Investigation of Compacted DNA Structures Induced by Na+ and K+ Monovalent Cations using Biological Nanopore

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 highly potential method 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 1M 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 study 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 affinities of each nucleotide to cations is different, the ability of DNA to fold and compact depends highly on the type of cations and nucleotides present. Our experimental results compare favorably with findings from previous molecular dynamics simulations for 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 about 30:1 and 15:1, at a pH of 7.2 and pH of 10 respectively. Our comparative studies reveal that Na+ monovalent cations have a greater compacting potential on the 15C-ssDNA than a K+ cation does.