Free energy considerations for nucleic acids with dangling ends near a surface: a coarse grained approach

Abstract

A coarse grain model for the thermodynamics of nucleic acid hybridization near surfaces has been extended and parameterized to consider unpaired dangling end contributions. The parameters of the model differ when representing a double stranded DNA section, or a single stranded DNA section. The thermodynamic effects of the possibility of different dangling end combinations were considered in the presence of different types of surfaces. Configurational sampling was achieved by Metropolis Monte Carlo. To have a more complete picture of the free energy changes, an estimation of the conformational entropy was included. We find a strong thermodynamic effect for dangling mismatches due to sequence requirements when they are nearer the surface as opposed to being held away from the surface.

Phage‐like packing structures with mean field sequence dependence

“…Such coarse-grained models are similar to other models which also treat DNA as polymeric chains of ion-penetrable spheres or ellipsoids with electrical double layer interactions and have been successfully applied to surface-bound DNA microarray experiments [39]-[41], as well as models of phage packaging [22]. Our choice of potential includes the full negative charges of the phosphate backbone with simple Gouy-Chapman double layer ionic-screening and depends only on the ionic-screening conditions as input variable parameters.…”

“…The form of our CG model uses ion‐penetrable spheres to represent six‐base pair segments of double‐stranded DNA which interact via an electrostatically repulsive potential derived from classic DLVO theory of charged colloids, given by where q = 12e − is the electrostatic charge from backbone phosphate groups L B = 7.135 Å is the Bjerrum length, κ = 0.31 Å −1 is the inverse Debye screening length, a = 19.9 Å is the radius of the DNA segments, and R is the separation between such segments. Such CG models are similar to other models which also treat DNA as polymeric chains of ion‐penetrable spheres or ellipsoids with electrical double layer interactions and have been successfully applied to surface‐bound DNA microarray experiments, as well as models of phage packaging . Our choice of potential includes the full negative charges of the phosphate backbone with simple Gouy‐Chapman double layer ionic‐screening and depends only on the ionic‐screening conditions as input variable parameters.…”

Target concentration dependence of DNA melting temperature on oligonucleotide microarrays

“…Recently, several investigations looking at the effect of different design parameters and their role in the thermodynamics and kinetics of the hybridization on the surface have emerged 8, 9, 19–29. These theoretical and experimental studies conclude that binding thermodynamics and dependency of T m could change due to the presence of the surface on which the probes are anchored.…”

Interactions of Nucleotide Bases with Decorated Si Surfaces from Molecular Dynamics Simulations

“…Thus, an accurate investigation of the configuration and dynamics of the adsorbed chains might be important to understand the mechanisms which take place at the deposition interfaces and would help develop robust strategies for creating efficient and selective DNA-based devices. Notwithstanding monolayers have been characterized from an experimental point of view using different techniques including, for example, Fourier transform infrared (FT-IR) spectroscopy, scanning tunneling microscopy (STM), , X-ray reflectivity, and atomic force microscopy (AFM); − only a small number of computational studies describing these systems at the atomic level have been reported to date. ,− Even fewer are the investigations which have used a classical all-atom molecular dynamics approach to estimate the free energy change upon adsorption of DNA strands at the aqueous SAM interface. − …”