Research ArticleBIOMATERIALS

The structure of DNA by direct imaging

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Science Advances  28 Aug 2015:
Vol. 1, no. 7, e1500734
DOI: 10.1126/sciadv.1500734

Figures

  • Fig. 1 A-DNA direct image and metrology.

    (A) HRTEM phase-contrast image of a single A-DNA helix bound to a 100 Å DNA bundle obtained by stacking two images acquired with 50 e/s Å2 at 80 keV. (B) Dotted line sharpens the DNA location. Major and minor grooves and the helix pitch of 26.5 Å are highlighted. (C) The principal lengths (the backbones, the base pairs (BPs), the diameter, and the rise per base pair) are indicated and reported in Table 1. The length difference between the purine and pyrimidine bases is also shown: a.u., arbitrary unit. (D) The tilt of the base pairs with respect to the helix axis is reported and measures 19°.

  • Fig. 2 Base propeller twist.

    A representative image of simulating different amounts of propeller twist of the A-T couple of bases in A-DNA is shown.

  • Fig. 3 A-DNA simulations.

    (A) Atomic model of A-DNA and corresponding HRTEM image simulations calculated using three defocus (Δf) values. (B) The A-DNA filament was subdivided into four plane slices of ¼t = 6.0 Å parallel to the helix axis. The black arrow indicates the electron beam propagation direction perpendicular to the planes. The corresponding electron exit wave functions at ¼t, ½t, ¾t, and t show phase variations directly correlated to specimen potential and atom position. Amplitude changes are negligible due to weak phase object approximation. In both (A) and (B), the lattice fringes form angles of 18° with respect to the helix axis, and the periodicity of minor and major grooves is in accordance with the double-helix atomic model.

Tables

  • Table 1 A-DNA structural lengths.

    Relevant measured lengths of A-DNA, as obtained by imaging data reported in Fig. 1 (see inset), are shown. The data reported for HRTEM imaging are coherent and comparable with the x-ray accepted values (1315, 30) and the simulations shown in Fig. 2.

    A-DNA structural
    characteristics
    HRTEM
    measurements* (Å)
    X-ray and
    simulation data (Å)
    Diameter21.223.0
    Rise/base pair along axis2.52.6
    Pitch/tum of helix26.528.2
    Phosphate + sugar
    (backbone A1)
    5.15.3
    Base (B1)3.64.0
    Base (B2)5.25.4
    Phosphate + sugar
    (backbone A2)
    5.05.3
    Base length (B1 + B2 +
    base interdistance)
    11.311.5
    Tilt of base pair relative
    to the axis
    19°19°

    *The statistical error for the measured lengths is estimated to be 1.5 Å from the inset of Fig. 1.

    †X-ray accepted values of relevant lengths as reported in (1315, 30).

    ‡Data obtained from the simulation of the twisted bases of Fig. 2 and as reported in (13).

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