Quantifying Mg2+ Binding to ssDNA Oligomers: A Self-Consistent Field Theory Study at Varying Ionic Strengths and Grafting Densities

Abstract

The performance of aptamer-based biosensors is crucially impacted by their interactions with physiological metal ions, which can alter their structures and chemical properties. Therefore, elucidating the nature of these interactions carries the utmost importance in the robust design of highly efficient biosensors. We investigated Mg 2 + binding to varying sequences of polymers to capture the effects of ionic strength and grafting density on ion binding and molecular reorganization of the polymer layer. The polymers are modeled as ssDNA aptamers using a self-consistent field theory, which accounts for non-covalent ion binding by integrating experimentally-derived binding constants. Our model captures the typical polyelectrolyte behavior of chain collapse with increased ionic strength for the ssDNA chains at low grafting density and exhibits the well-known re-entrant phenomena of stretched chains with increased ionic strength at high grafting density. The binding results suggest that electrostatic attraction between the monomers and Mg 2 + plays the dominant role in defining the ion cloud around the ssDNA chains and generates a nearly-uniform ion distribution along the chains containing varying monomer sequences. These findings are in qualitative agreement with recent experimental results for Mg 2 + binding to surface-bound ssDNA.

Paired aptamer capture and FISH detection of individual virions enables cell-free determination of infectious titer

“…5’ biotin-modified aptamers captured 1.615±0.055_fold more spike protein than the 3’ modified aptamers. The presence of MgCl 2 also had a positive effect on the quantity of spike protein captured with a 1.373±0.029 fold increase in absorbance over the condition where MgCl 2 was omitted, consistent with the previous work 22,23,24 ( Figure 1c ). Overall, 5’ biotin-modified 1C aptamers exhibit the highest affinity towards recombinant spike protein with MgCl 2 .…”

“…As a positive control, we immobilized biotinylated ACE2 protein to the streptavidin-coated polystyrene plates and used random aptamer sequences as our negative control ( Figure 1b ). We applied recombinant SARS-CoV-2 Spike protein to the immobilized capture reagents and performed a sandwich ELISA using an HRP-conjugated anti-Spike antibody followed by colorimetric detection 22,23,24 .…”

Divalent Cation Dependence Enhances Dopamine Aptamer Biosensing

“…Collectively, our findings illustrate that the differential behavior observed in terms of divalent cation sensitivity between the dopamine and serotonin aptamers is inherent to these sequences and is independent of whether the aptamers are tethered to (semiconductor) substrates or free in solution. Additional fluorescence-based strategies (e.g., FRET, fluorescence anisotropy, fluorescent nucleotide analogs), spectroscopic methods (e.g., surface-enhanced Raman spectroscopy), , mutational analysis, and theoretical modeling − will be useful for investigating target-induced aptamer conformational rearrangements and allosteric effects in greater detail. Moreover, the use of nuclear magnetic resonance (NMR), X-ray crystallography, or cryogenic electron microscopy, may enable atomically resolved structures to be solved, particularly with regard to target- and divalent-cation-bound aptamer conformations.…”

Phase Behavior of Ion-Containing Polymers in Polar Solvents: Predictions from a Liquid-State Theory with Local Short-Range Interactions

“…Phase equilibrium between the polymer-poor phase (denoted as phase I) and the polymer-rich phase (denoted as phase II) is determined by the equality of the electrochemical potential for all components (see Table 1 ) and the equality of the osmotic pressure [ 44 ]. Charge neutrality is enforced by introducing a Lagrange multiplier in the grand free energy minimization, similar to the approach conducted in earlier studies [ 44 , 118 , 119 ]. We have where the Lagrange multiplier has the interpretation of an electrostatic potential.…”