Investigation of compacted DNA structures induced by Na⁺and K⁺monovalent cations using biological nanopores

Abstract

In aqueous solutions, an elongated, negatively charged DNA chain can quickly change its conformation into a compacted globule in the presence of positively charged molecules, or cations. This well-known process, called DNA compaction, is a method with great potential for gene therapy and delivery. Experimental conditions to induce these compacted DNA structures are often limited to the use of common compacting agents, such as cationic surfactants, polymers, and multivalent cations. In this study, we show that in highly concentrated buffers of 1 M monovalent cation solutions at pH 7.2 and 10, biological nanopores allow real-time sensing of individual compacted structures induced by K and Na, the most abundant monovalent cations in human bodies. Herein, we studied the ratio between compacted and linear structures for 15-mer single-stranded DNA molecules containing only cytosine nucleotides, optimizing the probability of linear DNA chains being compacted. Since the binding affinity of each nucleotide to cation is different, the ability of the DNA strand to fold into a compacted structure greatly depends on the type of cations and nucleotides present. Our experimental results compare favorably with findings from previous molecular dynamics simulations for the DNA compacting potential of K and Na monovalent cations. We estimate that the majority of single-stranded DNA molecules in our experiment are compacted. From the current traces of nanopores, the ratio of compacted DNA to linear DNA molecules is approximately 30 : 1 and 15 : 1, at a pH of 7.2 and 10, respectively. Our comparative studies reveal that Na monovalent cations have a greater potential of compacting the 15C-ssDNA than K cations.

A signal-on fluorescent biosensor for mercury detection based on a cleavable phosphorothioate RNA fluorescent probe and metal–organic frameworks

“…The reaction buffer directly affects the sensitivity of the biosensor, so we next evaluated the effect of buffers with and without ionicity on the results because K + and Na + in the buffer stimulate cleavage site hydrolysis and induce self-folding and compaction of ssDNA. 21 PBS buffer was compared to some buffers without ionicity, including Tris–HCl, HEPES, and TE. The fluorescence intensities in the “blank” and “Hg 2+ ” groups minimally change for the TE buffer, as shown in Fig.…”

Recent advances in biological nanopores for nanopore sequencing, sensing and comparison of functional variations in MspA mutants

“…131 Additionally, identication of microcystin (MC) variants 132 and discerning the MC variants on the basis of their molecular interaction with a-hemolysin nanopore have also been carried out. 133 Currently, a-hemolysin nanopore has been used in exploring some new features of molecules, that is, the conformational heterogeneity of DNA assemblies, 134 DNA compaction instigated by Na + and K + ions, 135 determination of an intermediate in a catalyzed reaction cycle 136 unzipping mechanism of free and poly arginine-attached DNA-PNA duplexes to unveil the differences in their unzipping kinetics in a nano-conned space 137 and effect of glycerol and PEG molecules on the viscosity of aqueous solution together with their inuence on molecular motion of hairpin DNA. 138 Besides, early scanning of T790M drug resistance (infrequent mutation sequence) has become possible with a probe containing three locked nucleic acid (LNA) and a-hemolysin nanopore.…”