Determination of hydrodynamic degradation of DNA using flow birefringence techniques

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Shear degradation experiments on high molecular weight DNA have for the first time been carried out under uniform velocity gradient conditions. Precursory work on a calf thymus sample (molecular weight 31 x 106) indicates that a rate process is operative and that preferential molecular halving occurs. A gradient of 4 x 104 s-1 produces almost complete halving after shearing for seven minutes. Using an extended chain model for breakage this gradient corresponds to a critical breaking force for the DNA backbone of 1 x 10-4 dynes, which is an order of magnitude smaller than estimated theoretically. Flow birefringence measurements are reported which indicate that such an extended chain model is unrealistic : a loss in molecular anisometry during flow is implied, manifested in a time dependence anomaly of both birefringence and extinction angle. At high gradients, the extinction angle behaviour is further found to be associated with the molecular degradation which occurs. Extensive investigation of the time dependent anomaly, in an attempt to understand changes in DNA conformation during flow, has eliminated some of the possible mechanisms for this behaviour, such as, induced shear-denaturation, protein cross linkage and wall desorption. Quanlitalively, a molecular weight threshold for the time dependent behaviour of between two and five million has been established.