Electromigration of single DNA molecules in a crystalline array of silica colloids

A thin crystalline array of silica colloids was investigated as a possible sieving medium for fast DNA separation in electrophoresis. An optically transparent film comprised of 300-nm silica colloids was formed on glass as a transparent crystalline layer of 7 mum in thickness, with an effective pore size of 45 nm. Electric field as high as 200 V/cm can be applied to the crystalline array without causing any damages. The velocities and conformations of single DNA chains were probed as they electromigrated at varying electric field inside the array. The behaviors of individual lambda-DNA molecules (48,502 base pairs) electromigrating through this material were observed to be analogous to the behaviors of long DNA chains in electrophoresis gels, including chain extension, hooking of chains around the matrix, and hernia formation. The electrophoresic mobility of lambda-DNA in this dense, narrow-pore material is surprisingly high: 1.8 x 10-4 cm2/Vs at 10 V/cm, which is at least as high as for much wider-pore gels. Imaging of the single molecules revealed that higher field strength caused increased chain extension and increased mobility, which reached an apparent plateau just above 2.0 x 10-4 cm 2/Vs at 200 V/cm.; Electromigration of DNA with different chain lengths inside the crystalline array was probed under pulsed crossed electric field at 120° to one another. Single DNA chains were observed by fluorescence imaging to electromigrate in a "ratcheting" fashion and to complete the change of direction rapidly, similarly to long DNA chains in gels under pulsed crossed fields. Electric fields of 200 V/cm and 136 V/cm with pulse times of 0.1 s to 0.4 s, respectively, were applied to this material. Both field strength and pulse time are predicted to have effects on the resolution of separations using 120° pulsed crossed field electrophoresis with this material. Increasing the field strength or using a longer pulse time can improve the separation of the three DNA samples in this material with pore size of 45 nm. These results demonstrate that the rigid, inorganic material is promising in DNA electrophoresis for fast separation of long DNA chains within a short time.