Visualization of individual DNA molecules in a small-scale coating flow

Abstract

Individual DNA molecules in an ultradilute solution were observed with a fluorescence microscope as they flow between a scaled-down rotating roll and a stationary glass knife. The roll picks up a thin layer of liquid from a pool and drags it to the knife, establishing a bead delineated by two menisci. At low roll speed the flow is premetered and there is a large recirculation. The DNA experiences nearly rectilinear shear flow at the minimum gap position where there is a zero velocity surface. We report the mean and the distribution of fractional extension of DNA molecules and show that the mean fractional extension asymptotes to 0.5, in agreement with the results of Smith et al. ͓D. E. Smith et al., Science 283, 1724 ͑1999͔͒. Interestingly, no polymer distortion is observed at the two menisci. At high roll speed, capillarity is not strong enough to drive backflow; the big recirculation under the coverslip breaks into two smaller recirculations and two separation surfaces arise upstream and downstream of the location of the minimum gap. At the upstream separation surface, most DNA molecules are extended parallel to the knife as they traverse the field of view. We report the distribution of DNA extension and shape in this flow region. Slow, nodular recirculations are present under the upstream and downstream free surfaces. Notably, most DNA molecules stretch axially as they move in these slow recirculating regions.

The dynamics of single-molecule DNA in flow

“…In this context, fluorescentlytagged DNA chains can act as polymer configuration tracers in many complex flows. Recently Duggal and Pasquali [145] have provided just such study of a small-scale coating flow. In a different application, shear and sink flow have been shown to provide an excellent means of both creating fast concatenation or assembly of DNA [146] as well as controlled fragmentation of DNA for gene sequencing [147].…”

Single DNA molecule stretching in sudden mixed shear and elongational microflows

“…14,15 extension under constant shear grows asymptotically to approximately 50% of the contour length at very high Weissenberg numbers (w i > 150), where w i equals the strain rate perpendicular to flow, _ e e \ , multiplied by the longest polymer relaxation time, t relax . 18 The strain rate is a device property and, for purposes of roughly estimating w i , is the same on average for all DNA sizes,{ whereas the relaxation time grows with increasing DNA size. Consequently longer polymers, like the y50 and 185 kb DNA used here, are expected to tumble up to the funnel in a mixture of partially extended states.…”

Yield-stress fluid deposition in circular channels

“…Indeed, coating materials, such as paints and lacquers commonly used to prevent corrosion in automotive industry, often behave like non-Newtonian fluids. The deposition of various non-Newtonian fluids, such as polymer solutions or elastic fluids, has been addressed theoretically, numerically or experimentally (Gutfinger & Tallmadge 1965;Huzyak & Koelling 1997;Quéré 1999;Kamisli & Ryan 1999;Gauri & Koelling 1999;Kamisli & Ryan 2001;Kamışlı 2003;Weinstein & Ruschak 2004;Duggal & Pasquali 2004;Behr et al 2005;Quintella et al 2007;Ashmore et al 2008;Boehm et al 2011). In particular, for a shear-thinning or shear-thickening fluid, with a stress/strain-rate relationship in simple shear given by τ = kγ n (where n denotes the power-law index and k the consistency (in Pa.s n )), the same scaling arguments as for Newtonian fluids can be used (Gutfinger & Tallmadge 1965;Hewson et al 2009), thus yielding:…”