(577h) The Influence of Non-Ideal Effects On DNA Hybridization On Surfaces

The hybridization of single-stranded DNA in solution (the target molecule) to single-stranded DNA tethered to a surface (the probe molecule) is a key phenomenon involved in many technologies such as microarrays, DNA origami, self-assembly, templating, and surface biofunctionalization.  DNA is useful in these applications precisely because the hybridization process can be exploited to yield information and direct surface immobilization.  However, hybridization in these technologies occurs in an environment far removed from the cellular context, and the implications of these differences are not completely understood. 

One of the difficulties of studying hybridization on a surface is that no experimental technique exists to precisely determine the effects of the inhomogeneous environment on the process.  As such, molecular simulation has emerged as the primary method to investigate DNA-surface interactions.  In this role, simulation has provided a variety of insights into the process, but the vast majority of these studies have been done with relatively idealized systems.  The idealities include tethering the DNA to the surface at only one location and simulating only one probe hybridizing with only one target.  Studies to date that have used multiple surface probes have either not studied the hybridization process or started with a hybridized duplex and focused only on melting. 

This presentation will summarize several efforts to move away from the “ideal” cases and model the system in a manner that more closely approximates the real system.  Results will be presented on two major themes: tethering the probe to the surface at multiple locations and hybridization of a target to a group of probes.  The former is important because fabrication techniques do not always result in the probe extending perpendicular to the surface.  The latter is important because each “dot” of DNA on the surface consists of many probe molecules of the same sequence. 

In each case, replica exchange molecular dynamics and/or umbrella sampling were used to simulate hybridization, and the results offer surprising insights that are contrary to initial theories.  For example, it was hypothesized that tethering the probe to the surface at multiple locations would inhibit the ability of the target to hybridize and decrease duplex stability, but the opposite occurred.  It was also theorized that the presence of multiple probes on the surface—and the accompanying entanglements—would also destabilize the duplex, but the data showed an increase in stability.  These and other results that will be presented give a more complete picture of surface hybridization than previously understood and offer hope that future design improvements of DNA-surface technologies are possible.