Reduction of DNA Folding by Ionic Liquids and Its Effects on the Analysis of DNA–Protein Interaction Using Solid‐State Nanopore

Abstract

DNA folding is not desirable for solid-state nanopore techniques when analyzing the interaction of a biomolecule with its specific binding sites on DNA since the signal derived from the binding site could be buried by a large signal from the folding of DNA nearby. To resolve the problems associated with DNA folding, ionic liquids (ILs), which are known to interact with DNA through charge-charge and hydrophobic interactions are employed. 1-n-butyl-3-methylimidazolium chloride (C mim) is found to be the most effective in lowering the incident of DNA folding during its translocation through solid-state nanopores (4-5 nm diameter). The rate of folding signals from the translocation of DNA-C mim is decreased by half in comparison to that from the control bare DNA. The conformational changes of DNA upon complexation with C mim are further examined using atomic force microscopy, showing that the entanglement of DNA which is common in bare DNA is not observed when treated with C mim. The stretching effect of C mim on DNA strands improves the detection accuracy of nanopore for identifying the location of zinc finger protein bound to its specific binding site in DNA by lowering the incident of DNA folding.

From Water Solutions to Ionic Liquids with Solid State Nanopores as a Perspective to Study Transport and Translocation Phenomena

“…The usage of the room temperature ionic liquids in nanopore setups would be a big shift from classical aqueous solutions, as is evident from a low number of papers published within the community. [44][45][46][47][48] In order to make this novel field more approachable, we have used analogies to the well understood behavior in aqueous solutions. Our understanding of these systems is still in its infancy, so such analogies should be taken only as a guideline for future research.…”

“…[74] On the colloidal scale, besides DNA folding caused by strong pressure exhibited by the external source of voltage when DNA is near the nanopore, [75] the aggregation phenomenon can also reduce the accuracy of nucleotides sequencing. [47] In the case of [C 2 Mim] [Cl], the ion association decreased intra-repulsions via classical Manning condensation, which led to the undesired coil-globule transition. On the other hand, in the case of [C 8 Mim][Cl], the favorable overlap of the hydrophobic chains and the water exclusion caused the formation of DNA bundles which also blocked the translocation through the nanopore.…”

“…So far ionic liquids have seen only limited use with solid state nanopores both in theoretical modeling [41][42][43] and experiments. [44][45][46][47][48] Notable is the recent demonstration of the dramatic slowdown of DNA translocations in 2D nanopores with an interface between an aqueous KCl salt solution and a pure ionic liquid. [46] Our aim is to provide an overview of the related theoretical and experimental research done on ionic liquids, and put a perspective on ionic liquids and other classes of Coulomb fluids [49] in expanding the versatility of solid state nanopores as both single-molecular sensors and probes of nanoscale physics.…”

Nanopore Sensing Technique for Studying the Hofmeister Effect

“…For monovalent anions, only kosmotropic H 2 PO 4 shows a strong binding affinity to the positive charge of the nanopore resulting in a significant change in the rectification phenomenon. For the divalent anions, SO 4 2has no significant effect, whereas Furthermore, nanopores have also been used to study the ion interactions with not only nanopores but macromolecules such as polynucleotides [103][104][105] and proteins [106][107][108] translocating through there. It is important to notice that in Tabard-Cossa's recent work, they systematically studied and discussed how various factors of the Hofmeister effect would contribute to affecting the protein stability and change the protein confor-mation in solid-state nanopores using the interaction between monovalent streptavidin and LiCl, NaCl, and KCl (Figure 19).…”

Time-Dependent Growth of Gold Nanoparticles: Experimental Correlation of van der Waals Contact between DNA and Amino Acids with Polar Uncharged Side Chains

“…The DNA–protein interaction is the basic understanding of complex biological systems. , This interaction is quite different from covalent interactions even for the case of specific DNA-binding proteins. , The weak interactions, which are responsible for DNA–protein interactions specifically through the amino acids within proteins, are van der Waals contact, hydrogen bonding, and water-mediated bonding interactions . The theoretical predictions − and experimental proofs − of DNA–protein interactions are quite evident in the recent time literature.…”