Stochastic Binding Process of Blunt-End Stacking of DNA Molecules Observed by Atomic Force Microscopy

Abstract

Hydrophobic attraction is often a physical origin of nonspecific and irreversible (uncontrollable) processes observed for colloidal and biological systems, such as aggregation, precipitation, and fouling with biomolecules. On the contrary, blunt-end stacking of complementary DNA duplex chain pairs, which is also mainly driven by hydrophobic interaction, is specific and stable enough to lead to self-assemblies of DNA nanostructures. To understand the reason behind these contradicting phenomena, we measured forces operating between two self-assembled monolayers of duplexed DNA molecules with blunt ends (DNA-SAMs) and analyzed their statistics. We found the high specificity and stability of blunt-end stacking that resulted in the high resemblance between the interaction forces measured on approaching and retracting. The other finding is on the stochastic formation process of blunt-end stacking, which appeared as a significant fluctuation of the interaction forces at separations smaller than 2.5 nm. Based on these results, we discuss the underlying mechanism of the specificity and stability of blunt-end stacking.

Mono- and bilayer smectic liquid crystal ordering in dense solutions of “gapped” DNA duplexes

“…Our results presented above provide compelling evidence that two distinct layer structures characterize smectic ordering in GDNA solutions-one with periodicity approximately two duplexes, observed for gap lengths n 10, and the other with approximately one duplex period that predominates for n 10. One mechanism that would promote the stability of the two-duplex layer structure is the hydrophobic attraction between the blunt ends of different duplexes (6,(16)(17)(18), which could promote pairing of folded duplexes and their organization into a regular bilayer structure with end-end paired duplexes separated by thin layers containing the flexible single-strand segments of the GDNA constructs (Fig. 4D).…”

Gold Nanoparticle-Based Colorimetric Strategies for Chemical and Biological Sensing Applications

“…This transition reduces the electrostatic interaction between nanoparticles because the rigid structures of the duplexes favor binding with counter cations. Moreover, duplexes lower the entropic effect, which decreases the steric repulsion [64,65]. Notably, the dsDNA–AuNPs with a single-pair mismatch at the terminal position significantly increase the colloidal stability of the AuNPs and prevent the non-cross-linking aggregation.…”

Lab on a Tip: Atomic Force Microscopy as a Versatile Analytical Tool for Nano-bioscience

“…They observed hydrophobic attraction and water-induced repulsion for complementary DNA and mismatched DNA layers, respectively, indicating that the water structure and behavior strongly depend on the complementarity of terminal base pairs. (33,34) The above reports imply that biomolecules smartly use the interfacial water around them to function more than we expected.…”