Chemical conjugation of nucleic acid aptamers and synthetic polymers

Nerantzaki, Maria; Loth, Capucine; Lutz, Jean‐François

doi:10.1039/d1py00516b

Cited by 22 publications

(21 citation statements)

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“…Due to their stability and facility of selection and synthesis, DNA aptamers have been extensively applied in biosensing, biotechnology, and biomedicine, as promising alternatives to monoclonal antibodies. , Although these “chemical antibodies” are discovered using an enzymatic process, like most synthetic oligonucleotides, they are readily synthesized using solid-phase phosphoramidite chemistry, in an automated process that has now been practiced for several decades . This chemical synthesis allows the site-specific introduction of non-nucleotide linkers such as fluorescent dyes and mobility modifiers such as polyethylene glycol (PEG) linkers . Additionally, automated solid-phase synthesis allows for uniform postsynthetic modification of aptamers and site-selective polymer attachment of various functional groups.…”

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confidence: 99%

“…Postmodifications of chemically modified aptamers has yielded aptamer–polymer conjugates (APCs) with a variety of natural and synthetic polymers such as biodegradable polymers, graft copolymers, amphiphilic block copolymers, and dendritic polymers. − However, in all reported studies, the synthetic segments that have been coupled to aptamers are polydisperse macromolecules synthesized by conventional polymerization methods such as chain-growth or step-growth polymerizations . Thus, APCs usually lack the remarkable programmability, sequence selectivity, monodispersity, and fine structural control that DNA can offer.…”

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Precisely Defined Aptamer-b-Poly(phosphodiester) Conjugates Prepared by Phosphoramidite Polymer Chemistry

et al. 2021

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Uniform conjugates combining a DNA aptamer (either anti-MUC1 or ATP aptamer) and a synthetic polymer segment were synthesized by automated phosphoramidite chemistry. This multistep growth polymer chemistry enables the use of both natural (i.e. nucleoside phosphoramidites) and non-natural monomers (e.g. alkyl-and oligo(ethylene glycol)phosphoramidites). Thus, in the present work, six different aptamer-polymer conjugates were synthesized and characterized by ion-exchange HPLC, circular dichroism spectroscopy and electrospray mass spectrometry. All these methods evidenced the formation of uniform molecules with precisely-controlled chain-length and monomer sequences. Furthermore, aptamer folding was not affected by polymer bioconjugation. The method described herein is straightforward and allows covalent attachment of homopolymers and copolymers to biofunctional DNA aptamers.

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Precisely Defined Aptamer-b-Poly(phosphodiester) Conjugates Prepared by Phosphoramidite Polymer Chemistry

et al. 2021

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“…To form a strong amide bond, first, the activation of the -COOH group was performed via EDC/NHS chemistry. Therefore, 6 µL of 300 mM of EDC and 35 mM of NHS were dropcasted on top of WE and kept for 1 h as previously employed by Nerantzaki et al [ 46 ]. Afterward, on top of each WE, 6 µL of 1 µM aptamer dispersion (diluted in double-distilled water) was dropcasted and kept at 4 °C for 16 h. The reaction of these chemicals with the -COOH leads to a semi-stable amine-reactive NHS-ester group, which once exposed to the aptamers, reacts with the primary amines (found in aptamers) to form a strong and stable amide bond [ 45 ].…”

Section: Methodsmentioning

confidence: 99%

An Aptasensor Based on a Flexible Screen-Printed Silver Electrode for the Rapid Detection of Chlorpyrifos

Inam

Angeli

Douaki

et al. 2022

Sensors

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In this work, we propose a novel disposable flexible and screen-printed electrochemical aptamer-based sensor (aptasensor) for the rapid detection of chlorpyrifos (CPF). To optimize the process, various characterization procedures were employed, including Fourier transform infrared spectroscopy (FT-IR), electrochemical impedance spectroscopy (EIS), and cyclic voltammetry (CV). Initially, the aptasensor was optimized in terms of electrolyte pH, aptamer concentration, and incubation time for chlorpyrifos. Under optimal conditions, the aptasensor showed a wide linear range from 1 to 105 ng/mL with a calculated limit of detection as low as 0.097 ng/mL and sensitivity of 600.9 µA/ng. Additionally, the selectivity of the aptasensor was assessed by identifying any interference from other pesticides, which were found to be negligible (with a maximum standard deviation of 0.31 mA). Further, the stability of the sample was assessed over time, where the reported device showed high stability over a period of two weeks at 4 °C. As the last step, the ability of the aptasensor to detect chlorpyrifos in actual samples was evaluated by testing it on banana and grape extracts. As a result, the device demonstrated sufficient recovery rates, which indicate that it can find application in the food industry.

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“…Sequence-defined DNA amphiphiles are covalent polymer chains of monodisperse length and specific monomer order attached to single-stranded DNA, constructed efficiently and rapidly on an automated DNA synthesizer. [1][2][3][4][5][6][7][8][9][10] Self-assembly arises to minimize contact of the hydrophobic region with water, and the relative volume of the hydrophobic to hydrophilic block can play a major role in determining the assembly morphology. [11][12][13] Increasing the volume of the hydrophobic phase generally decreases the interfacial curvature (i.e., the curvature of the hydrophobic region at the interface between the two blocks) evolving the morphology from spheres to cylinders to lamellae.…”

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DNA Sequence and Length Dictate the Assembly of Nucleic Acid Block Copolymers

Rizzuto

Dore

Rafique

et al. 2022

Preprint

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The self-assembly of block copolymers is often rationalized by structure and microphase separation; pathways that diverge from this parameter space may provide new mechanisms of polymer self-assembly. Here, we show that the sequence and length of single-stranded DNA directly influence the self-assembly of sequence-defined DNA block copolymers. While increasing the length of DNA led to predictable changes in self-assembly, changing only the sequence of DNA produced three distinct structures: spherical micelles (spherical nucleic acids, SNAs) from flexible poly(thymine) DNA, fibers from semi-rigid mixed-sequence DNA, and networked superstructures from rigid poly(adenine) DNA. The secondary structure of poly(adenine) DNA strands drives a temperature-dependent polymerization and assembly mechanism: copolymers stored in an SNA reservoir form fibers after thermal activation, which then aggregate upon cooling to form interwoven networks. DNA is often used as a programming code that aids in nanostructure addressability and function; Here, we show that the inherent physical and chemical properties of single-stranded DNA sequences also make them an ideal material to direct self-assembled morphologies and select for new methods of supramolecular polymerization.

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Chemical conjugation of nucleic acid aptamers and synthetic polymers

Abstract: Nucleic acid aptamers are chemically-synthesized single-stranded oligonucleotides that fold into specific sequence-dependent configurations. Due to their exceptional recognition properties towards a variety of biological targets, they find applications in many...

Cited by 22 publications

References 101 publications

Precisely Defined Aptamer-b-Poly(phosphodiester) Conjugates Prepared by Phosphoramidite Polymer Chemistry

Precisely Defined Aptamer-b-Poly(phosphodiester) Conjugates Prepared by Phosphoramidite Polymer Chemistry

An Aptasensor Based on a Flexible Screen-Printed Silver Electrode for the Rapid Detection of Chlorpyrifos

DNA Sequence and Length Dictate the Assembly of Nucleic Acid Block Copolymers

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