DNA as a universal chemical substrate for computing and data storage

Yang, Shuo; Bögels, Bas W. A.; Wang, Fei; Xu, Can; Dou, Hongjing; Mann, Stephen; Fan, Chunhai; de Greef, Tom F. A.

doi:10.1038/s41570-024-00576-4

Cited by 21 publications

(5 citation statements)

References 226 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Lysolipids were able to provide a facile and indirect contact approach for determining the fate of enclosed and interconnected DIBs in aqueous environments, making this system suitable for the active release of chemical species and non-invasive manipulation of artificial cellular membranes. Since in-situ controlled release from eDIB platforms can be established by utilizing the chemical sensitivity of functional elements (e.g., encapsulants or membranes), next-generation sensing and release technologies can be developed in macromolecular computing 40 , and can serve as biomimetic self-repairing materials ranging from biomedical implants to future constructional matrices 41 .…”

Section: Introductionmentioning

confidence: 99%

Manipulation of encapsulated artificial phospholipid membranes using sub-micellar lysolipid concentrations

Dimitriou,

Li,

Jamieson

et al. 2024

Commun Chem

View full text Add to dashboard Cite

Droplet Interface Bilayers (DIBs) constitute a commonly used model of artificial membranes for synthetic biology research applications. However, their practical use is often limited by their requirement to be surrounded by oil. Here we demonstrate in-situ bilayer manipulation of submillimeter, hydrogel-encapsulated droplet interface bilayers (eDIBs). Monolithic, Cyclic Olefin Copolymer/Nylon 3D-printed microfluidic devices facilitated the eDIB formation through high-order emulsification. By exposing the eDIB capsules to varying lysophosphatidylcholine (LPC) concentrations, we investigated the interaction of lysolipids with three-dimensional DIB networks. Micellar LPC concentrations triggered the bursting of encapsulated droplet networks, while at lower concentrations the droplet network endured structural changes, precisely affecting the membrane dimensions. This chemically-mediated manipulation of enclosed, 3D-orchestrated membrane mimics, facilitates the exploration of readily accessible compartmentalized artificial cellular machinery. Collectively, the droplet-based construct can pose as a chemically responsive soft material for studying membrane mechanics, and drug delivery, by controlling the cargo release from artificial cell chassis.

show abstract

Section: Introductionmentioning

confidence: 99%

Manipulation of encapsulated artificial phospholipid membranes using sub-micellar lysolipid concentrations

Dimitriou,

Li,

Jamieson

et al. 2024

Commun Chem

View full text Add to dashboard Cite

show abstract

“…This technology also enables the execution of predictable, cascading DNA hybridization-based logic operations or intricate circuitry programs, which are crucial for detecting specific targets. [2,3] Functional DNA mainly comprises aptamers and DNAzymes. Aptamers are selected through the SELEX process, which stands for Systematic Evolution of Ligands by Exponential Enrichment, to bind specifically and strongly to their targets, similar to how antibodies function.…”

Section: Introductionmentioning

confidence: 99%

Construction of Multiply Guaranteed DNA Sensors for Biological Sensing and Bioimaging Applications

Wang,

Zou,

Wang

2024

ChemBioChem

View full text Add to dashboard Cite

Nucleic acids exhibit exceptional functionalities for both molecular recognition and catalysis, along with the capability of predictable assembly through strand displacement reactions. The inherent programmability and addressability of DNA probes enable their precise, on‐demand assembly and accurate execution of hybridization, significantly enhancing target detection capabilities. Decades of research in DNA nanotechnology have led to advances in the structural design of functional DNA probes, resulting in increasingly sensitive and robust DNA sensors. Moreover, increasing attention has been devoted to enhancing the accuracy and sensitivity of DNA‐based biosensors by integrating multiple sensing procedures. In this review, we summarize various strategies aimed at enhancing the accuracy of DNA sensors. These strategies involve multiple guarantee procedures, utilizing dual signal output mechanisms, and implementing sequential regulation methods. Our goal is to provide new insights into the development of more accurate DNA sensors, ultimately facilitating their widespread application in clinical diagnostics and assessment.

show abstract

“…With the rapid development of deoxyribonucleic acid (DNA) nanotechnology over the past decades, DNA has evolved far beyond its conventional roles as genetic materials. − It has been engineered to build diverse two-dimensional (2D) or three-dimensional (3D) structures with nanoscale precision. − Additionally, numerous DNA nanodevices and reaction networks have also been created capable of executing tasks, such as mechanical motion, biosensing, biocomputing, and smart drug delivery. − While most DNA nanodevices were actuated in response to chemical or physical stimuli, , they can also be programmed into ultrasmall instruments to sense and measure the input forces and energies at molecular scales. For example, a suite of DNA-based molecular sensors has been introduced to measure the pulling and compressive forces in living systems. − DNA-based calorimeters and thermometers have also been created for measuring heat changes in small open systems. − …”

Section: Introductionmentioning

confidence: 99%

Native Characterization of Noncanonical Nucleic Acid Thermodynamics via Programmable Dynamic DNA Chemistry

Wu,

Wang,

Yang

et al. 2024

J. Am. Chem. Soc.

View full text Add to dashboard Cite

Folding thermodynamics, quantitatively described using parameters such as ΔG fold °, ΔH fold °, and ΔS fold °, is essential for characterizing the stability and functionality of noncanonical nucleic acid structures but remains difficult to measure at the molecular level. Leveraging the programmability of dynamic deoxyribonucleic acid (DNA) chemistry, we introduce a DNAbased molecular tool capable of performing a free energy shift assay (FESA) that directly characterizes the thermodynamics of noncanonical DNA structures in their native environments. FESA operates by the rational design of a reference DNA probe that is energetically equivalent to a target noncanonical nucleic acid structure in a series of toehold-exchange reactions, yet is structurally incapable of folding. As a result, a free energy shift (ΔΔG rxn °) is observed when plotting the reaction yield against the free energy of each toehold-exchange. We mathematically demonstrated that ΔG fold °, ΔH fold °, and ΔS fold °of the analyte can be calculated based on ΔΔG rxn °. After validating FESA using six DNA hairpins by comparing the measured ΔG fold °, ΔH fold °, and ΔS fold °values against predictions made by NUPACK software, we adapted FESA to characterize noncanonical nucleic acid structures, encompassing DNA triplexes, G-quadruplexes, and aptamers. This adaptation enabled the successful characterization of the folding thermodynamics for these complex structures under various experimental conditions. The successful development of FESA marks a paradigm shift and a technical advancement in characterizing the thermodynamics of noncanonical DNA structures through molecular tools. It also opens new avenues for probing fundamental chemical and biophysical questions through the lens of molecular engineering and dynamic DNA chemistry.

show abstract

DNA as a universal chemical substrate for computing and data storage

Cited by 21 publications

References 226 publications

Manipulation of encapsulated artificial phospholipid membranes using sub-micellar lysolipid concentrations

Manipulation of encapsulated artificial phospholipid membranes using sub-micellar lysolipid concentrations

Construction of Multiply Guaranteed DNA Sensors for Biological Sensing and Bioimaging Applications

Native Characterization of Noncanonical Nucleic Acid Thermodynamics via Programmable Dynamic DNA Chemistry

Contact Info

Product

Resources

About