A study of the structure of highly concentrated phases of DNA by X-ray diffraction

Abstract

In aqueous solution, pure DNA forms multiple liquid crystalline and crystalline phases whose nature depends on the polymer concentration. The following phase sequence is observed when the DNA concentration increases : isotropic ↦ cholesteric ↦ columnar hexagonal ↦ crystalline phases. The aim of this work is to obtain structural information about the highly concentrated phases formed by 500 Å long DNA molecules — in particular about the crystalline phases — by means of X-ray diffraction. We show that in the two-dimensional (2D) ordered hexagonal phase a longitudinal order progressively appears between neighbouring DNA helices leading continuously to a three-dimensional (3D) ordered hexagonal phase. For higher concentrations the specimens undergo a discontinuous transition towards an orthorhombic phase. The characteristic structural parameters of these different phases have been determined. An important result is that the number of nucleotides per helix turn decreases continuously, when the DNA concentration increases, from 10.3±0.1 at the cholesteric ↦ hexagonal transition down to 9±0.1 without any apparent change of the B conformation of the molecules.

Molecular Dynamics Simulation of High Density DNA Arrays

“…Therefore, the rotational analog of the Lindemann empirical criterion [73] is a good proxy to establish the point of H → OR phase transition. We estimated [73] this transition to occur roughly at DNA concentrations between 700-800 and 500-700 mg/mL for the Na + and Na + -Spd 3+ counterions, respectively, which also compares favorably with the experimental estimations, i.e., ≈670 mg/mL [10,11]. A more consistent determination of the phase transition based on no additional assumptions or approximations could proceed from the free-energy landscape computed by enhanced sampling techniques.…”

“…Applying the large water reservoir simulation methodology in order to implement the osmotic isobaric ensemble, the DNA subphase can then be segregated from the large water reservoir by way of either a cylindrical [51] or a combined orthorhombic-hexagonal semipermeable boundary [73]. Changing the symmetry of the boundary confining the DNA subphase is a convinient approach to capture the phase transitions with a change of packing symmetry, such as the cholesteric (Ch) → line hexatic (LH) (or hexagonal columnar H) and/or the line hexatic → orthorhombic (OR) phase transitions [3,11,15,18].…”

“…It was only recently, through high resolution control of the osmotic pressure based on its known temperature variation [9,10], that a small discontinuous DNA density change became discernible, between the cholesteric and hexatic phases and between the hexatic and orthorhombic phases for long fragment DNA [10]. The exact sequence and identity of the phases actually depends on the DNA length [11,12] and is apparent also from a sudden discontinuous change in the corresponding order parameters [13,14]. The detailed sequence of mesophase ordering on increase of the DNA density has been identified as consisting of isotropic (I) → cholesteric (Ch) → line hexatic (LH) (or hexagonal columnar H) → orthorhombic (OR) phase [3,11,[15][16][17][18], with many details, including the complete DNA length dependence and the demarcation between the line hexatic and hexagonal order, still remaining to be systematically investigated [19].…”

“…The exact sequence and identity of the phases actually depends on the DNA length [11,12] and is apparent also from a sudden discontinuous change in the corresponding order parameters [13,14]. The detailed sequence of mesophase ordering on increase of the DNA density has been identified as consisting of isotropic (I) → cholesteric (Ch) → line hexatic (LH) (or hexagonal columnar H) → orthorhombic (OR) phase [3,11,[15][16][17][18], with many details, including the complete DNA length dependence and the demarcation between the line hexatic and hexagonal order, still remaining to be systematically investigated [19]. For multivalent counterions at concentrations above a critical value depending on their identity [20], the EoS exhibits pronounced van der Waals-like density discontinuities that are in general larger then in the case of monovalent salt solutions, signalling a buildup of attractive interactions [21,22], whose details can be inferred from complementary experiments [23], that eventually lead to DNA condensation [24].…”

Re-entrant cholesteric phase in DNA liquid-crystalline dispersion particles

“…Upon the increase of the linear ds DNA concentration in water-salt solution, the isotropic solution transforms (via either blue phases or precholesteric stages) into the cholesteric LC phase. Under poly(ethylene glycol)-PEG-osmotic pressure compression the hexagonal densely packed structure becomes favorable and more concentrated phases can be considered even as true crystals [15][16][17][18][19].…”