Simultaneous and Traceless Ligation of Peptide Fragments on DNA Scaffold

Templating Peptide Chemistry with Nucleic Acids: Toward Artificial Ribosomes, Cell-Specific Therapeutics, and Novel Protein-Mimetic Architectures

In biology, nanomachines like the ribosome use nucleic acid templates to synthesize polymers in a sequence-specific, programmable fashion. Researchers have long been interested in using the programmable properties of nucleic acids to enhance chemical reactions via colocalization of reagents using complementary nucleic acid handles. In this review, we describe progress in using nucleic acid templates, handles, or splints to enhance the covalent coupling of peptides to other peptides or oligonucleotides. We discuss work in several areas: creating ribosome-mimetic systems, synthesizing bioactive peptides on DNA or RNA templates, linking peptides into longer molecules and bioactive antibody mimics, and scaffolding peptides to build protein-mimetic architectures. We close by highlighting the challenges that must be overcome in nucleic acid-templated peptide chemistry in two areas: making full-length, functional proteins from synthetic peptides and creating novel protein-mimetic architectures not possible through macromolecular folding alone.

Detection of Cadmium(II) in Aquatic Products Using a Rolling-Circle Amplification-Coupled Ratio Fluorescent Probe Based on an Aptamer-Peptide Conjugate

The existing aptamers for cadmium (Cd2+), the common toxic heavy metal contaminant in food, cannot meet the requirements for detecting Cd2+ in rapid detection methods. In previous work, we found that coupling aptamer-peptide conjugates (APCs) with peptides and aptamers can provide a less disruptive method with a significantly improved affinity. Moreover, we found that the spatial conformation of aptamers and peptides is crucial for obtaining proper affinity in APC. Therefore, we describe a simple design strategy to obtain a series of APCs with different affinities by designing peptide orientations (N-terminal, C-terminal). The best affinity was found for APC(C1-N) with a binding constant (Ka) of 2.23 × 106 M-1, indicating that the APC(C1-N) affinity was significantly increased by 829.17% over aptamer. Finally, a rolling-circle amplification (RCA)-coupled ratio fluorescence-based biosensor for Cd2+ detection was established with a detection limit of 0.0036 nM, which has great potential for practical aquatic product detection.

High-Affinity Host-Guest Recognition for Efficient Assembly and Enzymatic Responsiveness of DNA Nanostructures

The combination of multiple orthogonal interactions enables hierarchical complexity in self-assembled nanoscale materials. Here, efficient supramolecular polymerization of DNA origami nanostructures is demonstrated using a multivalent display of small molecule host-guest interactions. Modification of DNA strands with cucurbit[7]uril (CB[7]) and its adamantane guest, yielding a supramolecular complex with an affinity of order 1010 m-1 , directs hierarchical assembly of origami monomers into 1D nanofibers. This affinity regime enables efficient polymerization; a lower-affinity β-cyclodextrin-adamantane complex does not promote extended structures at a similar valency. Finally, the utility of the high-affinity CB[7]-adamantane interactions is exploited to enable responsive enzymatic actuation of origami nanofibers assembled using peptide linkers. This work demonstrates the power of high-affinity CB[7]-guest recognition as an orthogonal axis to drive self-assembly in DNA nanotechnology.

RNA-templated chemical synthesis of proapoptotic L- and d-peptides

Nucleic acid-programmed reactions find application in drug screening and nucleic acid diagnosis, and offer prospects for a RNA-sensitive prodrug approach. We aim for the development of a nucleic acid-templated reaction providing nucleic acid-linked molecules that can act on intracellular protein targets. Such reactions would be useful for in situ drug synthesis and activity-based DNA-encoded library screening. In this report, we show native chemical ligation-like chemical peptidyl transfer reactions between peptide-PNA conjugates. The reaction proceeds on RNA templates. As a chemical alternative to ribosomal peptide synthesis access to both L- and d-peptides is provided. In reactions affording 9 to 14 amino acid long pro-apoptotic L- and d-peptides, we found that certain PNA sequence motifs and combinations of cell penetrating peptides (CPPs) cause surprisingly high reactivity in absence of a template. Viability measurements demonstrate that the products of templated peptidyl transfer act on HeLa cells and HEK293 cells. Of note, the presence of cysteine, which is required for NCL chemistry, can enhance the bioactivity. The study provides guidelines for the application of peptide-PNA conjugates in templated synthesis and is of interest for in situ drug synthesis and activity-based DNA-encoded library screening.

Proximity-enhanced synthesis of DNA-peptide-DNA triblock molecules

We report a proximity-enhanced method to synthesize a peptide flanked by two different oligonucleotide handles. Our method relies on sequential bioorthogonal reactions, and partial hybridization of the second handle to the first. We demonstrate the synthesis of a protease-responsive DNA "latch" and a cyclic bioactive peptide using this method.

Traceless Click-Assisted Native Chemical Ligation Enabled by Protecting Dibenzocyclooctyne from Acid-Mediated Rearrangement with Copper(I)

The scope of proteins accessible to total chemical synthesis via native chemical ligation (NCL) is often limited by slow ligation kinetics. Here we describe Click-Assisted NCL (CAN), in which peptides are incorporated with traceless "helping hand" lysine linkers that enable addition of dibenzocyclooctyne (DBCO) and azide handles. The resulting strain-promoted alkyne-azide cycloaddition (SPAAC) increases their effective concentration to greatly accelerate ligations. We demonstrate that copper(I) protects DBCO from acid-mediated rearrangement during acidic peptide cleavage, enabling direct production of DBCO synthetic peptides. Excitingly, triazole-linked model peptides ligated rapidly and accumulated little side product due to the fast reaction time. Using the E. coli ribosomal subunit L32 as a model protein, we further demonstrate that SPAAC, ligation, desulfurization, and linker cleavage steps can be performed in one pot. CAN is a useful method for overcoming challenging ligations involving sterically hindered junctions. Additionally, CAN is anticipated to be an important stepping stone toward a multisegment, one-pot, templated ligation system.

Enhancing native chemical ligation for challenging chemical protein syntheses

Native chemical ligation has enabled the chemical synthesis of proteins for a wide variety of applications (e.g., mirror-image proteins). However, inefficiencies of this chemoselective ligation in the context of large or otherwise challenging protein targets can limit the practical scope of chemical protein synthesis. In this review, we focus on recent developments aimed at enhancing and expanding native chemical ligation for challenging protein syntheses. Chemical auxiliaries, use of selenium chemistry, and templating all enable ligations at otherwise suboptimal junctions. The continuing development of these tools is making the chemical synthesis of large proteins increasingly accessible.

Traceless Templated Amide-Forming Ligations

Template assistance allows organic reactions to occur under highly dilute conditions-where intermolecular reactions often fail to proceed-by bringing reactants into close spatial proximity. This strategy has been elegantly applied to numerous systems, but always with the retention of at least one of the templating groups in the product. In this report, we describe a traceless, templated amide-forming ligation that proceeds at low micromolar concentration under aqueous conditions in the presence of biomolecules. We utilized the unique features of an acylboronate-hydroxylamine ligation, in which covalent bonds are broken in each of the reactants as the new amide bond is formed. By using streptavidin as a template and acylboronates and O-acylhydroxylamines bearing desthiobiotins that are cleaved upon amide formation, we demonstrate that traceless, templated ligation occurs rapidly even at submicromolar concentrations. The requirement for a close spatial orientation of the functional groups-achieved upon binding to streptavidin-is critical for the observed enhancement in the rate and quantity of product formed.