Project | YOKABIO2024

Background and problems

Recent advancements in precise structural control at the nanoscale have rapidly progressed, particularly through the use of DNA origami technology , which allows for the precise construction of structures with specific shapes and functions tailored for various applications, such as molecular transport, sensing, and filtration devices [1]. DNA, through the Watson-Crick base pairing mechanism, self-assembles with nanometer-level precision. Chemical modifications and functional molecules can also be incorporated into the design, underscoring the potential of this field of research.

DNA origami technology [2] is composed of a single long DNA strand (scaffold) and auxiliary strands (staples) that fold the scaffold. By leveraging sequence complementarity, this method enables the creation of intricate two- and three-dimensional shapes. The rigidity and stability of the structures can be controlled by adjusting the number and arrangement of staple strands.

Currently, a variety of structures utilizing DNA origami have been proposed, such as functional molecular robots [3], DNA-based logic circuits that operate as electrical alternatives [4], and cylindrical structures like nanopores, which serve as the foundation for this study. These structures hold great potential for applications in engineering and pharmaceutical research.

Nanopores refer to small channels or tubular structures on cell membranes, typically measuring several nanometers in size, and have been applied in sequencing technologies and analytical methods [5]. Recently, dynamic DNA nanopores have been reported, which enable the control of permeable substances by altering the pore diameter.

In general, the flow rate through narrow tubular structures like nanopores is defined by Poiseuille's Law[6]. According to this law, the volume of fluid flowing per unit time is proportional to the radius of the pore and inversely proportional to the length of the tube. Although novel DNA nanopores capable of dynamically controlling both the pore radius and tube length hold promise for unprecedented applications, they have yet to be realized.

Formula 1: Poiseuille's Law.

It describes the flow rate of a viscous fluid (such as water or air) through a narrow cylindrical tube.

To construct a nanopore that can control both the "inner diameter" and "length," we focused on the Kresling pattern [7]. The Kresling pattern is formed by placing isosceles triangles on the surface of a cylinder, in a way that offsets the top and bottom sections without rotating them, creating a twisted fold (Fig. 1a). This structure allows for a twisting transformation when force is applied (Fig. 1b).

Moreover, when this transformation occurs, the inner diameter of the cylinder changes. As the structure transforms from an open-form to a closed-form, the cylinder contracts vertically, and with the decrease in inner diameter, the surface area of the cylinder also reduces (Fig. 1c).

Figure. 1 Feature of kresling pattern.

(a) Isosceles triangles are twisted and arranged on the sides of the cylinder.
(b) The height of the structure changes as it transforms in a twisting motion.
(c) The difference in inner diameter between open-form and closed-form.

Kresling-Inspired-Tube-DNA origami (KIT-D)

In this project, we propose the Kresling-Inspired-Tube DNA Origami (KIT-D), which leverages features beyond those inherent to the Kresling pattern. This innovative structure is designed to function not only as a single-layer configuration but also as a multi-layered assembly. In this study, we focus on constructing a single-layer structure, the fundamental unit of the Kresling pattern (Fig. 2).

The KIT-D developed in this work introduces a novel capability, enabling simultaneous variation of both "inner diameter" and "length," a feature challenging to achieve with conventional techniques. This adaptability offers the potential for KIT-D to transform its structure in response to a broader range of conditions and applications, significantly enhancing its versatility and practical utility.

Figure. 2 The modeling of open- and closed-KIT-D.

[1] M. Madsen, K. V. Gothelf, Chem. Rev. 2019, 119, 6384-6458.
[2] P. W. K. Rothemund, Nature 2006, 440, 297-302.
[3] Y. Amir, E. Ben-Ishay, D. Levner, S. Ittah, A. Abu-Horowitz, I. Bachelet, Nat. Nanotechnol. 2014, 9, DOI 10.1038/nnano.2014.58.
[4] Z. Tang, Z.-X. Yin, X. Sun, J.-Z. Cui, J. Yang, R. Wang, Comput. Biol. Med. 2019, 109, 112-120.
[5] Y. Wang, Y. Zhao, A. Bollas, Y. Wang, K. F. Au, Nat. Biotechnol. 2021, 39, 1348-1365.
[6] S. P. Sutera, R. Skalak, Annu. Rev. Fluid Mech. 1993, 25, 1-20.
[7] B. Kresling, IASS-IACM 2008 Spanning Nano Mega 2008.