Modelling the melting of DNA oligomers with non-inert dangling ends

Abstract

In this work, we investigate the dependence of the melting temperature of low-valency DNA constructs on the length of non-inert dangling ends, controlling their sequence composition. We compare two computational models to evaluate their effectiveness and limitations in predicting the melting behavior of DNA oligomers (bivalent linkers) and more complex structures (trivalent nanostars), benchmarking the results against experimental spectroscopic data. Our results suggest that the length of non-inert dangling ends has minimal impact on the melting point of the DNA duplex for the duplexes we studied, informing the future design of DNA supramolecular constructs.

Keywords: DNA nanotechnology; NUPACK; melting curves; molecular dynamics; oxDNA; umbrella sampling.

FIGURE 1

Schematic of the building blocks employed in this study: (a) Linker “LS12” with a 12-nucleotide-long sticky end. Linear sequence representation and three-dimensional representation showing the approximate volume the construct occupies. (b) Linker “LS6” with a 6-nucleotide-long sticky end. As in (a), we show a linear sequence and three-dimensional representations giving the approximate volume the construct occupies. (c) A trivalent nanostar (Y-shape) joined with a double-stranded linker LS6, justifying the rational design of our non-inert sequences, although here we performed simulations and experiments only on the individual building blocks. (d) Potential energy contributions included in the oxDNA model, used to calculate intra- and inter-strand interactions.

FIGURE 2

Melting curves as a function of temperature, obtained from (a) UV-visible absorbance experiments, (b) NUPACK statistical mechanics treatment, and (c) oxDNA MD unbiased simulations for dimers with dangling ends of different length and for a Y-shape. Error bars in (a) are obtained from the values measured in heating and cooling ramps.

FIGURE 3

Melting temperature as a function of the length of the sticky ends from UV-visible absorbance experiments (squares), NUPACK statistical treatment (triangles), and oxDNA MD unbiased simulations (circles).