Terminal Sequence-Specific Interparticle Attraction between DNA Duplex-Carrying Polystyrene Microparticles in Aqueous Salt Solution Assessed by Optical Tweezers

Abstract

The dispersion behavior of DNA duplex-carrying colloidal particles in aqueous high-salt solutions shows extraordinary selectivity against the duplex terminal sequence. We investigated the interparticle force between DNA duplex-carrying polystyrene (dsDNA-PS) microparticles in aqueous salt solutions and examined their behavior in relation to the duplex terminal sequences. Force−distance (F−D) curves for a pair of dsDNA-PS particles were recorded with a dual-beam optical tweezers system with the two optically trapped particles closely approaching each other. Interestingly, only 3− 5% of the oligo-DNA strands on the dsDNA-PS particles formed a duplex with complementary DNAs, and the F−D curves showed a distinct specificity to the duplex terminal sequences in the interparticle force at a high-NaCl concentration; a clear attraction peak was observed in F−D curves only when the duplex terminal was a complementary base pair. The attractive strength reached 2.6 ± 0.5 pN at 500 mM NaCl and 4.3 ± 1.0 pN at 750 mM NaCl. By sharp contrast, no significant attraction occurred for the particles with mismatched duplex terminals even at 750 mM NaCl. Similar duplex terminal-specificity in the interparticle force was also confirmed for dsDNA-PS particles in divalent MgCl 2 solutions. Considering that the duplex terminal sequences on the dsDNA-PS particles showed only a negligible difference in their surface charges under identical salt conditions, we concluded that the interparticle attraction observed only for the dsDNA-PS particles with complementary duplex terminals is attributable to the salt-facilitated stacking interaction between the paired terminal nucleobases (i.e., blunt-end stacking) on the dsDNA-PS surfaces. Our results thus demonstrate the occurrence of a duplex terminal-specific interparticle force between dsDNA-PS particles under high-salt conditions.

A Simple Colorimetric Assay of Bleomycin‐Mediated DNA Cleavage Utilizing Double‐Stranded DNA‐Modified Gold Nanoparticles

“…Such behavior may be due to differences between the attractive blunt‐end stacking at the matched dsDNA terminal and the repulsive mismatched dsDNA terminal on the particle. In fact, the analysis of the force‐distance curve between the dsDNA layers in atomic force microscopy supported the assumption [54,55] . It was also found that single‐base protrusions on dsDNA‐AuNPs exhibited high colloidal stability even in high ionic aqueous solutions [56] .…”

“…In fact, the analysis of the force‐distance curve between the dsDNA layers in atomic force microscopy supported the assumption. [ 54 , 55 ] It was also found that single‐base protrusions on dsDNA‐AuNPs exhibited high colloidal stability even in high ionic aqueous solutions. [56] The high colloidal stability with a dangling end on dsDNA‐AuNPs allowed more reliable human‐related cytochrome P450 2C19 gene SNP genotyping, which plays a role in the metabolism of pharmaceutical agents.…”

Demonstration of a Magic Reaction: Accelerating DNA Functionalization of Gold Nanoparticles by Freezing

“…The results could be ascribed to the entropic repulsion among the DNA-AuNPs produced by the free bases at the outermost surface, since the resulting T-T mismatch at the penultimate position disturbs the G-C base pairing at the distal end. 18,19 The corresponding results obtained by the other group are shown in Figure S3. By introducing the basic knowledge of plasmon resonance, the students could learn the unique optical property of AuNP, and that the shortening of interparticle distance leads to the coupling of the plasmon resonance and thereby the red-topurple color change of the AuNPs.…”