Microfluidic systems for single DNA dynamics

Abstract

Recent advances in microfluidics have enabled the molecular-level study of polymer dynamics using single DNA chains. Single polymer studies based on fluorescence microscopy allow for the direct observation of non-equilibrium polymer conformations and dynamical phenomena such as diffusion, relaxation, and molecular stretching pathways in flow. Microfluidic devices have enabled the precise control of model flow fields to study the non-equilibrium dynamics of soft materials, with device geometries including curved channels, cross-slots, and microfabricated obstacles and structures. This review explores recent microfluidic systems that have advanced the study of single polymer dynamics, while identifying new directions in the field that will further elucidate the relationship between polymer microstructure and bulk rheological properties.

Fig. 1

Schematics of several microfluidic platforms highlighted in this review. For each schematic, the direction of fluid flow is indicated by the arrows. (a) Straight channel; (b) planar micro-contraction; (c) planar 90° bend; (d) channel-based micro-curvilinear flow device; (e) hyperbolic contraction; (f) linear converging channels; (g) cross-slot geometry; (h) single obstacle; (i) ordered array of obstacles; and (j) slit-like confinement.

Fig. 2

Conformations of single DNA molecules in steady shear flow at Wi = 19. Time between images is (A) 6 seconds, (B) 0.84 seconds, or (C) 6 seconds. Scale bar: 5 μm. From D. E. Smith, H. P. Babcock and S Chu, Science, 1999, 283, 1724-1727. Reprinted with permission from AAAS.

Fig. 3

DNA conformation along the channel centreline as a function of axial position in the device. The representative images indicate the dramatic stretching of the molecule due to the elongational flow at the channel entrance, and the recovery of its equilibrium conformation as it travels through the channel and into the downstream reservoir. From Ref. , with kind permission from Springer Science + Business Media.

Fig. 4

Single molecule images show distinct modes of DNA migration through polymer solutions in the presence of electric fields. White dots are superimposed as reference points for entanglement coupling mechanisms. Adapted with permission from T. N. Chiesl, K. W. Putz, M. Babu, P. Mathias, K. A. Shaikh, E. D. Goluch, C. Liu and A. E. Barron, Analytical Chemistry, 2006, 78, 4409-4415. Copyright 2006 American Chemical Society.

Fig. 5

DNA stretching in a planar extensional flow uncovered the effects of initial polymer conformation on the transient extension of single DNA molecules, thereby revealing "molecular individualism." Top to bottom: dumbbell, kinked, half-dumbbell, and folded conformations (sketches of molecular configurations are included on the left). Time between images is 0.13 seconds. Inset: planar extensional flow. From T. T. Perkins, D. E. Smith and S. Chu, Science, 1997, 276, 2016-2021. Reprinted with permission from AAAS.

Fig. 6

Schematic of a single DNA-post collision, with parameters including the polymer radius of gyration R_g, obstacle size R_obs, and offset between centres of masses b.

Fig. 7

Classifications for hooking collisions of DNA molecules with a single post: (a) U symmetric hooks, (b) J asymmetric hooks, (c) W entangled hooks, and (d) X continuously extending hooks. Time between images is 1.33 seconds. Adapted with permission from G. C. Randall and P. S. Doyle, Macromolecules, 2006, 39, 7734-7745. Copyright 2006 American Chemical Society.

Fig. 8

Schematics comparing polymer conformations in bulk solution, slit-like confinement, and tube-like confinement given polymer radius of gyration R_g and confinement dimensions h and d. Adapted from Ref. , with kind permission from Springer Science + Business Media and the Korean Society of Rheology.

Fig. 9

Deformation of a DNA molecule that is electrokinetically driven into confinement between a stationary oil "slug" and microchannel wall. Reprinted figure with permission from S.-F. Hsieh and H.-H. Wei, Physical Review E, 79, 021901, 2009. Copyright (2009) by The American Physical Society.

Fig. 10

Schematics of polymer behaviour in tube-like confinement: (A) a relaxed polymer molecule is recoils by entropic forces across interface at nanochannel entrance; (B) a folded molecule unfolds and recoils simultaneously; (C) a molecule driven electrophoretically into the nanochannel relaxes to an equilibrium extension length; (D) a molecule driven partially into the nanochannel relaxes and recoils simultaneously. Reprinted from Biophysical Journal, 90 (12), J. T. Mannion, C. H. Reccius, J. D. Cross and H. G. Craighead, Conformational Analysis of Single DNA Molecules Undergoing Entropically Induced Motion in Nanochannels, 4538-4545, Copyright (2006), with permission from Elsevier.