Specific and nonspecific metal ion-nucleotide interactions at aqueous/solid interfaces functionalized with adenine, thymine, guanine, and cytosine oligomers

Ultra-sensitive dielectrophoretic surface charge multiplex detection inside a micro-dielectrophoretic device

Label-free dielectrophoretic force-based surface charge detection has shown great potential for highly sensitive and selective sensing of metal ions and small biomolecules. However, this method suffers from a complex calibration process and measurement signal interference in simultaneous multi-analyte detection, thus creating difficulties in multiplex detection. We have developed a method to overcome these issues based on the optical discrimination of the dielectrophoretic behaviors of multiple microparticle probes considering the surface charge difference before and after self-assembling conjugation. In this report, we demonstrate and characterize this dielectrophoretic force-based surface charge detection method with particle probes functionalized by various biomolecules. This technique achieved an attomolar limit of detection (LOD) for Hg²⁺ in distilled water and a femtomolar LOD in drinking water using DNA aptamer-functionalized particle probes. More importantly, using two different DNA aptamer-functionalized particle probes for Hg²⁺ and Ag⁺, label-free dielectrophoretic multiplex detection of these species in drinking water with a femtomolar and a nanomolar LOD was achieved for the first time.

Hydration and Charge-Transfer Effects of Alkaline Earth Metal Ions Binding to a Carboxylate Anion, Phosphate Anion, and Guanine Nucleobase

To investigate the ability of alkaline earth metal ions to tune ion-mediated DNA adsorption, hydrated Mg²⁺, Ca²⁺, Sr²⁺, and Ba²⁺ ions bound to a carboxylate anion, phosphate anion, and guanine nucleobase were modeled using density functional theory (DFT) and a combined explicit and continuum solvent model. The large first solvation shell of Ba²⁺ requires a larger solute cavity defined by a solvent-accessible surface, which is used to model all hydrated ions. Alkaline earth metal ions bind indirectly or directly to each binding site. DFT binding energies decrease with increasing ion size, which is likely due to ion size and hydration structure, rather than quantum effects such as charge transfer. However, charge transfer explains weaker ion binding to guanine compared to phosphate or carboxylate. Overall, carboxylate and phosphate anions are expected to compete equally for hydrated Mg²⁺, Ca²⁺, Sr²⁺, and Ba²⁺ ions and larger alkaline earth metal ions may induce weaker ion-mediated adsorption. The ion size and hydration structure of alkaline earth metal ions may effectively tune ion-mediated adsorption processes, such as DNA adsorption to functionalized surfaces.

A simple reagent-less approach using electrical discharge as a substitution for chelating agent in addressing genomic assay inhibition by divalent cations

Electrical discharge treatment was shown to be a viable substitution for chelating agent in genomic assays. Divalent cation Mg2+ inhibits the performance of DNA hybridization based genomic assays by binding to the DNA and disrupting DNA hybridization. Until now, chelating agents such as ethylenediaminetetraacetic acid (EDTA) was the only option to address the presence of Mg2+ in samples. However, EDTA is a well-known environmental contaminant. In this work, we successfully employed electrical discharge instead of EDTA to render Mg2+ insipid. Its preliminary efficacy was first observed via circular dichroism (CD) and zeta potential analyses. After electrical discharge treatment, the reduction in CD shift at 280 nm was significant for samples with 10-3 and 10-8 M Mg2+. The zeta potential of Mg2+ laden samples were also restored from -4.71 ± 1.38 to -20.59 ± 6.37 mV after electrical discharge treatment. Both CD shift and change in zeta potential suggested that 2 min of electrical discharge treatment could prevent Mg2+ from binding to DNA. The complete efficacy of electrical discharge treatment was demonstrated with the performance recovery (within ∼15% of the control) of a genomic assay variant (NanoGene assay) while analyzing Mg2+ laden samples (10-5-10-3 M). Assuming 10 million samples are analyzed annually, the proposed electrical discharge treatment (∼50 mW per sample) would allow us to trade environmental contamination by ∼50 kg of hazardous EDTA with a single 250 W STC (standard test conditions) solar panel.

Molecular dynamics simulations of alkaline earth metal ions binding to DNA reveal ion size and hydration effects

Classical molecular dynamics simulations reveal size-dependent trends of alkaline earth metal ions binding to DNA are due to ion size and hydration behavior.

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

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 Mg2+ 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 Mg2+ 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 Mg2+ binding to surface-bound ssDNA.

Adsorption of 2-vinyl thiophene on Si(100)2 × 1: A van Der Waals corrected DFT study

Oligo- and polythiophenes on surfaces play a fundamental role in building molecular circuits and organic-based electronics and may be assembled via interaction of the monomer units with the surface. In this framework, the nature of interaction of 2-vinyl thiophene (2VTP), a conjugated heteroaromatic monomer unit, with the Si (100) surface was studied by means of density functional theory (DFT). In particular, structural optimizations were performed comparing the effects of the inclusion of van der Waals (VdW) forces. It came out that the adsorption through the double bond is energetically favored, if VdW forces are included, whereas the adsorption through both aromatic ring and double bond simultaneously is more stable, if they are excluded. Physisorbed states were singled out and the barriers between two of them and the corresponding chemisorbed states were calculated along with the imaginary frequencies of the transition states. Also the transition energies have different values if the VdW forces are included.

The thermal reorganization of DNA immobilized at the silica/buffer interface: a vibrational sum frequency generation investigation

Vibrational SFG reveals that C–H stretches associated with the nucleobase rather than the phosphate-sugar backbone are most sensitive to DNA duplex “melting” at the silica/buffer interface.

Noncanonical structures and their thermodynamics of DNA and RNA under molecular crowding: beyond the Watson-Crick double helix

How does molecular crowding affect the stability of nucleic acid structures inside cells? Water is the major solvent component in living cells, and the properties of water in the highly crowded media inside cells differ from that in buffered solution. As it is difficult to measure the thermodynamic behavior of nucleic acids in cells directly and quantitatively, we recently developed a cell-mimicking system using cosolutes as crowding reagents. The influences of molecular crowding on the structures and thermodynamics of various nucleic acid sequences have been reported. In this chapter, we discuss how the structures and thermodynamic properties of nucleic acids differ under various conditions such as highly crowded environments, compartment environments, and in the presence of ionic liquids, and the major determinants of the crowding effects on nucleic acids are discussed. The effects of molecular crowding on the activities of ribozymes and riboswitches on noncanonical structures of DNA- and RNA-like quadruplexes that play important roles in transcription and translation are also described.

Choline ion interactions with DNA atoms explain unique stabilization of A-T base pairs in DNA duplexes: a microscopic view

Under physiological conditions, G-C base pairs are more stable than A-T base pairs. In a previous study, we showed that in the hydrated ionic liquid of choline dihydrogen phosphate, the stabilities of these base pairs are reversed. In the present study, we elucidated the unique binding interactions of choline ions with DNA atoms from a microscopic viewpoint using molecular dynamics simulations. Three times more choline ions bind to the DNA duplex than sodium ions. Sodium ions bind closely but not stably; in contrast, the choline ions bind through multiple hydrogen bonding networks with DNA atoms stably. The affinity of choline ion for the minor groove of A-T base pairs is more than 2 times that for other groove areas. In the narrow A-T minor groove, choline ion has high affinity for the ribose atoms of thymine. Choline ions also destabilize the formation of hydrogen bonds between G-C base pairs by binding to base atoms preferentially for both of duplex and single-strand DNA, which are associated with the bonds between G-C base pairs. Our new finding will not only lead to better control of DNA stability for use in DNA nanodevices, but also provide new insight into the stability of DNA duplexes under crowding conditions found in living cells.

Counting the number of magnesium ions bound to the surface-immobilized thymine oligonucleotides that comprise spherical nucleic acids

Label-free studies carried out under aqueous phase conditions quantify the number of Mg(2+) ions binding to surface-immobilized T40 sequences, the subsequent reordering of DNA on the surface, and the consequences of Mg(2+) binding for DNA-DNA interactions. Second harmonic generation measurements indicate that, within error, 18-20 Mg(2+) ions are bound to the T40 strand at saturation and that the metal-DNA interaction is associated with a near 30% length contraction of the strand. Structural reordering, evaluated using vibrational sum frequency generation, atomic force microscopy, and dynamic light scattering, is attributed to increased charge screening as the Mg(2+) ions bind to the negatively charged DNA, reducing repulsive Coulomb forces between nucleotides and allowing the DNA single strands to collapse or coil upon themselves. The impact of Mg(2+) binding on DNA hybridization and duplex stability is assessed with spherical nucleic acid (SNA) gold nanoparticle conjugates in order to determine an optimal working range of Mg(2+) concentrations for DNA-DNA interactions in the absence of NaCl. The findings are consistent with a charge titration effect in which, in the absence of NaCl, (1) hybridization does not occur at room temperature if an average of 17.5 or less Mg(2+) ions are bound per T40 strand, which is not reached until the bulk Mg(2+) concentration approaches 0.5 mM; (2) hybridization proceeds, albeit with low duplex stability having an average Tm of 31(3)°C, if an average of 17.5-18.0 Mg(2+) ions are bound; and (3) highly stable duplexes having a Tm of 64(2)°C form if 18.5-19.0 Mg(2+) ions are bound, corresponding to saturation of the T40 strand.

Rapid dissolution of DNA in a novel bio-based ionic liquid with long-term structural and chemical stability: successful recycling of the ionic liquid for reuse in the process

DNA from salmon testes was solubilised in two bio-based ionic liquids up to 3.5% w/w in 6 h. No structural degradation of the molecule was observed for the sample solubilised in choline-indole-3-acetate (chol-IAA). However, the molecule was found to be denatured in choline-indole-3-butyrate (chol-IBA). The structural and chemical stability of the DNA molecules after six months of storage in the former was established. Further recyclability of the ionic liquid with very high yield (90-95%) for consecutive reuse in the redissolution of DNA was demonstrated.

Importance of length and sequence order on magnesium binding to surface-bound oligonucleotides studied by second harmonic generation and atomic force microscopy

The binding of magnesium ions to surface-bound single-stranded oligonucleotides was studied under aqueous conditions using second harmonic generation (SHG) and atomic force microscopy (AFM). The effect of strand length on the number of Mg(II) ions bound and their free binding energy was examined for 5-, 10-, 15-, and 20-mers of adenine and guanine at pH 7, 298 K, and 10 mM NaCl. The binding free energies for adenine and guanine sequences were calculated to be -32.1(4) and -35.6(2) kJ/mol, respectively, and invariant with strand length. Furthermore, the ion density for adenine oligonucleotides did not change as strand length increased, with an average value of 2(1) ions/strand. In sharp contrast, guanine oligonucleotides displayed a linear relationship between strand length and ion density, suggesting that cooperativity is important. This data gives predictive capabilities for mixed strands of various lengths, which we exploit for 20-mers of adenines and guanines. In addition, the role sequence order plays in strands of hetero-oligonucleotides was examined for 5'-A(10)G(10)-3', 5'-(AG)(10)-3', and 5'-G(10)A(10)-3' (here the -3' end is chemically modified to bind to the surface). Although the free energy of binding is the same for these three strands (averaged to be -33.3(4) kJ/mol), the total ion density increases when several guanine residues are close to the 3' end (and thus close to the solid support substrate). To further understand these results, we analyzed the height profiles of the functionalized surfaces with tapping-mode atomic force microscopy (AFM). When comparing the average surface height profiles of the oligonucleotide surfaces pre- and post- Mg(II) binding, a positive correlation was found between ion density and the subsequent height decrease following Mg(II) binding, which we attribute to reductions in Coulomb repulsion and strand collapse once a critical number of Mg(II) ions are bound to the strand.

Binding and cleavage of DNA with the restriction enzyme EcoR1 using time-resolved second harmonic generation

The binding of EcoR1 to a 90-bp DNA duplex attached to colloidal microparticles and the subsequent cleavage by the enzyme was observed in real time and label-free with time-resolved second harmonic (SH) spectroscopy. This method provides a unique way to investigate biomolecular interactions based on its sensitivity to changes in structure and electrical charge on formation of a complex and subsequent dynamics. The binding of EcoR1 to the recognition sequence in DNA appears as a rapid increase in the SH signal, which is attributed to the enzyme-induced change in the DNA conformation, going from a rod-like to a bent shape. In the presence of the cofactor Mg(2+), the subsequent decay in the SH signal was monitored in real time as the following processes occurred: cleavage of DNA, dissociation of the enzyme from the DNA, and diffusion of the 74-bp fragment into the bulk solution leaving the 16-bp fragment attached to the microparticle. The observed decay was dependent on the concentration of Mg(2+), which functions as a cofactor and as an electrolyte. With SH spectroscopy the rehybridization dynamics between the rehybridized microparticle bound and free cleaved DNA fragments was observed in real time and label-free following the cleavage of DNA. Collectively, the experiments reported here establish SH spectroscopy as a powerful method to investigate equilibrium and time-dependent biological processes in a noninvasive and label-free way.

Divalent metal cation speciation and binding to surface-bound oligonucleotide single strands studied by second harmonic generation

The binding of Sr(II), Ca(II), Mg(II), Ba(II), Mn(II), Zn(II), and Cd(II) to silica/water interfaces functionalized with A(15)T(6) oligonucleotides was quantified at pH 7 and 10 mM NaCl using the Eisenthal χ((3)) technique. The binding free energies range from -31.1(6) kJ/mol for Ba(II) to -33.8(4) kJ/mol for Ca(II). The ion densities were found to range from 2(1) ions/strand for Zn(II) to 11(1) ions/strand for Cd(II). Additionally, we quantified Mg(II) binding in the presence of varying background electrolyte concentrations which showed that the binding free energies changed in a linear fashion from -39.3(8) to -27(1) kJ/mol over the electrolyte concentration range of 1-80 mM, respectively. An adsorption free energy versus interfacial potential analysis allowed us to elucidate the speciation of the bound Mg(II) ions and to identify three possible binding pathways. Our findings suggest that Mg(II) binds as a fully hydrated divalent cation, most likely displacing DNA-bound Na ions. These measurements will serve as a benchmark for computer simulations of divalent metal cation/DNA interactions for geochemical and biosensing applications.