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 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 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 binding to surface-bound ssDNA.
Highlights
Aptamers are an important class of biomolecules consisting of single-stranded DNA, RNA, or peptides that can fold into unique secondary and tertiary structures for shape-specific target recognition [1]
Divalent metal ion binding to surface-grafted nucleic acid oligomers is investigated by studying the effects of the ionic strength and grafting density on the oligomer structure and chemistry, with a field theoretic molecular model
Quantitative assessment of the ion cloud around the oligomers shows a uniform distribution of the ions around different sequences and reinforces the dominance of non-specific electrostatic attraction between the nucleobases and the cations as the driving force for the cation binding [33,44]
Summary
Aptamers are an important class of biomolecules consisting of single-stranded DNA (ssDNA), RNA, or peptides that can fold into unique secondary and tertiary structures for shape-specific target recognition [1]. Due to the highly specific and selective nature of their target binding, aptamers are widely studied for a range of applications from biosensing [2,3] to drug design [4,5,6]. Charge regulation and counterion binding in aptamers, or polyelectrolytes in general, are modulated by the metal ions present in the system, which can non-trivially alter their chemical and structural properties [8,9,10,11,12,13]. The presence of metal ions affects the performance of the aptamers as biosensing probes or therapeutics [14,15,16] due to the electrostatic screening of the charges on their surface, which changes their structure and chemistry
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