title: Randomized ligation control for chromosome conformation capture.
abstract: In experiments using chromosome conformation capture followed by PCR (3C-PCR) or chromosome conformation capture carbon copy (5C), it is critical to control for intrinsic biases in the restriction fragments of interest and the probes or primers used for detection. Characteristics such as GC%, annealing temperature, efficiency of 3C primers or 5C probes, and length of restriction fragment can cause variations in primer or probe performance and fragment ligation efficiency. Bias can be measured empirically by production of a random control library, as described here, to be used with the 3C library of interest.
authors.affiliation: Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605.
authors.forename: Jon-Matthew
authors.initials: JM
authors.lastname: Belton
authors.affiliation: Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605.
authors.forename: Job
authors.initials: J
authors.lastname: Dekker
mesh_terms: D002874:Chromosome Mapping; D002875:Chromosomes; D017931:DNA Primers; D015723:Gene Library; D023281:Genomics / Q000379:methods*; D009690:Nucleic Acid Conformation; D016133:Polymerase Chain Reaction; D015003:Yeasts
chemical_list: D017931:DNA Primers