Peeling Single-Stranded DNA from Graphite Surface to Determine Oligonucleotide Binding Energy by Force Spectroscopy

Abstract

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 k B T and 8.3±0.7 k B T in the cases of thymine and cytosine nucleotides. The equilibrium free-energy profile simulated using molecular dynamics had a potential well of 18.9 k B T for thymidine, showing that non-electrostatic 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.Interactions of polyelectrolytes with solid substrates have several important applications in materials science and engineering. 1, 2 On complexation with neutral particles, polyelectrolytes convert these particles into charged species, enabling dispersions in aqueous media, and find use in detergents, cosmetics, gels, food additives, and oil recovery. In a biological context, our interest is in the interaction between single and double-stranded DNA (ssDNA and dsDNA) and substrates such as graphite and carbon-nanotubes (CNTs) that can potentially play a vital role in biomedicine, 3, 4 nanotechnology, 5,6 and relevant for the understanding of the origin of life. 7 Importantly, ssDNA has been used successfully for dispersion and solution-based manipulation of CNTs -ssDNA forms a stable hybrid with a nanotube by wrapping around the CNT in helical fashion. 8,9 The hybrid is useful for dispersion, sorting, 8,9 and patterned placement of nanotubes, 6 for transportation of DNA into cells, and for killing cancer cells by thermal ablation. 3 Strength of dispersion, ability to sort, and stability in the cellular environment all depend on the interaction between DNA and a CNT. 10 Individual DNA bases also bind to a graphitic surface through non-covalent π-π interactions. [11][12][13][14] Very little is known quantitatively about the strength of binding between ssDNA and CNT's in spite of the fundamental importance of understanding such interactions. 8,[15][16][17] As a first

Adsorption and Desorption of DNA on Graphene Oxide Studied by Fluorescently Labeled Oligonucleotides

“…31 Previous work has focused on characterization of the adsorption of single nucleotides or nucleosides by atomic force microscopy (AFM), 32 isothermal titration calorimetry, 33 and theoretical calculations. [34][35][36] It was concluded that non-electrostatic interactions dominate the binding, 32 and the purine bases bind more strongly than the pyrimidines. 33,35,36 The adsorption of DNA on carbon nanotubes has also been studied.…”

“…33,35,36 The adsorption of DNA on carbon nanotubes has also been studied. [37][38][39][40][41][42][43] GO and nanotubes, however, are fundamentally different and the adsorption/desorption of oligonucleotides on GO have not been systematically tested as a function of solution conditions. We believe such studies can serve as a basis for further design and optimization of GO and DNA-based biosensors.…”

Comparison of Graphene Oxide and Reduced Graphene Oxide for DNA Adsorption and Sensing

“…21 Fundamental studies on the interaction between DNA and GO were also carried out. 11,[22][23][24][25][26][27][28][29][30][31][32] GO is a loosely defined material, and the oxygen content can vary quite a lot depending on the preparation condition. The adsorption affinity of DNA is likely to depend on the oxygen content.…”

Mechanisms of DNA Sensing on Graphene Oxide

“…The attractive forces between DNA and GO include - stacking, hydrophobic interaction, hydrogen bonding and van der Waals force. [3][4][5] Without a covalent linkage, 6 DNA adsorption is reversible. For example, adsorbed DNA can be desorbed by adding its complementary DNA (cDNA) to form a duplex.…”