Exploring the thermal stability of DNA-linked gold nanoparticles in ionic liquids and molecular solvents

Abstract

While water is the most commonly used solvent for DNA, many co-solvents have been added for various applications. Ionic liquids (ILs) are molten salts at around room temperature. ILs have been tested as a green solvent for many reactions and many biopolymers can also be dissolved in ILs. In this work, we study DNAlinked gold nanoparticles (AuNPs) in seven types of ILs. DNA-functionalized AuNPs possess 10 a high density of negative charges and thus may generate new physical properties in ILs. We have identified the role of ILs to transit from salts to increase DNA duplex stability to solvents to decrease DNA melting temperature. The onset of this transition depends on the structure of ILs, where more hydrophobic cations destabilize DNA at lower IL concentrations. This trend is opposite to molecular solvents (e.g. ethanol, DMSO, ACN and DMF) that destabilize DNA at low solvent concentration. 15 Specific DNA base pairing is disrupted at high DMSO concentrations, and AuNPs are held together by non-specific interactions. The other tested molecular solvents are able to maintain DNA base pairs, although strong non-specific interactions are also present. Several ILs can release proton and thus drastically change pH, which also changes the melting temperature of DNA. This study also reveals the feasibility of using ILs as solvents for DNA-functionalized nanomaterials.

Strand-Exchange Nucleic Acid Circuitry with Enhanced Thermo-and Structure- Buffering Abilities Turns Gene Diagnostics Ultra-Reliable and Environmental Compatible

“…Meanwhile, the non-catalytic reaction rate (without C1) still kept unchanged “zero” in the same recipe, about 500-fold less than that of catalytic reaction. Above surprising improvement could be partially explained by earlier finding17181920212223242526272829 and our experiments (Figure S5) that formamide could accelerate the hybridization rate. Being identically consistent with one other pioneering literature22, we also observed formamide could linearly decrease duplex melting temperature at a rate of approximate −6.5 °C/volume fraction (×100) formamide (Figure S6), suggesting formamide was meanwhile destabilizing the nucleobase pairs.…”

“…In the following several decades, these properties of formamide have been successively employed for increasing reaction rate or accuracy of many novel nucleic acid interactions20212223242526272829, including those milestones such as polymerase chain reaction20, sequencing21 and nanostructure assembly262729. Inspired by these early findings, here we deeply explored the amide (especially formamide)-assistant mechanism in the CHA reaction and showed dramatic enhancement in the buffering ability of a CHA against unexpected self-folding or temperature-cooling.…”

Trifluoromethylated nucleic acid analogues capable of self-assembly through hydrophobic interactions

“…3 Assembly of such building blocks creates well-defined structures with applications in highly sensitive and selective sensors or detectors, 4 nano-scale electronics, 5 and nanomachines. 6 The replacement of Watson-Crick hydrogen bonding with strictly hydrophobic interactions confers new properties and facilitates the construction of complex DNA nano-devices, expanding the repertoire of DNA nanotechnology beyond the boundaries of Watson-Crick base pairing.…”

DNA duplex stabilization in crowded polyanion solutions

“…DNA melting was thus monitored by fluorescence enhancement. [15][16][17][18][19] The melting curves in the presence of increasing concentrations of NaPAA1200 are shown in Figure 2A, where typical DNA melting transitions are observed. The temperature corresponding to the maximal of the first 65 derivative of a melting curve is Tm.…”