Aptamer‐Mediated Protein Molecular Recognition Driving a DNA Tweezer Nanomachine

Abstract

Nucleic acid-mediated nanomachines have significant potential in biomedical applications but new approaches that link molecular recognition of proteins to change in nucleic acid structure and function are required. Here, a split DNA aptamer is integrated into G-quadruplex tweezers, which close in the presence of the malaria biomarker protein Plasmodium falciparum lactate dehydrogenase (PfLDH). Closing of the tweezers enables G-quadruplex hemin mediated peroxidase activity, which can be observed colorimetrically. The PfLDH aptamer is split within an asymmetric internal loop and incorporated into the tweezers maintaining aptamer binding capability. Spacing between the G-quadruplex structure and split aptamer, together with extent of complementarity, is found to be critical for optimization to enhance catalytic performance. The integrated split aptamer is observed to maintain the high specificity to Plasmodium falciparum lactate dehydrogenase of the parent aptamer. Split aptamer approaches have significant potential to functionalize nucleic acid nanostructures for protein molecular recognition. www.adv-biosys.com

Principles and Applications of Nucleic Acid Strand Displacement Reactions

“…Following the development of the DNA tweezers as the first DNA machine driven by strand displacement processes, a large variety of similar switchable devices were developed. Yurke and Simmel described a variation of the tweezers that could stretch, relax, contract, and thus cycle between three distinct mechanical states. , In later work, DNA tweezers were modified with various aptamer-based functionalities, which made their opening and closing dependent on the presence small molecules like adenosine or proteins such as thrombin , or the malaria biomarker PfLDH (Plasmodium falciparum lactate dehydrogenase) …”

Bioderived DNA Nanomachines for Potential Uses in Biosensing, Diagnostics, and Therapeutic Applications

“…In 2017, Tanner and co‐workers demonstrated a colorimetric aptamer‐based sensor to detect a malarial biomarker by incorporating a split version (similar to that of Funabashi and co‐workers) of the Plasmodium falciparum lactate dehydrogenase aptamer within DNA tweezers. In the presence of the protein, the split aptamer binds the protein and forces a split G‐quadruplex to form and bind to hemin, which, in the presence of hydrogen peroxide, can oxidize ABTS, thus allowing a colorimetric readout . Consequently, it is easy to visualize the massive advantage that smart DNA nanomachines have in site‐specific, targeted therapeutic delivery and diagnostics when they incorporate these natural aptamer sequences.…”

“…This flexibility allows engineers to create hybrid nanostructures with both DNA and other materials, thus expanding the range of what DNA nanotechnology can be designed for. We can also include within these synthetic DNA structures, the potential for responsiveness to pH, light, or small molecule targets through incorporating DNA secondary structures such as DNA triplex structures or the intercalated cytosine motif, thus allowing us to create responsive nanostructures that can be classified as nanomachines. This responsiveness can also be derived from pre‐existing artificially selected for motifs called “aptamers” which selectively bind proteins and small molecules .…”

Asymmetric patterning drives the folding of a tripodal DNA nanotweezer

“…This large-scale motion may find applications in molecular robotics, biosensing schemes with amplification, and cellular probes that interrogate and influence large sections of the cell membrane. 26,[28][29][30][31][32][33][34][35][36][37][38][39] Herein, we report the synthesis of an extended DNA tweezer with a trivalent synthetic molecule as the core and three rigid and long DNA arms of different sequences (Fig. 1).…”