DNA Binding to the Silica Surface

Abstract

We investigate the DNA-silica binding mechanism using molecular dynamics simulations. This system is of technological importance, and also of interest to explore how negatively charged DNA can bind to a silica surface, which is also negatively charged at pH values above its isoelectric point near pH 3. We find that the two major binding mechanisms are attractive interactions between DNA phosphate and surface silanol groups and hydrophobic bonding between DNA base and silica hydrophobic region. Umbrella sampling and the weighted histogram analysis method (WHAM) are used to calculate the free energy surface for detachment of DNA from a binding configuration to a location far from the silica surface. Several factors explain why single-stranded DNA (ssDNA) has been observed to be more strongly attracted to silica than double-stranded (dsDNA): (1) ssDNA is more flexible and therefore able to maximize the number of binding interactions. (2) ssDNA has free unpaired bases to form hydrophobic attachment to silica while dsDNA has to break hydrogen bonds with base partners to get free bases. (3) The linear charge density of dsDNA is twice that of ssDNA. We devise a procedure to approximate the atomic forces between biomolecules and amorphous silica to enable large-scale biomolecule-silica simulations as reported here.

Adsorption and Desorption of Single‐Stranded DNA from Single‐Walled Carbon Nanotubes

“…In the case of the ssDNA adsorbed onto the SWCNTs, the N:P ratio remains constant while the amount of N increases relative to C. This indicates that the ssDNA remains adsorbed and the carbon lost was probably amorphous or adventitious carbon. The strong adsorption of ssDNA to SWCNTs is supported by various theoretical studies and its strong adsorption to other substrates …”

“…Prior to investigating ssDNA desorption from SWCNTs, ssDNA adsorption was investigatedt ob oth confirm adsorption and to determine baseline values for characterizing subsequent desorption. (GT) 20 was chosen as the model ssDNA oligomer because it has been used for the chirality-specifics eparation of SWCNTsa nd because we have found that longer ssDNA strandsy ield ah igher concentration of SWCNT in suspension after probe sonication and centrifugation (typical optical density x dilution factor 20-30, see Figure S1 in the Supporting Information). [5b] The photographs of the suspension in Figure 1(a) shows the produced SWCNT suspension was stable (for months) and recorded azeta potential of À42 mV,which is similar to other reports of CNT-DNA suspensions and similar in magnitude to SWCNT suspensions with anionic surfactant sodium deoxycholate ( Figure S2).…”

Microscopic origin of wall slip during flow of an entangled DNA solution in microfluidics: Flow induced chain stretching versus chain desorption

“…Note that it has been demonstrated by molecular dynamics simulations that DNA can still bind to a (a negatively charged) silica surface effectively and the repulsion between silica and DNA can be weak due to the screening effect of the counterions near both surfaces. 71 Furthermore, the DNA binding to silica nanoparticles also has been detected experimentally in a salt-free solution at pH ¼ 7. 72 The details of surface modification are described in the supplementary material.…”

Nanoparticles: synthesis and applications

“…Thus, to provide insight into important issues such as the mechanism behind DNA binding to silica is of great interest. Using molecular dynamics simulations, Shi et al (2015) showed that the two major mechanisms for binding of DNA to silica are attractive interactions between DNA phosphate and surface silanol groups and hydrophobic bonding between DNA base and hydrophobic region of silica surface. These short-range attractions can be sufficiently strong to overcome the electrostatic repulsion between negatively charged DNA and negatively charged silica surface.…”