Cation-Size-Dependent DNA Adsorption Kinetics and Packing Density on Gold Nanoparticles: An Opposite Trend

Liu, Biwu; Kelly, Erin Y.; Liu, Juewen

doi:10.1021/la503188h

Cited by 29 publications

(40 citation statements)

References 45 publications

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“…From a pure electrostatic standpoint, we would expect Li + to be a more potent inhibitor due to its higher charge density. For example, Li + can increase the melting temperature of DNA more than Na + or K + ( 46 ).…”

Section: Resultsmentioning

confidence: 99%

Misfolding of a DNAzyme for ultrahigh sodium selectivity over potassium

Chen

Huang

et al. 2018

Nucleic Acids Research

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Herein, the excellent Na+ selectivity of a few RNA-cleaving DNAzymes was exploited, where Na+ can be around 3000-fold more effective than K+ for promoting catalysis. By using a double mutant based on the Ce13d DNAzyme, and by lowering the temperature, increased 2-aminopurine (2AP) fluorescence was observed with addition of both Na+ and K+. The fluorescence increase was similar for these two metals at below 10 mM, after which K+ took a different pathway. Since 2AP probes its local base stacking environment, K+ can be considered to induce misfolding. Binding of both Na+ and K+ was specific, since single base mutations could fully inhibit 2AP fluorescence for both metals. The binding thermodynamics was measured by temperature-dependent experiments revealing enthalpy-driven binding for both metals and less coordination sites compared to G-quadruplex DNA. Cleavage activity assays indicated a moderate cleavage activity with 10 mM K+, while further increase of K+ inhibited the activity, also supporting its misfolding of the DNAzyme. For comparison, a G-quadruplex DNA was also studied using the same system, where Na+ and K+ led to the same final state with only around 8-fold difference in Kd. This study provides interesting insights into strategies for discriminating Na+ and K+.

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Section: Resultsmentioning

confidence: 99%

Misfolding of a DNAzyme for ultrahigh sodium selectivity over potassium

Chen

Huang

et al. 2018

Nucleic Acids Research

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“…For this, the opposite was observed: the intensity with Li + was lower than with Na + (Figure F). We attribute this to the higher charge density of Li + , thus making 17E more compact and less accessible to Tb 3+ . Because 17E is much smaller than Ce13d, we also performed the experiment with a larger DNAzyme, Pb‐C30: there was lower emission in Li + (Figure S1).…”

Section: Resultsmentioning

confidence: 99%

“…We attribute this to the higher charged ensity of Li + ,t hus making 17E more compact and less accessible to Tb 3 + . [46,47] Because 17E is much smaller than Ce13d, we also performed the experiment with al arger DNAzyme,P b-C30: [16] there was lower emission in Li + ( Figure S1). Therefore, Tb 3 + is ag ood probe for Na + binding by Ce13d, [39] and it was used for the rest of this study.…”

Section: Resultsmentioning

confidence: 99%

A Selective Na⁺ Aptamer Dissected by Sensitized Tb³⁺ Luminescence

2016

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A previous comparative study between two RNA-cleaving DNAzymes named NaA43 and Ce13d revealed the possibility of a common Na + aptamer in these two DNAzymes. Since Na + binding by DNA is a very fundamental biochemical problem, herein the interaction between Ce13d and Na + is studied in detail using sensitized Tb 3+ luminescence spectroscopy. Na + displaces Tb 3+ from the DNAzyme, and thus quenches the emission from Tb 3+ . The overall requirement for Na + binding includes the hairpin and the highly conserved 16-nucleotide loop in the enzyme strand along with a few unpaired nucleotides in the substrate. Mutations studies indicate a good correlation between Na + binding and the DNAzyme cleavage activity, suggesting the critical role of Na + binding for the enzyme activity. Ce13d displays a Kd of ~20 mM Na + , while other monovalent cations are in the ~40-60 mM range. The measured Kd for other metal ions are mainly due to non-specific competition. With a single nucleotide mutation, the specific Na + binding is lost, while another mutant improved the Kd to 8 mM Na + . This study has demonstrated a Na + aptamer with important biological implications and analytical applications. It has also defined the structural requirements for Na + binding and produced an improved mutant.

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“…According to this model, the DNA needs to approach the particle in order to displace the citrate and is then adsorbed in a latter step. The neutralization of the negative charges of citrate by salt addition favors the process, which is also faster in the case of larger cations, due to them being more dehydrated than the small ones and as such better at screening long range electrostatic repulsions . Upon adsorption, the DNA may change conformation to maximize contact points with the surface.…”

Section: Interactions Between Aunps and Oligonucleotidesmentioning

confidence: 99%

Covalent and Non‐Covalent DNA–Gold‐Nanoparticle Interactions: New Avenues of Research

et al. 2016

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The interactions of DNA, whether long, hundred base pair chains or short-chained oligonucleotides, with ligands play a key role in the field of structural biology. Its biological activity not only depends on the thermodynamic properties of DNA-ligand complexes, but can and often is conditioned by the formation kinetics of those complexes. On the other hand, gold nanoparticles have long been known to present excellent biocompatibility with biomolecules and are themselves remarkable for their structural, electronic, magnetic, optical and catalytic properties, radically different from those of their counterpart bulk materials, and which make them an important asset in multiple applications. Therefore, thermodynamic and kinetic studies of the interactions of DNA with nanoparticles acting as small ligands are key for a better understanding of those interactions to allow for their control and modulation and for the opening of new venues of research in nanomedicine, analytic and biologic fields. The interactions of gold nanoparticles with both DNA polymers and their smaller subunits; special focus is placed on those interactions taking place with nonfunctionalized gold nanoparticles are reviewed in the present work.

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Cation-Size-Dependent DNA Adsorption Kinetics and Packing Density on Gold Nanoparticles: An Opposite Trend

Cited by 29 publications

References 45 publications

Misfolding of a DNAzyme for ultrahigh sodium selectivity over potassium

Misfolding of a DNAzyme for ultrahigh sodium selectivity over potassium

A Selective Na⁺ Aptamer Dissected by Sensitized Tb³⁺ Luminescence

Covalent and Non‐Covalent DNA–Gold‐Nanoparticle Interactions: New Avenues of Research

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Cation-Size-Dependent DNA Adsorption Kinetics and Packing Density on Gold Nanoparticles: An Opposite Trend

Cited by 29 publications

References 45 publications

Misfolding of a DNAzyme for ultrahigh sodium selectivity over potassium

Misfolding of a DNAzyme for ultrahigh sodium selectivity over potassium

A Selective Na+ Aptamer Dissected by Sensitized Tb3+ Luminescence

Covalent and Non‐Covalent DNA–Gold‐Nanoparticle Interactions: New Avenues of Research

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A Selective Na⁺ Aptamer Dissected by Sensitized Tb³⁺ Luminescence