two proteins that always associate with the same DNA fragment have complete co-occupancy; no co-occupancy occurs when the proteins can only associate in mutually-exclusive sub-populations of the DNA strand; partial co-occupancy means that some DNA molecules have both proteins, while others have one or the other. If SeqChIP testing is one procedure in the strand of biology, it provides scientists with the possibility of applying singular results to an entire genomic structure.