Exploring the mechanisms of DNA hybridization on a surface

Abstract

DNA microarrays are a potentially disruptive technology in the medical field, but their use in such settings is limited by poor reliability. Microarrays work on the principle of hybridization and can only be as reliable as this process is robust, yet little is known at the molecular level about how the surface affects the hybridization process. This work uses advanced molecular simulation techniques and an experimentally parameterized coarse-grain model to determine the mechanism by which hybridization occurs on surfaces. The results show that hybridization proceeds through a mechanism where the untethered (target) strand often flips orientation. For evenly lengthed strands, the surface stabilizes hybridization (compared to the bulk system) by reducing the barriers involved in the flipping event. For unevenly lengthed strands, the surface destabilizes hybridization compared to the bulk, but the degree of destabilization is dependent on the location of the matching sequence. Taken as a whole, the results offer an unprecedented view into the hybridization process on surfaces and provide some insights as to the poor reproducibility exhibited by microarrays.

An experimentally-informed coarse-grained 3-site-per-nucleotide model of DNA: Structure, thermodynamics, and dynamics of hybridization

“…The same mechanism was observed in simulations of surface hybridization. [25][26][27] The offset nucleation observed in past work was influenced by the relatively rigid, helical structure of ssDNA in 3SPN.1. Because the two strands were predominantly helical, the only way for hybridization to succeed was for the strands to wrap around each other, followed by "slithering."…”

“…3SPN.1, a subsequent refinement of the model, enabled a description of denaturation and renaturation as a function of temperature and ionic strength. 11 This model has been used to explore the pathways for hybridization in the bulk 23,24 and on surfaces, [25][26][27] and has provided new insights into DNA bending, 28 DNA melting, 29 and DNA-based hybrid structures. 30 It has since been extended to include explicit ions [30][31][32] and water.…”

Regimes of streaming potential in cylindrical nano-pores in presence of finite sized ions and charge induced thickening: An analytical approach

“…31,32 Miniaturized devices have been employed for a wide variety of applications ranging from chemical separation, [33][34][35][36][37][38][39][40] mixing, [41][42][43][44][45][46][47][48][49] analysis, 35,50 DNA hybridization, [51][52][53][54][55] etc. Realizing the importance and wide-range applicability of these phenomena, there have been several attempts to theoretically model the coupled electrical and hydrodynamic phenomena.…”

Coarse-graining DNA for simulations of DNA nanotechnology

“…53,54,111,118,119 For oxDNA, hybridization normally occurs by the formation of a nucleus of a few correct base pairs, followed by the "zippering" up of the rest of the duplex as bases are transferred from the relatively unstructured single- Fig. 7(d)), (c) the formation of a kissing complex at 296 K between two hairpins with 20-base complementary loops ( Fig.…”