Polymer support for exonucleolytic sequencing

The effect of wall depletion and hydrodynamic interactions on stress-gradient-induced polymer migration

We generalize our recent continuum theory for the stress-gradient-induced migration of polymers [Zhu et al., J. Rheol., 2016, 60, 327-343] by incorporating the effect of solid boundaries on concentration variations. For a model flow in a channel with periodic slip wall velocity, which can in principle be produced by an electric field in the presence of a sinusoidal wall charge, we obtain theoretical results for the steady-state distribution of dilute solutions of polymer dumbbells using a systematic perturbation analysis in Weissenberg number Wi. We find that the presence of a thin wall depletion zone changes the lowest order solution from second to first in Wi and drastically affects the concentration field far from the depletion layer, due both to a coupling of the second derivative of the velocity field to the concentration gradient, and to convection of the polymer-depleted fluid in this layer into the bulk of the fluid. Additional effects induced by wall hydrodynamic interaction (HI) are assessed by incorporating polymer flux from the wall-HI migration theory of Ma and Graham into our continuum theory. We establish the range of validity of our theory by comparing the theoretical results with Brownian dynamics (BD) simulations: excellent agreement is achieved for relatively small molecules, while the theory breaks down when the Gradient number Gd is greater than 0.5, where Gd is the ratio of polymer coil size to the length scale over which the velocity gradient changes. The BD simulations are also extended to the case of long Hookean chains with numbers of springs per chain ranging from 1 to 32, where it is found that for fixed Gd and Wi, the results are nearly identical, showing that all important phenomena are captured by a simple dumbbell model, thus supporting the continuum theory which was derived for the case of dumbbells. In addition, the Stochastic Rotation Dynamics (SRD) method is employed to evaluate the role of HI on the migration pattern, producing effects consistent with the continuum theory incorporating the wall-migration flux. In general, we demonstrate that the polymer concentrates in drastically different regions of the channel depending on Gd and Wi.

Drop drying on surfaces determines chemical reactivity - the specific case of immobilization of oligonucleotides on microarrays

BACKGROUND

Drop drying is a key factor in a wide range of technical applications, including spotted microarrays. The applied nL liquid volume provides specific reaction conditions for the immobilization of probe molecules to a chemically modified surface.

RESULTS

We investigated the influence of nL and μL liquid drop volumes on the process of probe immobilization and compare the results obtained to the situation in liquid solution. In our data, we observe a strong relationship between drop drying effects on immobilization and surface chemistry. In this work, we present results on the immobilization of dye labeled 20mer oligonucleotides with and without an activating 5'-aminoheptyl linker onto a 2D epoxysilane and a 3D NHS activated hydrogel surface.

CONCLUSIONS

Our experiments identified two basic processes determining immobilization. First, the rate of drop drying that depends on the drop volume and the ambient relative humidity. Oligonucleotides in a dried spot react unspecifically with the surface and long reaction times are needed. 3D hydrogel surfaces allow for immobilization in a liquid environment under diffusive conditions. Here, oligonucleotide immobilization is much faster and a specific reaction with the reactive linker group is observed. Second, the effect of increasing probe concentration as a result of drop drying. On a 3D hydrogel, the increasing concentration of probe molecules in nL spotting volumes accelerates immobilization dramatically. In case of μL volumes, immobilization depends on whether the drop is allowed to dry completely. At non-drying conditions, very limited immobilization is observed due to the low oligonucleotide concentration used in microarray spotting solutions. The results of our study provide a general guideline for microarray assay development. They allow for the initial definition and further optimization of reaction conditions for the immobilization of oligonucleotides and other probe molecule classes to different surfaces in dependence of the applied spotting and reaction volume.

N log N method for hydrodynamic interactions of confined polymer systems: Brownian dynamics

A Brownian dynamics simulation technique is presented where a Fourier-based N log N approach is used to calculate hydrodynamic interactions in confined flowing polymer systems between two parallel walls. A self-consistent coarse-grained Langevin description of the polymer dynamics is adopted in which the polymer beads are treated as point forces. Hydrodynamic interactions are therefore included in the diffusion tensor through a Green's function formalism. The calculation of Green's function is based on a generalization of a method developed for sedimenting particles by Mucha et al. [J. Fluid Mech. 501, 71 (2004)]. A Fourier series representation of the Stokeslet that satisfies no-slip boundary conditions at the walls is adopted; this representation is arranged in such a way that the total O(N2) contribution of bead-bead interactions is calculated in an O(N log N) algorithm. Brownian terms are calculated using the Chebyshev polynomial approximation proposed by Fixman [Macromolecules 19, 1195 (1986); 19, 1204 (1986)] for the square root of the diffusion tensor. The proposed Brownian dynamics simulation methodology scales as O(N1.25 log N). Results for infinitely dilute systems of dumbbells are presented to verify past predictions and to examine the performance and numerical consistency of the proposed method.

Advances in sequencing technology

Faster sequencing methods will undoubtedly lead to faster single nucleotide polymorphism (SNP) discovery. The Sanger method has served as the cornerstone for genome sequence production since 1977, close to almost 30 years of tremendous utility [Sanger, F., Nicklen, S., Coulson, A.R, DNA sequencing with chain-terminating inhibitors, Proc. Natl. Acad. Sci. U.S.A. 74 (1977) 5463-5467]. With the completion of the human genome sequence [Venter, J.C. et al., The sequence of the human genome, Science 291 (2001) 1304-1351; Lander, E.S. et al., Initial sequencing and analysis of the human genome, Nature 409 (2001) 860-921], there is now a focus on developing new sequencing methodologies that will enable "personal genomics", or the routine study of our individual genomes. Technologies that will lead us to this lofty goal are those that can provide improvements in three areas: read length, throughput, and cost. As progress is made in this field, large sections of genomes and then whole genomes of individuals will become increasingly more facile to sequence. SNP discovery efforts will be enhanced lock-step with these improvements. Here, the breadth of new sequencing approaches will be summarized including their status and prospects for enabling personal genomics.

Shear-induced migration in flowing polymer solutions: Simulation of long-chain DNA in microchannels

We simulate dilute solution dynamics of long flexible polymer molecules in pressure driven flow in channels with widths of roughly 0.1-10 times the polymer bulk radius of gyration. This is done using a self-consistent coarse-grained Langevin description of the polymer dynamics and a numerical simulation of the flow in the confined geometry that is generated by the motions of polymer segments. Results are presented for a model of DNA molecules of approximately 10-100 microm contour length in micron-scale channels. During flow, the chains migrate toward the channel centerline, in agreement with well-known experimental observations. The thickness of the resulting hydrodynamic depletion layer increases with molecular weight at constant flow strength; higher molecular weight chains therefore move with a higher average axial velocity than lower molecular weight chains. In contrast, if the hydrodynamic effects of the confining geometry are neglected, depletion of concentration is observed in the center of the channel rather than at the walls, contradicting experimental observations. The mechanisms for migration are illustrated using a simple kinetic theory dumbbell model of a confined flexible polymer. The simple theory correctly predicts the trends observed in the detailed simulations. We also examine the steady-state stretch of DNA chains as a function of channel width and flow strength. The flow strength needed to stretch a highly confined chain away from its equilibrium length is shown to increase with decreasing channel width, independent of molecular weight; this is fairly well explained using a simple blob picture.

DNA dynamics in a microchannel

An extended Brownian dynamics simulation method is used to characterize the dynamics of long DNA molecules flowing in microchannels. The relaxation time increases due to confinement in agreement with scaling predictions. During flow the molecules migrate toward the channel center line, and thereby segregate according to molecular weight. Capturing these effects requires the detailed incorporation of solvent flow in the simulation method, demonstrating the importance of hydrodynamic effects in the dynamics of confined macromolecules.

Progress towards single-molecule DNA sequencing: a one color demonstration

Single molecules of fluorescently labeled nucleotides were detected during the cleavage of individual DNA fragments by a processive exonuclease. In these experiments, multiple (10-100) strands of DNA with tetramethyl rhodamine labeled dUMP (TMR-dUMP) incorporated into the sequence were anchored in flow upstream of the detection region of an ultra sensitive flow cytometer. A dilute solution of Exonuclease I passed over the microspheres. When an exonuclease attached to a strand, processive digestion of that strand began. The liberated, labeled bases flowed through the detection region and were detected at high efficiency at the single-molecule level by laser-induced fluorescence. The digestion of a single strand of DNA by a single exonuclease was discernable in these experiments. This result demonstrates the feasibility of single-molecule DNA sequencing. In addition, these experiments point to a new and practical means of arriving at a consensus sequence by individually reading out identical sequences on multiple fragments.