Understanding the origin of liquid crystal ordering of ultrashort double-stranded DNA

Recent experiments have shown that short double-stranded DNA (dsDNA) fragments having six- to 20-base pairs exhibit various liquid crystalline phases. This violates the condition of minimum molecular shape anisotropy that analytical theories demand for liquid crystalline ordering. It has been hypothesized that the liquid crystalline ordering is the result of end-to-end stacking of dsDNA to form long supramolecular columns which satisfy the shape anisotropy criterion necessary for ordering. To probe the thermodynamic feasibility of this process, we perform molecular dynamics simulations on ultrashort (four base pair long) dsDNA fragments, quantify the strong end-to-end attraction between them, and demonstrate that the nematic ordering of the self-assembled stacked columns is retained for a large range of temperature and salt concentration.

Figure 1

PMF profiles at 300 K for a pair of 4-bp DNA fragments. End-to-end PMF for blunt-end DNA (GTAC) fragments in (a) FH configuration and (b) SH configuration. (c) PMF for shifted-end DNA (GCTA) as well as (d) PMF for blunt-end DNA fragments placed side-by-side. The insets show the definition of the reaction coordinates for each PMF calculation and the initial systems corresponding to different windows along the reaction coordinate.

Figure 2

(a) Mechanism of LC phase formation in aggregates of ultrashort dsDNA. (b) Nematic phase of blunt-end (GTAC) DNA system with SH initial configuration for $\mathrm{\Phi }$ of 52% at 280 K. (c) Isotropic phase of blunt-end DNA system with SH initial configuration for $\mathrm{\Phi }$ of 20% at 280 K.

Figure 3

(a) Average nematic order parameter at different volume fractions $\left(\mathrm{\Phi }\right)$ for different systems at 280 K. (b) Variation of order parameter with salt concentration (black) for blunt-end DNA (GTAC) system with an initial FH configuration at $\mathrm{\Phi }$ of 52% and temperature (red) for blunt-end DNA (GTAC) system with an initial SH configuration at $\mathrm{\Phi }$ of 52%.

Figure 4

(a) $\phi$ distribution for blunt-end DNA (GTAC) system with FH initial configuration and (b) SH initial configuration for $\mathrm{\Phi }$ of 52% and 20% at $T=280$ K.