Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2024 Sep 10;15(1):7894.
doi: 10.1038/s41467-024-51721-y.

Controlled mechanochemical coupling of anti-junctions in DNA origami arrays

Fiona Cole #  1   2 , Martina Pfeiffer #  1   2 , Dongfang Wang #  3   4   5   6 , Tim Schröder  1   2 , Yonggang Ke  7   8 , Philip Tinnefeld  9   10
Affiliations

Controlled mechanochemical coupling of anti-junctions in DNA origami arrays

Fiona Cole et al. Nat Commun. .

Abstract

Allostery is a hallmark of cellular function and important in every biological system. Still, we are only starting to mimic it in the laboratory. Here, we introduce an approach to study aspects of allostery in artificial systems. We use a DNA origami domino array structure which-upon binding of trigger DNA strands-undergoes a stepwise allosteric conformational change. Using two FRET probes placed at specific positions in the DNA origami, we zoom in into single steps of this reaction cascade. Most of the steps are strongly coupled temporally and occur simultaneously. Introduction of activation energy barriers between different intermediate states alters this coupling and induces a time delay. We then apply these approaches to release a cargo DNA strand at a predefined step in the reaction cascade to demonstrate the applicability of this concept in tunable cascades of mechanochemical coupling with both spatial and temporal control.

PubMed Disclaimer

Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1. Concept for following the transformation reaction of reconfigurable DNA origami array structures on the single-molecule level in real time.
a Scheme of the DNA origami array model structure transforming upon addition of DNA trigger strands. Red and green FRET probes (ATTO647N-IowaBlack RQ and ATTO542-BHQ2, red/ black and blue/ purple circles) are placed at the positions at which the transformation reaction is studied. The transformation process occurs diagonally, starting either from the top right corner, as shown in the sketch, or from the bottom right corner. b Sketch of conformational flipping of a single anti-junction. Blue DNA strands represent sections of the scaffold strand, whereas pink and orange strands represent different staple strands. c, d AFM images of the DNA origami array (c) before and (d) after overnight incubation with trigger strands indicate a successful transformation of the structure. e, f Exemplary TIRF images of the DNA origami array structure before and after incubation with and without trigger strands. Fluorescence of ATTO647N is shown in red, fluorescence of ATTO542 in blue and co-localized fluorescence of both in white.
Fig. 2
Fig. 2. Real-time imaging of the transformation reaction of DNA origami arrays.
a Representative single-molecule fluorescence intensity transients of DNA origami array with a green and a red FRET probe incorporated after addition of five trigger DNA strands at 0 s. The time the transformation occurs at the red and the green FRET probe positions is marked with an arrow. Fluorescence of ATTO647N and ATTO542 is shown in red and blue, respectively. b Transformation time after the addition of five trigger DNA strands at the position of the red FRET probe (red) and the green FRET probe (blue). c Scheme of the different positions used for the placement of the FRET probes on DNA origami arrays for tracking the transformation reaction. d–g Time difference between the transformation occurring at the positions of the green and red FRET probes for different FRET probe positions. h Proposed, simplified energy landscape of the transformation reaction. The intermediates at which the studied positions switch their conformation are marked with numbers.
Fig. 3
Fig. 3. Reversibility and coupling in the transformation reaction upon addition of different numbers of trigger DNA strands.
a Representative single-molecule fluorescence intensity transients of DNA origami arrays with FRET probes placed at different positions upon the addition of all five trigger DNA strands (upper row) and only the upper four trigger strands (middle and lower row) at 0 s. Fluorescence of ATTO647N and ATTO542 is shown in red and blue, respectively. b Fraction of structures exhibiting fluctuations between the untransformed and transformed conformation at the different positions of the FRET probes upon addition of all five or the upper four trigger strands. Error bars represent the standard error of at least 80 structures. c Mean absolute time differences for the transformation occurring at the different positions upon addition of five trigger strands and upon the addition of the upper four trigger DNA strands. For designs in which the majority of structures exhibited a time delay between the transformation at the different positions, only non-perfectly coupled structures with △t≠0s were considered. All plots show the mean values and standard errors of Gaussian fits to the corresponding time difference distributions. d–g Coupling histograms for DNA origami array structures with the FRET probes at different positions. The fraction of structures exhibiting full coupling is indicated by an orange bar. h, i Scheme of the transformation reaction upon addition of five and the upper four trigger strands. j Proposed, simplified energy landscape of the transformation reaction with four and five trigger strands. The potential wells at which the studied positions switch their conformation are marked with numbers.
Fig. 4
Fig. 4. Temporal decoupling of different steps in the transformation reaction by artificially introducing energy barriers.
a, b Mechanisms used to engineer the energy landscape. d1 corresponds to the unmodified reference, d2 to a system with a locking unit incorporated and d3 and d4 to systems with missing central anti-junctions. c Lag times for the transformation to progress from Position 2 to Position 3 upon addition of all five trigger DNA strands in the systems shown in (b). Error bars represent the standard deviation of the Gaussian fit of the corresponding time difference histograms. For designs in which the majority of structures exhibited a time delay between the transformation at the different positions, only non-perfectly coupled structures with △t≠0s were considered. All plots show the mean values and standard errors of Gaussian fits to the corresponding time difference distributions. d–f Corresponding coupling histograms. The fraction of structures exhibiting full coupling (C > 0.95) is indicated by an orange bar.
See this image and copyright information in PMC

Similar articles

See all similar articles

References

    1. MONOD, J. & JACOB, F. Teleonomic mechanisms in cellular metabolism, growth, and differentiation. Cold Spring Harb. symposia Quant. Biol.26, 389–401 (1961). 10.1101/SQB.1961.026.01.048 - DOI - PubMed
    1. Monod, J., Changeux, J.-P. & Jacob, F. Allosteric proteins and cellular control systems. J. Mol. Biol.6, 306–329 (1963). 10.1016/S0022-2836(63)80091-1 - DOI - PubMed
    1. Monod, J., Wyman, J. & Changeux, J.-P. On the nature of allosteric transitions: a plausible model. J. Mol. Biol.12, 88–118 (1965). 10.1016/S0022-2836(65)80285-6 - DOI - PubMed
    1. Koshland, D. E., Némethy, G. & Filmer, D. Comparison of experimental binding data and theoretical models in proteins containing subunits. Biochemistry5, 365–385 (1966). 10.1021/bi00865a047 - DOI - PubMed
    1. Changeux, J.-P. & Edelstein, S. J. Allosteric mechanisms of signal transduction. Sci. (N. Y., N. Y.)308, 1424–1428 (2005).10.1126/science.1108595 - DOI - PubMed

LinkOut - more resources