DNA nanocomputer detect antibodies and could be used to control drug delivery into the bloodstream

Researchers at Eindhoven University of Technology (TU/e) present a new method that should enable controlled drug delivery into the bloodstream using DNA computers. In the journal Nature Communications the team, led by biomedical engineer Maarten Merkx, describes how it has developed the first DNA computer capable of detecting several antibodies in the blood and performing subsequent calculations based on this input. This is an important step towards the development of smart, ‘intelligent’ drugs that may allow better control of the medication for rheumatism and Crohn’s disease, for example, with fewer side-effects and at lower cost.

An analogy for the method presented by the TU/e researchers is a security system that opens the door depending on the person standing in front of it. If the camera recognizes the person, the door unlocks, but if the person is unknown, the door remains locked. “Research into diagnostic tests tends to focus on the ‘recognition’, but what is special about this system is that it can think and that it can be connected to actuation such as drug delivery,” says professor of Biomedical Chemistry Maarten Merkx.

DNA computer

To be able to perform such an action, ‘intelligence’ is needed, a role that is performed in this system by a DNA computer. DNA is best known as a carrier of genetic information, but DNA molecules are also highly suitable for performing molecular calculations. The sequence within a DNA molecule determines with which other DNA molecules it can react, which allows a researcher to program desired reaction circuits.

DNA-based molecular circuits allow complex signal processing in antibody detection.

Nature Communications – Antibody-controlled actuation of DNA-based molecular circuits

Antibodies

To date biomedical applications of DNA computers have been limited because the input of DNA computers typically consists of other DNA and RNA molecules. To determine whether someone has a particular disease, it is essential to measure the concentration of specific antibodies – agents that our immune system produces when we are ill. Merkx and his colleagues are the first to have succeeded in linking the presence of antibodies to a DNA computer.

Drug delivery

Their method translates the presence of each antibody into a unique piece of DNA whereby the DNA computer can decide on the basis of the presence of one or more antibodies whether drug delivery, for example, is necessary. “The presence of a particular DNA molecule sets in motion a series of reactions whereby we can get the DNA computer to run various programs,” explains PhD student and primary author Wouter Engelen. “Our results show that we can use the DNA computer to control the activity of enzymes, but we think it should also be possible to control the activity of a therapeutic antibody.”

Medication

In treating chronic diseases like rheumatism or Crohn’s disease, such therapeutic antibodies are used as medication. One of the potential applications of this system is to measure the quantity of therapeutic antibodies in the blood and decide whether it is necessary to administer any extra medication. Merkx: “By directly linking the measurement of antibodies to the treatment of the disease, we may be able to prevent side-effects and reduce costs in the future.”

Abstract

DNA-based molecular circuits allow autonomous signal processing, but their actuation has relied mostly on RNA/DNA-based inputs, limiting their application in synthetic biology, biomedicine and molecular diagnostics. Here we introduce a generic method to translate the presence of an antibody into a unique DNA strand, enabling the use of antibodies as specific inputs for DNA-based molecular computing. Our approach, antibody-templated strand exchange (ATSE), uses the characteristic bivalent architecture of antibodies to promote DNA-strand exchange reactions both thermodynamically and kinetically. Detailed characterization of the ATSE reaction allowed the establishment of a comprehensive model that describes the kinetics and thermodynamics of ATSE as a function of toehold length, antibody–epitope affinity and concentration. ATSE enables the introduction of complex signal processing in antibody-based diagnostics, as demonstrated here by constructing molecular circuits for multiplex antibody detection, integration of multiple antibody inputs using logic gates and actuation of enzymes and DNAzymes for signal amplification.

They have shown that Antibody-Templated Strand Exchange (ATSE) of peptide-functionalized DNA strands provides a unique and robust molecular approach to translate the presence of an antibody into a ssDNA output. Both thermodynamic and kinetic effects contribute to the remarkable efficiency of ATSE. First, the bivalent peptide-dsDNA product of the ATSE reaction forms a highly stable 1:1 cyclic complex with its bivalent target antibody, thus making the displacement reaction thermodynamically favourable. Second, colocalization of the peptide-functionalized oligonucleotides on the two antigen binding domains increases their effective concentration, hence enhancing the rate of the exchange reaction. An important application of the ATSE reaction is that it allows the use of DNA-based molecular circuits in antibody-based diagnostics, introducing complex signal-processing capabilities beyond those achievable in convential immunoassays. In addition to the logic gates and multiplex detection demonstrated in this work, many other features of DNA-based molecular circuits could be employed, including tresholding, signal amplification, feedback and signal modulation. The importance of ATSE to the field of DNA-nanotechnology is that it provides a generic method to use antibodies as inputs for DNA-based molecular computing and the actuation of 3D DNA-nanoarchitectures. Since antibodies can be generated that bind with high affinity and specificity to almost any molecular target, any of these biomarkers can now also be considered as potential inputs for DNA-based molecular circuits, by competing with ATSE-mediated generation of DNA input strands. As a generic mechanism that allows protein-based control of DNA circuits, ATSE complements previously developed molecular approaches for DNA-based control of protein activity. The development of these and other molecular strategies to integrate the rich functional properties of antibodies and other proteins with the inherent programmability of DNA-nanotechnology will provide access to truly autonomous biomolecular systems with sophisticated signal integration, processing and actuation properties.

SOURCES- Nature Communications, Eindhoven University of Technology

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