Unraveling Molecular Dynamics
Supercoiled DNA states, char-
acteristic for interactions with mol- ecules, such as other nucleic acids, DNA-specific enzymes, etc., can drive partial “unzipping” of the double-stranded DNA regions [21]. It is generally driven by a torsional stress around the strand axis. Once the molecule is dehybridized, and due to the hydrophobic organic base backbone, the single strands twist around the axis to minimize contact with water (Figure 3). Several X-ray structural models
Figure 3: Selected frames from a 6915-frame-long high-speed DNA bubble rehybridization sequence, showing individual single-stranded DNA conformation states, imaged with a temporal resolution of 25 ms. The lower left insets indicate the backtraced shapes of the metastable DNA bubble. XY-scaling of the amplitude AFM images is 100×100 nm2
.
additional epitopes. Currently we are working on fine-tuning the streptavidin- biotin binding by using enhanced mono- and bivalent streptavidin protocols [11].
predicted that the very hierarchical structure of collagen type I involves different structural intermediates, one of which is a microfibrillar unit (4–5 nm) that ultimately gives rise to thicker fibrillar structures with a char- acteristic D-banding of 67 nm [22,23]. Our results show that the dynamics of collagen type I fibrillogenesis can be studied successfully with high-speed AFM, while also indicating the exis- tence of several structural intermedi- ates in the fibril formation (Figure 4).
Te identified 5–8 nm wide fibrillar units, aſter accounting for certain AFM tip convolution, can be attributed to the already- mentioned microfibrillar units. Te sub-D-banding periodicity,
Figure 4: High-speed imaging of collagen type I fibril formation at 15 frames/sec, studied over near 3900 frames. Cross-section profile P1 identifies the repeating characteristic D-band (67 nm) and shows the existing sub-D-banding structure. Profile P2 is used for identification of several speculative microfibrillar units in the fibrillar films.
2022 May •
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