DYNAMICS AND COMPACTION OF CONGESTED AND/OR CONFINED DNA

In the first part of this thesis, the dynamics of both linear and circular DNA is discussed. The mean square displacement (MSD), reorientation correlation, and the radius of gyration of entangled lambda-phage DNA and the MSD of cosmid DNA were obtained with fluorescence microscopy. From an analysis of the end-segment MSD of lambda DNA with Doi-Edwards theory, the Rouse relaxation time, tube renewal time, tube step length, and tube end-to-end distance are obtained. The concentration dependencies of the tube renewal and reorientation times agree with the relevant scaling laws for reptation dynamics indicateing coupled translational and rotational motion of DNA in the entangled regime. From a comparison of the MSD of cosmid DNA with that of colloid beads, an essential similarity is found indicating circular DNA molecules behave like spherical particles in an entangled system. In the second part, the effects of the like-charged proteins, bovine serum albumin (BSA) and hemoglobin, on the conformation and compaction of single DNA molecule confined in rectangular nanochannels were investigated with fluorescence microscopy. Anisotropic nanoconfinement facilitates compaction of DNA by negatively charged protein. Tentatively, it is interpreted that this behavior in terms of enhanced depletion interaction between segments of the DNA molecule due to orientation order imposed by the channel walls.

Author dc:creator

• GONG ZONG YING

• reptation, entangled polymer, concentration dependency, DNA compaction, nanochannel