Preparation and Characterization of a Set of Linear DNA Molecules for Polymer Physics and Rheology Studies

Abstract

Imaging of single DNA molecules has enabled detailed studies of dilute polymer dynamics and rigorous testing of assumptions and predictions of molecular theories. It is of interest to extend these methods to the study of entangled polymers and to correlate molecular dynamics with rheology measurements. Progress in this direction has been hampered, however, by a lack of available DNA samples in sufficient quantities and covering a wide range of lengths. Here we describe the preparation of a suitable set of molecules ranging in length from ∼3 to 300 kilobase pairs. These constructs are replicated as plasmids or as fosmids or bacterial artificial chromosomes fitted with an inducible high-copy number origin of replication. DNA sequences were chosen to allow molecules to be linearized by single-cutting restriction enzymes. We show that these molecules can be imaged and characterized by fluorescence microscopy and can be prepared in sufficient quantities for bulk rheology measurements.