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Peeling DNA from graphite (with Dmitri Vezenov/Chemistry@Lehigh)

We measured the force required to peel single-stranded DNA molecules from single-crystal graphite using chemical force microscopy. Force traces during retraction of a tip chemically modified with oligonucleotides displayed characteristic plateaus with abrupt force jumps, which we interpreted as a steady state peeling process punctuated by complete detachment of one or more molecules. We were able to differentiate between bases in pyrimidine homopolymers; peeling forces were 85.3 ± 4.7 pN for polythymine and 60.8 ± 5.5 pN for polycytosine, substantially independent of salt concentration and the rate of detachment. We developed a model for peeling a freely jointed chain from the graphite surface and estimated the average binding energy per monomer to be 11.5 ± 0.6 kBT and 8.3 ± 0.7 kBT in the cases of thymine and cytosine nucleotides, respectively. The equilibrium free-energy profile simulated using molecular dynamics had a potential well of 18.9 kBT for thymidine, showing that nonelectrostatic interactions dominate the binding. The discrepancy between the experiment and theory indicates that not all bases are adsorbed on the surface or that there is a population of conformations in which they adsorb. Force spectroscopy using oligonucleotides covalently linked to AFM tips provides a flexible and unambiguous means to quantify the strength of interactions between DNA and a number of substrates, potentially including nanomaterials such as carbon nanotubes.

"Peeling Single-Stranded DNA from Graphite Surface to Determine Oligonucleotide Binding Energy by Force Spectroscopy" Suresh Manohar†, Amber R. Mantz‡, Kevin E. Bancroft‡, Chung-Yuen Hui§, Anand Jagota*† and Dmitri V. Vezenov*‡

We have analyzed the statistical thermodynamics of peeling single-stranded DNA (ssDNA) from the surface of graphite. Using recently measured parameters, we model ssDNA as a freely jointed chain strongly adsorbed to a frictionless substrate. Under force control, we have obtained several exact closed-form results that, in agreement with single-molecule experiments, predict peeling under a steady force and provide a relation between this force and the underlying adhesion free energy. During peeling under displacement control we predict that, for finite length chains (< 25 bases), the equilibrium response will display spikes in force that decrease in magnitude with increasing end-to-end distance of the desorbed chain. These force spikes carry information about the underlying sequence of ssDNA, which might thus be measurable with a sufficiently stiff loading system.

(Manohar and Jagota, PRE 2010)