Hello Watson and Crick, we are mortise and mortise

With the unique property of sequence complementarity, nucleic acid molecules stand out among many biological macromolecules and become one of
the research hotspots in synthetic biology.
Taking DNA as an example, there are strict matching rules between the four components of the DNA molecule A, T, C, and G - Watson-Crick base complementary pairing (A and T pairing, C and G pairing).

This matching rule between the bases in turn results in the specific recognition between the base sequence and the base sequence, that is, sequence complementarity
.
For any single strand of DNA, the sequence of its complementary strand is unambiguous and unique; Incorrectly matched sequences reduce the rate of binding between the two chains and greatly reduce
the stability of the resulting double helix structure.
Based on the specific recognition between DNA sequences, researchers have greatly expanded the study of DNA, no longer as a single carrier of genetic information, but also as a molecular probe and molecular robot, so that DNA molecules in many fields such as drug delivery, biological computing, disease diagnosis, super-resolution imaging and many other fields show extremely promising application prospects
.
At the same time, in the continuous exploration of DNA nanostructure design, people's understanding of structural complexity, flexibility and functionalization has become more and more deep, and relevant design concepts and design experience have been continuously accumulated and enriched
.

In the field of DNA nanostructures, researchers generally achieve recognition
between structures by designing sticky ends.
These artificially designed sticky ends have a specific length and sequence, and only between the two sticky ends whose sequences complement each other form perfect recognition, thus guiding the static or dynamic assembly of DNA nanostructures
.
Theoretically, a viscous end of length N (base number) can form 4^N
sequences.
However, in practical designs, the length and sequence of the viscous ends are often limited to a certain extent, so that the type of final specific sequence is greatly reduced
exponentially.
For example, for four bases, a viscous end with a length of 2 bases can only form 4²=16 complementary pairs, and a viscous end with a length of 1 base can only form 4¹=4 complementary pairs
.
How to optimize and improve the ability to recognize between sticky ends in actual design has become a major focus
of DNA molecular research.

In this study, the authors took inspiration from the tenon and tenon structure of traditional Chinese wood craftsmanship to design a new way of identifying between the sticky ends of DNA—specific recognition
that relies on geometric configuration.
Unlike the recognition method that relies on the complementary pairing of sequences, this recognition method is completely independent of the diversity of sequences, but is based on the shape fit between the multiple geometric configurations of the
DNA double helix structure.
The authors show that even in the most extreme design scenarios – where the viscous end is only 1 base in length and the base species is only C-G paired, it is still possible to promote only 1 complementary pair to at least 10 complementary pairs, significantly improving the ability to
recognize between the viscous ends of DNA.

Figure 1.
Geometric-based specific recognition
of DNA molecules.
(A) The contrast
between the specific recognition method relying on the geometric configuration and the specific recognition method relying on sequence complementarity.
(B) In the specific identification method that relies on geometric configuration, the binding will occur only when the specific geometric configuration requirements are met between the two sticky ends; Bonding does not occur when specific geometric requirements are not met between the two viscous ends
.

Using simple four-arm branched DNA nanostructures as templates, the authors design optimization of the viscous ends at their branches, and the bonded interface of the sticky ends presents a variety of different geometric configurations by inserting a specific number of base pairs
.
Binding occurs only when the two ends are connected so that the overall geometry satisfies the helix parameters of type B DNA, otherwise stable binding cannot occur at the two ends
.
The two-dimensional self-assembly results of four-arm branched DNA nanostructures were used to verify and analyze the feasibility
of specific identification methods that rely on geometric configurations.
This identification method was then used to successfully achieve a wide variety of 2D and 3D assemblies
that were strictly in line with the design expectations.

Figure 2.
Application of DNA sticky ends that depend on geometry in four-arm branched DNA nanostructures
.
(A) Design details and two-dimensional self-assembly activity of four-arm branched DNA nanostructures
.
(B) Design details
of DNA sticky ends that rely on geometric configurations.
(C) The bonded interface at the viscous end exhibits a number of different geometric configurations and exhibits different assembly activities
.
Two-dimensional assembly occurs only when the two ends are connected so that the overall geometry satisfies the helix parameters of type B DNA
.

This study expands the recognition method of DNA viscous ends, establishes a new bonding mechanism and regulation method, improves the recognition ability between DNA molecules, and is of great significance
for the design and application of high-sensitivity and high-precision DNA molecular probes and molecular machines in the future.

The research results were completed by the Wei Diming Molecular Design Group (MADlab) of the School of Life Sciences of Tsinghua University, and the paper was entitled "Design of orthogonal DNA sticky end cohesion based on configuration-specific molecular recognition".
Published in the Journal of the American Chemical Society on September 30, 2022
.
Zhang Tianqing, a 2017 doctoral student in the School of Life Sciences of Tsinghua University, is the first author and co-corresponding author of this paper, and the whole process from project conception, specific implementation to final thesis writing is basically completed independently, and the other co-corresponding author is Associate Professor Wei Diming of the School of Life Sciences of Tsinghua University, who provided assistance
in project conception and writing.
The research was supported by funds from the Ministry of Science and Technology and the Tsinghua-Peking University Joint Center for
Life Sciences.

Paper Link: https://pubs.
acs.
org/doi/10.
1021/jacs.
2c07181