What Controls the Hybridization Thermodynamics of Spherical Nucleic Acids?

Abstract

The hybridization of free oligonucleotides to densely packed, oriented arrays of DNA modifying the surfaces of spherical nucleic acid (SNA)–gold nanoparticle conjugates occurs with negative cooperativity; i.e., each binding event destabilizes subsequent binding events. DNA hybridization is thus an ever-changing function of the number of strands already hybridized to the particle. Thermodynamic quantification of this behavior reveals a 3 orders of magnitude decrease in the binding constant for the capture of a free oligonucleotide by an SNA conjugate as the fraction of pre-hybridized strands increases from 0 to ∼30%. Increasing the number of pre-hybridized strands imparts an increasing enthalpic penalty to hybridization that makes binding more difficult, while simultaneously decreasing the entropic penalty to hybridization, which makes binding more favorable. Hybridization of free DNA to an SNA is thus governed by both an electrostatic barrier as the SNA accumulates charge with additional binding events and an effect consistent with allostery, where hybridization at certain sites on an SNA modify the binding affinity at a distal site through conformational changes to the remaining single strands. Leveraging these insights allows for the design of conjugates that hybridize free strands with significantly higher efficiencies, some of which approach 100%.

Particle-by-Particle Charge Analysis of DNA-Modified Nanoparticles Using Tunable Resistive Pulse Sensing

“…Previous studies have illustrated that the kinetics of target DNA capture is influenced by DNA probe density at a surface [67][68][69][70] . At high DNA probe densities, the ssDNA forms a dense packed polymer brush 56 , the DNA forms a rigid polymer coating who's thickness is equal to the length of the extended DNA sequence, H 72 .…”

What Controls the “Off/On Switch” in the Toehold-Mediated Strand Displacement Reaction on DNA Conjugated Gold Nanoparticles?

“…We suspect that the attenuation of the DNA hybridization for the toehold domain is related to the large electrostatic repulsion between the negatively charge probes and the highly stretched brush-like conformation for the tethered oligonucleotide strands at high surface probe density on AuNP-1. 30,31,45 These properties induce a high enthalpic impediment for the linkerprotector complex to move close to and insert into the oliogonucleotide layer of DNA-AuNP-1.…”

“…26 Besides, toehold-mediated strand displacement reaction has been utilized to improve the selectivity and sensitivity of DNA sensing, such as the graphene oxide (GO)-based FRET assays 27,28 or quartz crystal microbalance (QCM)-based biosensor. 29 The ability for DNA strands from solution anchored to AuNPs to hybridize to their complementary oligonucleotides in a robust and efficient manner is crucial to AuNPs assembly, 30 and DNA hybridization occurring at interfacial environments differs greatly from the solution-phase hybridization. [31][32][33] Proceeding of this process needs the DNA target from solution to first penetrate into the dense layer of oligonucleotide strand, implying the crucial role of properties of oligonucleotide layer in the DNA hybridization on AuNP surfaces.…”

The competing effects of core rigidity and linker flexibility in the nanoassembly of trivalent small molecule-DNA hybrids (SMDH3s)–a synergistic experimental-modeling study

“…This results in a quantitative mismatch of the predicted dimer populations. We note in passing that while ionic contributions, such as explicit treatment of the counterions and polyanionic effects of the DNA backbone, have been incorporated into CGMD model, 38 their deployment herein would only impact the predicted melting behavior via the size and range of thermal fluctuations of the DNA arms.…”

“…To this end, our CGMD model can allow chemists and material scientists to begin to predict the outcomes of DNA-directed nanoassembly of SMDH 3 comonomers as a function of the supramolecular design parameters. Thanks to the simplicity of CGMD modeling and its low computational cost, this innovative model can be further improved, with inputs from spectroscopic studies, to capture factors such as core-DNA hydrophobic collapse, 9 polyanionic repulsions between CG beads, 38 and degrees of freedom of the DNA arms. With these improvements, it can continually evolve into a comprehensive framework for the design and improvement of DNA-hybrid nanomaterials for various applications.…”