Cooperativity in the annealing of DNA origamis

*authors contributed equally to this work 2 DNA origami is a robust molecular assembly technique by which a single-stranded DNA template is folded by annealing it with hundreds of short 'staple' strands. 1-4 The guiding design principle of nanofabrication by DNA self-assembly is that the target structure is the single most stable configuration; 5 however, the pathway and kinetics of origami assembly are poorly understood. The folding transition is cooperative 4,6,7 , and there is a strong analogy with protein folding: both are governed by information encoded in polymer sequence. [8][9][10][11] Misfolded structures are kinetic traps. The yield of well-folded DNA origami can be low: 2 yield is improved by titration of cations 2,12 or by following empirical design rules, 12,13 but it is frequently necessary to separate wellfolded origami from misfolded objects. 2, 3, 14-16 Here, we present an origami structure that is designed to reveal the assembly process. Our system has the unusual property of having a small set of distinguishable, well-folded shapes that represent discrete and approximately degenerate energy minima in a vast folding landscape. We obtain a high yield of well-folded origami structures, demonstrating the existence of efficient folding pathways. The distribution of shapes provides information about individual trajectories through the folding landscape. We show that the assembly pathway can be steered by rational design and identify similarities to protein folding: assembly is highly cooperative; reversible bond-formation is important in recovering from transient misfoldings; and the early formation of long-range connections can be very effective in forcing particular folds. Expanding the rational design process to include the assembly pathway is the key to reproducible synthesis, which is essential if nucleic acid selfassembly is to continue its rapid development 1-3,17-19 and become a reliable manufacturing technology. 20 3This study is based on a simplified version of the archetypal origami tile 1 and, in particular, on the distribution of observed folds of a 'dimer' variant which contains two copies of the template sequence in head-to-tail repeat. The 'monomer' tile ( Fig. . 1) (Fig. 1c); approximately 80% of tiles appear to be well folded.The 'dimer' template is also circular. It contains two identical copies of the monomer joined head-to-tail and can therefore bind two copies of each staple (Fig. 2). Each pair of body and seam staples can bind in one of two configurations (Fig. 2a) to form either an internal link within each copy of the monomer sequence or a pair of cross-links between the two copies.The total number of possible domain pairings is 2 76 ≈ 10 23 . Although many of these configurations are sterically inaccessible it is clear that the result of reducing the specificity of staple binding is that, as in the case of protein folding, the number of possible states of the system is overwhelmingly greater than the number of well-folded structures. However, in contrast to proteins (and t...

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“…( 11 , 01 ) = + exp ( ∆ 01 , 11 0,duplex ) × M ( 6 ) where 11 denotes the state in which the staple is bound to the template with both domains.…”

Section: Rates Modelmentioning

confidence: 99%

Guiding the folding pathway of DNA origami

Dunn

Dannenberg

Ouldridge

et al. 2015

Nature

157

188

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“…Arbona et al postulate that the binding of one staple to the origami might facilitate the binding of a second by shortening the loop which it must enclose [26].…”

Section: Introductionmentioning

confidence: 99%

“…An understanding of general principles for optimizing yield and folding rate would allow the improvement of current designs and the assembly of larger and more complex structures. A number of recent experiments have probed the details of origami folding [22][23][24][25][26][27][28]. Assembly is cooperative [23,26], occurs across a narrow temperature window [23], exhibits hysteresis [23,26,27] and is highly sensitive to staple design [24][25][26].…”

Section: Introductionmentioning

confidence: 99%

“…In particular, such an approach cannot describe cooperative interactions whereby the presence of a bound staple affects the binding of other staples to the scaffold. Recent evidence suggests that cooperative interactions affect origami folding significantly [23,26,27], leading to sharp formation transitions as the temperature is lowered and contributing to hysteresis in heating and cooling experiments.…”

Section: Introductionmentioning

confidence: 99%

“…Staples bind to the scaffold only, not to other staples, and can hybridize to the same number of scaffold domains at any stage of assembly. Arbona et al [22,26] have presented a model of origami folding in which cooperativity arises from two effects.…”

Section: Introductionmentioning

confidence: 99%

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Modelling DNA origami self-assembly at the domain level

Dannenberg

Dunn

Bath

et al. 2015

The Journal of Chemical Physics

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We present a modelling framework, and basic model parameterization, for the study of DNA origami folding at the level of DNA domains. Our approach is explicitly kinetic and does not assume a specific folding pathway. The binding of each staple is associated with a free-energy change that depends on staple sequence, the possibility of coaxial stacking with neighbouring domains, and the entropic cost of constraining the scaffold by inserting staple crossovers. A rigorous thermodynamic model is difficult to implement as a result of the complex, multiply connected geometry of the scaffold: we present a solution to this problem for planar origami. Coaxial stacking of helices and entropic terms, particularly when loop closure exponents are taken to be larger than those for ideal chains, introduce interactions between staples. These cooperative interactions lead to the prediction of sharp assembly transitions with notable hysteresis that are consistent with experimental observations. We show that the model reproduces the experimentally observed consequences of reducing staple concentration, accelerated cooling and absent staples. We also present a simpler methodology that gives consistent results and can be used to study a wider range of systems including non-planar origami.

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Detection of Short DNA Sequences with DNA Nanopores**

Yang

Cullin²,

Elezgaray³

2022

ChemPhysChem

Self Cite

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Several studies suggest strong correlation between different types of cancer and the relative concentration of short circulating RNA sequences (miRNA). Because of short length and low concentration, miRNA detection is not easy. Standard methods such as RT-PCR require both the standard PCR amplification step and a preliminary additional step of reverse transcription. In this paper, we investigate the use of DNA nanopores as a tool to detect short oligonucleotide sequences at the single molecule level. These nanostructures show two different conformations depending on the presence of DNA analogues of miRNA sequences. By monitoring current across a lipid bilayer, we show that this change of conformation translates to different levels of conductance.

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Cooperativity in the annealing of DNA origamis

Cited by 30 publications

References 33 publications

Guiding the folding pathway of DNA origami

Guiding the folding pathway of DNA origami

Modelling DNA origami self-assembly at the domain level

Detection of Short DNA Sequences with DNA Nanopores**

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