Discrete Assembly of Synthetic Peptide–DNA Triplex Structures from Polyvalent Melamine–Thymine Bifacial Recognition

Heat-activated growth of metastable and length-defined DNA fibers expands traditional polymer assembly

Biopolymers such as nucleic acids and proteins exhibit dynamic backbone folding, wherein site-specific intramolecular interactions determine overall structure. Proteins then hierarchically assemble into supramolecular polymers such as microtubules, that are robust yet dynamic, constantly growing or shortening to adjust to cellular needs. The combination of dynamic, energy-driven folding and growth with structural stiffness and length control is difficult to achieve in synthetic polymer self-assembly. Here we show that highly charged, monodisperse DNA-oligomers assemble via seeded growth into length-controlled supramolecular fibers during heating; when the temperature is lowered, these metastable fibers slowly disassemble. Furthermore, the specific molecular structures of oligomers that promote fiber formation contradict the typical theory of block copolymer self-assembly. Efficient curling and packing of the oligomers - or 'curlamers' - determine morphology, rather than hydrophobic to hydrophilic ratio. Addition of a small molecule stabilises the DNA fibers, enabling temporal control of polymer lifetime and underscoring their potential use in nucleic-acid delivery, stimuli-responsive biomaterials, and soft robotics.

2-Amino-5-methylene-pyrimidine-4,6-dione-based Janus G-C nucleobase as a versatile building block for self-assembly

This communication reports a nature-inspired Janus G-C nucleobase featuring two recognition sites: DDA (G mimic) and DAA (C mimic), which is capable of forming a linear tape-like supramolecular polymer structure. As demonstrated herein, the amino group of this self-assembling system can be further modified to yield a highly stable quadruple H-bonding system as well as a masked self-assembling system cleavable upon exposure to light.

Intracellular RNA and DNA tracking by uridine-rich internal loop tagging with fluorogenic bPNA

The most widely used method for intracellular RNA fluorescence labeling is MS2 labeling, which generally relies on the use of multiple protein labels targeted to multiple RNA (MS2) hairpin structures installed on the RNA of interest (ROI). While effective and conveniently applied in cell biology labs, the protein labels add significant mass to the bound RNA, which potentially impacts steric accessibility and native RNA biology. We have previously demonstrated that internal, genetically encoded, uridine-rich internal loops (URILs) comprised of four contiguous UU pairs (8 nt) in RNA may be targeted with minimal structural perturbation by triplex hybridization with 1 kD bifacial peptide nucleic acids (bPNAs). A URIL-targeting strategy for RNA and DNA tracking would avoid the use of cumbersome protein fusion labels and minimize structural alterations to the RNA of interest. Here we show that URIL-targeting fluorogenic bPNA probes in cell media can penetrate cell membranes and effectively label RNAs and RNPs in fixed and live cells. This method, which we call fluorogenic U-rich internal loop (FLURIL) tagging, was internally validated through the use of RNAs bearing both URIL and MS2 labeling sites. Notably, a direct comparison of CRISPR-dCas labeled genomic loci in live U2OS cells revealed that FLURIL-tagged gRNA yielded loci with signal to background up to 7X greater than loci targeted by guide RNA modified with an array of eight MS2 hairpins. Together, these data show that FLURIL tagging provides a versatile scope of intracellular RNA and DNA tracking while maintaining a light molecular footprint and compatibility with existing methods.

Supernatural: Artificial Nucleobases and Backbones to Program Hybridization-Based Assemblies and Circuits

The specificity and predictability of hybridization make oligonucleotides a powerful platform to program assemblies and networks with logic-gated responses, an area of research which has grown into a field of its own. While the field has capitalized on the commercial availability of DNA oligomers with its four canonical nucleobases, there are opportunities to extend the capabilities of the hardware with unnatural nucleobases and other backbones. This Topical Review highlights nucleobases that favor hybridizations that are empowering for assemblies and networks as well as two chiral XNAs than enable orthogonal hybridization networks.

Structural and Thermodynamic Control of Supramolecular Polymers and DNA Assemblies with Cyanuric Acid: Influence of Substituents and Intermolecular Interactions

Understanding the interactions and thermodynamic parameters that govern the structure and stability of supramolecular polymers is challenging because of their flexible nature and high sensitivity to weak intermolecular interactions. The application of both experimental and computational analyses reveals the role that substituents on cyanuric acid (Cy), and other nitrogen-containing heterocycles, play in the formation of novel helical supramolecular structures. In this report, we focus on how noncovalent interactions, including steric and stacking interactions, modulate the structural and physical properties of these assemblies. In-depth analyses and several examples of critical steric and electrostatic effects provide insight into the relationship between intermolecular interactions of Cy with nucleic acids and the structure and thermodynamic stability of the supramolecular polymers they form.

Structural Analysis of the Poly(thymidine)-Melamine Assembly

Hydrogen bonding between the DNA nucleobases and small organic molecules, such as melamine, is a new strategy for the design of novel DNA materials. Poly(thymidine) DNA and melamine self-assemble into a duplex structure containing two antiparallel DNA strands hydrogen bonded to central melamine units. In this Article, molecular dynamics simulations rationalize the observed antiparallel duplex structure. Alternative duplex and triplex structures with parallel and antiparallel strand orientations are shown to be unstable because of the increase in unfavorable interactions between the DNA backbones.

Perspectives on conformationally constrained peptide nucleic acid (PNA): insights into the structural design, properties and applications

Peptide nucleic acid or PNA is a synthetic DNA mimic that contains a sequence of nucleobases attached to a peptide-like backbone derived from N-2-aminoethylglycine. The semi-rigid PNA backbone acts as a scaffold that arranges the nucleobases in a proper orientation and spacing so that they can pair with their complementary bases on another DNA, RNA, or even PNA strand perfectly well through the standard Watson-Crick base-pairing. The electrostatically neutral backbone of PNA contributes to its many unique properties that make PNA an outstanding member of the xeno-nucleic acid family. Not only PNA can recognize its complementary nucleic acid strand with high affinity, but it does so with excellent specificity that surpasses the specificity of natural nucleic acids and their analogs. Nevertheless, there is still room for further improvements of the original PNA in terms of stability and specificity of base-pairing, direction of binding, and selectivity for different types of nucleic acids, among others. This review focuses on attempts towards the rational design of new generation PNAs with superior performance by introducing conformational constraints such as a ring or a chiral substituent in the PNA backbone. A large collection of conformationally rigid PNAs developed during the past three decades are analyzed and compared in terms of molecular design and properties in relation to structural data if available. Applications of selected modified PNA in various areas such as targeting of structured nucleic acid targets, supramolecular scaffold, biosensing and bioimaging, and gene regulation will be highlighted to demonstrate how the conformation constraint can improve the performance of the PNA. Challenges and future of the research in the area of constrained PNA will also be discussed.

Synthesis of Bifacial Peptide Nucleic Acids with Diketopiperazine Backbones

We report a synthesis of bifacial peptide nucleic acids (bPNAs) with novel diketopiperazine (DKP) backbones that display unnatural melamine (M) bases, as well as native bases. To examine the structure-function scope of DKP bPNAs, we synthesized a set of bPNAs by using diaminopropionic acid, diaminobutyric acid, ornithine, and lysine derivatives to display the base-tripling motifs, which result in one, two, three, or four carbons linking the alpha carbon to the side-chain amine. Thermal denaturation of DNA hybrids with these bPNAs revealed that the optimal side-chain linkage was four carbons, corresponding to the lysine derivative. Accordingly, monomers displaying two bases per side-chain were prepared through double reductive alkylation of the ε-amine of Fmoc-lysine with acetaldehyde derivatives of adenine, cytidine, uridine, and melamine. With these building blocks in hand, DKP bPNAs were prepared to display a combination of native and synthetic (melamine) bases. Preliminary melting studies indicate binding signatures of cytidine- and melamine-displaying bPNAs to T-rich DNAs of noncanonical structure, though full characterization of this behavior is ongoing. The convenient and potentially scalable method described enables rapid access to DNA-binding scaffolds of low (<1 kD) molecular weight and previously established cell permeability. We expect that this straightforward and efficient approach to nucleic acid binders will enable studies on noncanonical nucleic acid hybridization.

Impact of bPNA Backbone Structural Constraints and Composition on Triplex Hybridization with DNA

We report herein a study on the impact of bifacial peptide nucleic acid (bPNA) amino acid composition and backbone modification on DNA binding. A series of bPNA backbone variants with identical net charge were synthesized to display either 4 or 6 melamine (M) bases. These bases form thymine-melamine-thymine (TMT) base-triples, resulting in triplex hybrid stem structures with T-rich DNAs. Analyses of 6 M bPNA-DNA hybrids suggested that hybrid stability was linked to amino acid secondary structure propensities, prompting a more detailed study in shorter 4 M bPNAs. We synthesized 4 M bPNAs predisposed to adopt helical secondary structure via helix-turn nucleation in 7-residue bPNAs using double-click covalent stapling. Generally, hybrid stability improved upon stapling, but amino acid composition had a more significant effect. We also pursued an alternative strategy for bPNA structural preorganization by incorporation of residues with strong backbone amide conformational preferences such as 4R- and 4S-fluoroprolines. Notably, these derivatives exhibited an additional improvement in hybrid stability beyond both unsubstituted proline bPNA analogues and the helically patterned bPNAs. Overall, these findings demonstrate the tunability of bPNA-DNA hybrid stability through bPNA backbone structural propensities and amino acid composition.

Fluorobenzene Nucleobase Analogues for Triplex-Forming Peptide Nucleic Acids

2,4-Difluorotoluene is a nonpolar isostere of thymidine that has been used as a powerful mechanistic probe to study the role of hydrogen bonding in nucleic acid recognition and interactions with polymerases. In the present study, we evaluated five fluorinated benzenes as nucleobase analogues in peptide nucleic acids designed for triple helical recognition of double helical RNA. We found that analogues having para and ortho fluorine substitution patterns (as in 2,4-difluorotoluene) selectively stabilized Hoogsteen triplets with U-A base pairs. The results were consistent with attractive electrostatic interactions akin to non-canonical F to H-N and C-H to N hydrogen bonding. The fluorinated nucleobases were not able to stabilize Hoogsteen-like triplets with pyrimidines in either G-C or A-U base pairs. Our results illustrate the ability of fluorine to engage in non-canonical base pairing and provide insights into triple helical recognition of RNA.

Enhanced Triplex Hybridization of DNA and RNA via Syndiotactic Side Chain Presentation in Minimal bPNAs

General design principles for recognition at noncanonical interfaces of DNA and RNA remain elusive. Triplex hybridization of bifacial peptide nucleic acids (bPNAs) with oligo-T/U DNAs and RNAs is a robust recognition platform that can be used to define structure-function relationships in synthetic triplex formation. To this end, a set of minimal (mw < 1 kD) bPNA variants was synthesized to probe the impact of amino acid secondary structural propensity, stereochemistry, and backbone cyclization on hybridization with short, unstructured T-rich DNA and U-rich RNAs. Thermodynamic parameters extracted from optical melting analyses of bPNA variant hybrids indicated that there are two bPNA backbone modifications that significantly improve hybridization: alternating (d, l) configuration in open-chain dipeptides and homochiral dipeptide cyclization to diketopiperazine. Further, binding to DNA is preferred over RNA for all bPNA variants. Thymine-uracil substitutions in DNA substrates revealed that the methyl group of thymine accounts for 71% of ΔΔGDNA-RNA for open-chain bPNAs but only 40% of ΔΔGDNA-RNA for diketopiperazine bPNA, suggesting a greater sensitivity to RNA conformation and more optimized stacking in the cyclic bPNA. Together, these data reveal pressure points for tuning triplex hybridization at the chiral centers of bPNA, backbone conformation, stacking effects at the base triple, and the nucleic acid substrate itself. A structural blueprint for enhancing bPNA targeting of both DNA and RNA substrates includes syndiotactic base presentation (as found in homochiral diketopiperazines and d, l peptides), expansion of base stacking, and further investigation of bPNA backbone preorganization.

Screening of Minimalist Noncanonical Sites in Duplex DNA and RNA Reveals Context and Motif-Selective Binding by Fluorogenic Base Probes

We hypothesize that programmable hybridization to noncanonical nucleic acid motifs may be achieved by macromolecular display of binders to individual noncanonical pairs (NCPs). As each recognition element may individually have weak binding to an NCP, we developed a semi-rational approach to detect low affinity interactions between selected nitrogenous bases and noncanonical sites in duplex DNA and RNA. A set of fluorogenic probes was synthesized by coupling abiotic (triazines, pyrimidines) and native RNA bases to thiazole orange (TO) dye. This probe library was screened against duplex nucleic acid substrates bearing single abasic, single NCP, and tandem NCP sites. Probe engagement with NCP sites was reported by 100-1000× fluorescence enhancement over background. Binding is strongly context-dependent, reflective of both molecular recognition and stability: less stable motifs are more likely to bind a synthetic probe. Further, DNA and RNA substrates exhibit entirely different abasic and single NCP binding profiles. While probe binding in the abasic and single NCP screens was monotonous, much richer binding profiles were observed with the screen of tandem NCP sites in RNA, in part due to increased steric accessibility. In addition to known binding interactions between the triazine melamine (M) and T/U sites, the NCP screens identified new targeting elements for pyrimidine-rich motifs in single NCPs and 2×2 internal bulges. We anticipate that semi-rational approaches of this type will lead to programmable noncanonical hybridization strategies at the macromolecular level.

A signal-on fluorescent aptasensor by sensitized Tb3+ luminescence for detection of melamine in milk

A fluorescent aptasensor based on sensitized terbium(III) luminescence was constructed to detect melamine in milk. Tb³⁺ as the fluorescence probe can be sensitized by a guanine-rich single-stranded DNA sequence, so the complementary sequence of the polythymidine aptamer (cDNA) was modified with six consecutive guanine bases (G6). In the absence of melamine, melamine aptamer combined with cDNA to form a double helix structure, and G6 hybridized with the extended cytosine bases in the aptamer, resulting in low fluorescence intensity of Tb³⁺. In the presence of melamine, cDNA was released due to the specific recognition of melamine to the aptamer, resulting in stronger sensitized fluorescence intensity of Tb³⁺. Under the optimum conditions, the linear concentration of melamine in the milk ranged from 1.0 μg/mL to 10.0 μg/mL. This aptasensor can be used for the accurate and rapid detection of melamine in milk with a detection limit of 0.02 μg/mL, and has the advantages of high sensitivity, high efficiency, simple operation and low cost.

Three in One: Triple G-C-T Base-Coded Brahma Nucleobase Amino Acid: Synthesis, Peptide Formation, and Structural Features

This note reports the synthesis and peptide formation of a novel triple G-C-T nucleobase amino acid (NBA) building block featuring three recognition faces: DDA (G mimic), DAA (C mimic), and ADA (T mimic). Readily obtainable in multigram scale in a remarkably easy one-step reaction, this unique NBA building block offers scope for wide ranging applications for nucleic acid recognition and nucleic acid peptide/protein interaction studies.

Revealing the Hydrogen Bonding Interaction of DNA with Unnatural Bases via Plasmonic Antenna Enhanced Infrared Spectroscopy

The incorporation of unnatural bases in DNA programming can break through the limits of Watson-Crick and Hoogsteen base pairing to expand the diversity of DNA structures. Thus, understanding the interaction between DNA and unnatural bases is of great importance in DNA nanotechnology. Here, we propose an approach of plasmonic antenna enhanced infrared spectroscopy to study the hydrogen bonding interaction between poly(thymine) DNA (poly T DNA) and melamine. The formation of multiple hydrogen bonds between melamine and thymine of poly T DNA is revealed by the appearance of a new infrared (IR) feature of the NH₂ deformation vibration at 1680 cm^-1. The binding rate constant (k_b) and the dissociation rate constant (k_d) of the affinity reaction reach 39.70 M^-1·s^-1 and 4.49 × 10^-5 s^-1, respectively. This work offers a valuable IR technique to study DNA nanostructures at the molecular level, providing unique physicochemical views of the interaction mechanism between DNA and unnatural bases in DNA programming.

Bifacial PNAs Destabilize MALAT1 by 3' A-Tail Displacement from the U-Rich Internal Loop

We report herein a new class of synthetic reagents for targeting the element for nuclear expression (ENE) in MALAT1, a long noncoding RNA upregulated in many cancers. The cis-acting ENE contains a U-rich internal loop (URIL) that forms an 11 base UAU-rich triplex stem with the truncated 3' oligo-A tail of MALAT1, protecting the terminus from exonuclease digestion and greatly extending transcript lifetime. Bifacial peptide nucleic acids (bPNAs) similarly bind URILs via base triple formation between two uracil bases and a synthetic base, melamine. We synthesized a set of low molecular weight bPNAs composed of α-linked peptide, isodipeptide, and diketopiperazine backbones and evaluated their ENE binding efficacy in vitro via oligo-A strand displacement and consequent exonuclease sensitivity. Degradation was greatly enhanced by bPNA treatment in the presence of exonucleases, with ENE half-life plunging to 6 min from >24 h. RNA digestion kinetics could clearly distinguish between bPNAs with similar URIL affinities, highlighting the utility of functional assays for evaluating synthetic RNA binders. In vitro activity was mirrored by a 50% knockdown of MALAT1 expression in pancreatic cancer (PANC-1) cells upon treatment with bPNAs, consistent with intracellular digestion triggered by a similar ENE A-tail displacement mechanism. Pulldown from PANC-1 total RNA with biotinylated bPNA enriched MALAT1 > 4000× , supportive of bPNA-URIL selectivity. Together, these experiments establish the feasibility of native transcript targeting by bPNA in both in vitro and intracellular contexts. Reagents such as bPNAs may be useful tools for the investigation of transcripts stabilized by cis-acting poly(A) binding RNA elements.

Chemical approaches to discover the full potential of peptide nucleic acids in biomedical applications

Peptide nucleic acid (PNA) is arguably one of the most successful DNA mimics, despite a most dramatic departure from the native structure of DNA. The present review summarizes 30 years of research on PNA's chemistry, optimization of structure and function, applications as probes and diagnostics, and attempts to develop new PNA therapeutics. The discussion starts with a brief review of PNA's binding modes and structural features, followed by the most impactful chemical modifications, PNA enabled assays and diagnostics, and discussion of the current state of development of PNA therapeutics. While many modifications have improved on PNA's binding affinity and specificity, solubility and other biophysical properties, the original PNA is still most frequently used in diagnostic and other in vitro applications. Development of therapeutics and other in vivo applications of PNA has notably lagged behind and is still limited by insufficient bioavailability and difficulties with tissue specific delivery. Relatively high doses are required to overcome poor cellular uptake and endosomal entrapment, which increases the risk of toxicity. These limitations remain unsolved problems waiting for innovative chemistry and biology to unlock the full potential of PNA in biomedical applications.

Peptide nucleic acids and their role in gene regulation and editing

The unique properties of peptide nucleic acid (PNA) makes it a desirable candidate to be used in therapeutic and biotechnological interventions. It has been broadly utilized for numerous applications, with a major focus in regulation of gene expression, and more recently in gene editing. While the classic PNA design has mainly been employed to date, chemical modifications of the PNA backbone and nucleobases provide an avenue to advance the technology further. This review aims to discuss the recent developments in PNA based gene manipulation techniques and the use of novel chemical modifications to improve the current state of PNA mediated gene targeting.

Preparation of Artificial Hexaplex Composed of Non-Natural Nucleic Acid

This article describes synthetic procedures for acyclic D-threoninol nucleic acid tethering of bifacial nucleobases. Because these nucleobases have complementary hydrogen bonding sites on both sides, their oligomers can form a hexaplex. These hexaplexes are suitable for use as metal or pH sensors and as supramolecular motifs. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Synthesis of D-threoninol backbone Basic Protocol 2: Synthesis of D-aTNA tethering cyanuric acid Basic Protocol 3: Synthesis of D-aTNA tethering a 2-aminopyrimidine moiety Basic Protocol 4: Synthesis of D-aTNA tethering a 2,4,6-triaminopyrimidine moiety Basic Protocol 5: Synthesis of D-aTNA oligomer tethering cyanuric acid, 2-aminopyrimidine, or 2,4,6-triaminopyrimidine.

A novel miniaturized homogeneous label-free electrochemical biosensing platform combining integrated microelectrode and functional nucleic acids

A miniaturized platform combining integrated microelectrode (IME) and functional nucleic acids was developed for homogeneous label-free electrochemical biosensing. IME was constructed with a carbon fiber microelectrode and a platinum wire in a θ type glass tube as a two-electrode system for electrochemical monitoring at microliter level. A newly reported G-triplex/methylene blue (G3/MB) complex was used as the signal generator in the homogeneous label-free electrochemical biosensor. G3 has strong affinity with MB and it can cause significant decrease of the diffusion current of MB after binding. Melamine was chosen as the model target. Since melamine can interact with nucleobase thymine (T) to form T-melamine-T structure through complementary hydrogen bonds, a single-strand functional DNA hairpin structure with poly T and G3 elaborately blocked via base pairing was designed. The presence of melamine can trigger the conformation switching of the DNA hairpin to release the G3. The released G3 combined with MB could therefore change the diffusion current, leading to a simple and rapid detection of melamine. The combination of functional DNA hairpin as target recognition element, G3/MB as signal generator, and IME as transducer provided a "Mix and Measure" miniaturized platform for the construction of homogeneous label-free electrochemical biosensors.

Triazine-Based Janus G-C Nucleobase as a Building Block for Self-Assembly, Peptide Nucleic Acids, and Smart Polymers

This communication reports on the utility of a triazine-based self-assembling system, reminiscent of a Janus G-C nucleobase, as a building block for developing (1) supramolecular polymers, (2) peptide nucleic acids (PNAs), and (3) smart polymers. The strategically positioned self-complementary triple H-bonding arrays DDA and AAD facilitate efficient self-assembly, leading to a linear supramolecular polymer.

SYBR Green I promotes melamine binding to poly-thymine DNA and FRET-based ratiometric sensing

Using SYBR Green I for DNA melting experiments, polythymine DNA binding to melamine was found to be an intramolecular reaction, allowing the design of a FRET-based biosensor and its sensitivity was enhanced by SYBR Green I.

Unnatural bases for recognition of noncoding nucleic acid interfaces

The notion of using synthetic heterocycles instead of the native bases to interface with DNA and RNA has been explored for nearly 60 years. Unnatural bases compatible with the DNA/RNA coding interface have the potential to expand the genetic code and co-opt the machinery of biology to access new macromolecular function; accordingly, this body of research is core to synthetic biology. While much of the literature on artificial bases focuses on code expansion, there is a significant and growing effort on docking synthetic heterocycles to noncoding nucleic acid interfaces; this approach seeks to illuminate major processes of nucleic acids, including regulation of transcription, translation, transport, and transcript lifetimes. These major avenues of research at the coding and noncoding interfaces have in common fundamental principles in molecular recognition. Herein, we provide an overview of foundational literature in biophysics of base recognition and unnatural bases in coding to provide context for the developing area of targeting noncoding nucleic acid interfaces with synthetic bases, with a focus on systems developed through iterative design and biophysical study.

A poly(thymine)-melamine duplex for the assembly of DNA nanomaterials

The diversity of DNA duplex structures is limited by a binary pair of hydrogen-bonded motifs. Here we show that poly(thymine) self-associates into antiparallel, right-handed duplexes in the presence of melamine, a small molecule that presents a triplicate set of the hydrogen-bonding face of adenine. X-ray crystallography shows that in the complex two poly(thymine) strands wrap around a helical column of melamine, which hydrogen bonds to thymine residues on two of its three faces. The mechanical strength of the thymine-melamine-thymine triplet surpasses that of adenine-thymine base pairs, which enables a sensitive detection of melamine at 3 pM. The poly(thymine)-melamine duplex is orthogonal to native DNA base pairing and can undergo strand displacement without the need for overhangs. Its incorporation into two-dimensional grids and hybrid DNA-small-molecule polymers highlights the poly(thymine)-melamine duplex as an additional tool for DNA nanotechnology.

Context-Sensitive Cleavage of Folded DNAs by Loop-Targeting bPNAs

Herein, we demonstrate context-dependent molecular recognition of DNA by synthetic bPNA iron and copper complexes, using oxidative backbone cleavage as a chemical readout for binding. Oligoethylenimine bPNAs displaying iron·EDTA or copper·phenanthroline sites were found to be efficient chemical nucleases for designed and native structured DNAs with T-rich single-stranded domains. Cleavage reactivity depends strongly on structural context, as strikingly demonstrated with DNA substrates of the form (GGGTTA)_n. This repeat sequence from the human telomere is known to switch between parallel and antiparallel G-quadruplex (G4) topologies with a change from potassium to sodium buffer: notably, bPNA-copper complexes efficiently cleave long repeat sequences into ∼22-nucleotide portions in sodium, but not potassium, buffer. We hypothesize preferential cleavage of the antiparallel topology (Na⁺) over the parallel topology (K⁺) due to the greater accessibility of the TTA loop to bPNA in the antiparallel (Na⁺) form. Similar ion-sensitive telomere shortening upon treatment with bPNA nucleases can be observed in both isolated and intracellular DNA from PC3 cells by quantitative polymerase chain reaction. Live cell treatment was accompanied by accelerated cellular senescence, as expected for significant telomere shortening. Taken together, the loop-targeting approach of bPNA chemical nucleases complements prior intercalation strategies targeting duplex and quadruplex DNA. Structurally sensitive loop targeting enables discrimination between similar target sequences, thus expanding bPNA targeting beyond simple oligo-T sequences. In addition, bPNA nucleases are cell membrane permeable and therefore may be used to target native intracellular substrates. In addition, these data indicate that bPNA scaffolds can be a platform for new synthetic binders to particular nucleic acid structural motifs.

Modulation of DNA and RNA by PNA

Peptide nucleic acid (PNA), a synthetic DNA mimic that is devoid of the (deoxy)ribose-phosphate backbone yet still perfectly retains the ability to recognize natural nucleic acids in a sequence-specific fashion, can be employed as a tool to modulate gene expressions via several different mechanisms. The unique strength of PNA compared to other oligonucleotide analogs is its ability to bind to nucleic acid targets with secondary structures such as double-stranded and quadruplex DNA as well as RNA. This digest aims to introduce general readers to the advancement in the area of modulation of DNA/RNA functions by PNA, its current status and future research opportunities, with emphasis on recent progress in new targeting modes of structured DNA/RNA by PNA and PNA-mediated gene editing.

Prebiotic Peptides: Molecular Hubs in the Origin of Life

The fundamental roles that peptides and proteins play in today's biology makes it almost indisputable that peptides were key players in the origin of life. Insofar as it is appropriate to extrapolate back from extant biology to the prebiotic world, one must acknowledge the critical importance that interconnected molecular networks, likely with peptides as key components, would have played in life's origin. In this review, we summarize chemical processes involving peptides that could have contributed to early chemical evolution, with an emphasis on molecular interactions between peptides and other classes of organic molecules. We first summarize mechanisms by which amino acids and similar building blocks could have been produced and elaborated into proto-peptides. Next, non-covalent interactions of peptides with other peptides as well as with nucleic acids, lipids, carbohydrates, metal ions, and aromatic molecules are discussed in relation to the possible roles of such interactions in chemical evolution of structure and function. Finally, we describe research involving structural alternatives to peptides and covalent adducts between amino acids/peptides and other classes of molecules. We propose that ample future breakthroughs in origin-of-life chemistry will stem from investigations of interconnected chemical systems in which synergistic interactions between different classes of molecules emerge.

Triplex Hybridization of siRNA with Bifacial Glycopolymer Nucleic Acid Enables Hepatocyte-Targeted Silencing

Herein, we describe a versatile non-covalent strategy for packaging nucleic acid cargo with targeting modalities, based on triplex hybridization of oligo-uridylate RNA with bifacial polymer nucleic acid (bPoNA). Polyacrylate bPoNA was prepared and side chain-functionalized with N-acetylgalactosamine (GalNAc), which is known to enable delivery to hepatocytes and liver via binding to the asialoglycoprotein receptor (ASGPR). Polymer binding resulted in successful delivery of both native and synthetically modified siRNAs to HepG2 cells in culture, yielding in low nanomolar IC50 silencing of the endogenous ApoB target, in line with observations of expected Dicer processing of the polymer-siRNA targeting complex. Indeed, in vitro Dicer treatment of the polymer complex indicated that triplex hybridization does not impede RNA processing and release from the polymer. The complex itself elicited a quiescent immunostimulation profile relative to free RNA in a cytokine screen, setting the stage for a preliminary in vivo study in a high-calorie-diet mouse model. Gratifyingly, we observed significant ApoB silencing in a preliminary animal study, validating bPoNA as an in vivo carrier platform for systemic siRNA delivery. Thus, this new siRNA carrier platform exhibits generally useful function and is accessible through scalable synthesis. In addition to its utility as a carrier, the triplex-hybridizing synthetic platform could be useful for optimization screens of siRNA sequences using the identical polymer carriers, thus alleviating the need for covalent ligand modification of each RNA substrate.

Duplex Stem Replacement with bPNA+ Triplex Hybrid Stems Enables Reporting on Tertiary Interactions of Internal RNA Domains

We report herein the synthesis and DNA/RNA binding properties of bPNA+, a new variant of bifacial peptide nucleic acid (bPNA) that binds oligo T/U nucleic acids to form triplex hybrids. By virtue of a new bivalent side chain on bPNA+, similar DNA affinity and hybrid thermostability can be obtained with half the molecular footprint of previously reported bPNA. Lysine derivatives bearing two melamine bases (K2M) can be prepared on multigram scale by double reductive alkylation with melamine acetaldehyde, resulting in a tertiary amine side chain that affords both peptide solubility and selective base-triple formation with 4 T/U bases; the Fmoc-K2M derivative can be used directly in solid phase peptide synthesis, rendering bPNA+ conveniently accessible. A compact bPNA+binding site of two U6 domains can be genetically encoded to replace existing 6 bp stem elements at virtually any location within an RNA transcript. We thus replaced internal 6 bp RNA stems that supported loop regions with 6 base-triple hybrid stems using fluorophore-labeled bPNA+. As the loop regions engaged in RNA tertiary interactions, the labeled hybrid stems provided a fluorescent readout; bPNA+ enabled this readout without covalent chemical modification or introduction of new structural elements. This strategy was demonstrated to be effective for reporting on widely observed RNA tertiary interactions such as intermolecular RNA-RNA kissing loop dimerization, RNA-protein binding, and intramolecular RNA tetraloop-tetraloop receptor binding, illustrating the potential general utility of this method. The modest 6 bp stem binding footprint of bPNA+ makes the hybrid stem replacement method practical for noncovalent installation of synthetic probes of RNA interactions. We anticipate that bPNA+ structural probes will be useful for the study of tertiary interactions in long noncoding RNAs.

Synthetic bPNAs as allosteric triggers of hammerhead ribozyme catalysis

The biochemistry and structural biology of the hammerhead ribozyme (HHR) have been well elucidated. The secondary and tertiary structural elements that enable sugar-phosphate bond scission to be catalyzed by this RNA are clearly understood. We have taken advantage of this knowledge base to test the extent to which synthetic molecules, may be used to trigger structure in secondary structure and tertiary interactions and thereby control HHR catalysis. These molecules belong to a family of molecules we generally call "bPNAs" based on our work on bifacial peptide nucleic acid (bPNA). This family of molecules displays the "bifacial" heterocycle melamine, which acts as a base-triple upon capturing two equivalents of thymine or uracil. Loosely structured internal oligouridylate bulges of 4-20 nucleotides can be restructured as triplex hybrid stems upon binding bPNAs. As such, a duplex stem element can be replaced with a bPNA triplex hybrid stem; similarly, a tertiary loop-stem interaction can be replaced with a loop-bPNA-stem complex. The ability to control RNA structure-function facilitates elucidation of these critical aspects of RNA recognition. In this chapter, we discuss how bPNAs are prepared and applied to study structure-function turn on in the hammerhead ribozyme system.

Facile detection of melamine by a FAM-aptamer-G-quadruplex construct

The development of a novel method for melamine detection that uses a FAM-aptamer-G-quadruplex construct due to the efficient quenching ability of an aptamer-linked G-quadruplex is reported herein. The construct, which is labeled with the fluorescent dye 6-carboxyfluorescein (FAM), consists of two parts: a melamine-binding aptamer and a G-rich sequence that can form a G-quadruplex structure. Because of the specific recognition of melamine by the T-rich aptamer, this aptamer folds into a hairpin structure in the presence of melamine, which draws the G-quadruplex closer to the FAM fluorophore, leading to the quenching of the fluorescence of FAM. Thus, a highly sensitive and selective fluorescence strategy for assaying melamine was established. Under optimal conditions, the fluorescence quenching is proportional to the concentration of melamine within the range 10-90 nM, and the method has a detection limit of 6.32 nM. Further application of the method to plastic cup samples suggested that it permitted recoveries of between 97.15% ± 1.02 and 101.92% ± 2.07. The detected amounts of melamine spiked into the plastic cup samples and the corresponding amounts measured by HPLC were in good accordance, indicating that this fluorescent method is reliable and practical. Owing to its high sensitivity, excellent selectivity, and convenient procedure, this strategy represents a promising alternative method of melamine screening. Graphical abstract.

Supramolecular self-assembly of triazine-based small molecules: targeting the endoplasmic reticulum in cancer cells

The endoplasmic reticulum (ER) is one of the most important organelles controlling myriads of cellular functions including protein folding/misfolding/unfolding, calcium ion homeostasis and lipid biosynthesis. Subsequently, due to its functional dysregulation in cancer cells, it has emerged as an interesting target for anti-cancer therapy. However, specific targeting of the ER in cancer cells remains a major challenge due to the lack of ER-selective chemical tools. Furthermore, for performing multiple cellular functions the ER is dependent on the nucleus through complicated cross-talk. Herein, we have engineered a supramolecular self-assembled hexameric rosette structure from two small molecules: tri-substituted triazine and 5-fluorouracil (5-FU). This rosette structure consists of an ER-targeting moiety with a fluorescence tag, an ER-stress inducer and a nuclear DNA damaging drug simultaneously, which further self-assembled into an ER-targeting spherical nano-scale particle (ER-NP). These ER-NPs internalized into HeLa cervical cancer cells by macropinocytosis and specifically localized into the ER to induce ER stress and DNA damage leading to cell death through apoptosis. Interestingly, ER-NPs initiated autophagy, inhibited by a combination of ER-NPs and chloroquine (CQ) to augment cancer cell death. This work has the potential to exploit the concept of supramolecular self-assembly into developing novel nano-scale materials for specific sub-cellular targeting of multiple organelles for future anti-cancer therapy.

Melamine-mediated supramolecular assembly of nucleobase-modified poly(l-lysine)

Melamine (M) was used to drive the supramolecular assembly of thymine (T)-modified poly(l-lysine) into fibers or spherical micelles through simply adjusting the substitution degree of T and the concentration of M.

Universal and label-free photosensitization colorimetric assays enabled by target-induced termini transformation of dsDNA resistant to Exo III digestion

A label-free and universal colorimetric assay was developed via the combination of CHA, Exo III digestion, and photosensitization colorimetry.

Target-switched triplex nanotweezer and synergic fluorophore translocation for highly selective melamine assay

This paper describes a triplex DNA nanotweezer to specifically capture melamine (MEL). The triplex-forming oligonucleotide (TFO) arm can be switched from the open state to the closed state once MEL binds to the abasic site (AP site) in duplex via the bifacial hydrogen bonding with thymines. Following this nanotweezer operation, the AP site-bound fluorophore is translocated to the terminal triplet to subsequently light up the nanotweezer. The TFO arm is found to be pivotal for permitting the AP site binding. The synergic processes of target competition and fluorophore translocation support a high selectivity for the MEL assay even against the inherent adenosine and the MEL hydrolysis products. Chelerythrine is employed as the fluorescent probe. The detection limit of MEL was estimated to be about 140 nM assuming a signal-to-noise ratio of 3. It was applied to the determination of MEL in spiked milk samples without any separation procedure. Conceivably, this method opens a new avenue towards highly selective triplex-based sensors by making use of other commercially available DNA modifications for recognizing other analytes. Graphical abstract Schematic presentation of a triplex nanotweezer with an open-to-close conversion upon the abasic site binding of melamine. The assay is based on a synergic fluorophore translocation. The corresponding duplex otherwise shows no binding with melamine. Chelerythrine (CHE) with a yellow-green emission peaking at 544 nm is employed as the fluorescent probe.

Electrochemical DNA-Based Sensors for Molecular Quality Control: Continuous, Real-Time Melamine Detection in Flowing Whole Milk

The ability to monitor specific molecules in real-time directly in a flowing sample stream and in a manner that does not adulterate that stream could greatly augment quality control in, for example, food processing and pharmaceutical manufacturing. Because they are continuous, reagentless, and able to work directly in complex samples, electrochemical DNA-based (E-DNA) sensors, a modular and, thus, general sensing platform, are promising candidates to fill this role. In support, we describe here an E-DNA sensor supporting the continuous, real-time measurement of melamine in flowing milk. Using target-driven DNA triplex formation to generate an electrochemical output, the sensor responds to rising and falling melamine concentration in seconds without contaminating the product stream. The continuous, autonomous, real-time operation of sensors such as this could provide unprecedented safety, convenience, and cost-effectiveness relative to the batch processes historically employed in molecular quality control.

Simple and Label-Free Fluorescent Detection of Melamine Based on Melamine⁻Thymine Recognition

In the past few years, melamine has been illegally added into dairy products to increase the apparent crude protein levels. If humans or animals drink the milk adulteration of melamine, it can form insoluble melamine–cyanurate crystals in their kidneys which causes kidney damage or even death. In the present work, we constructed a simple and label-free fluorescent method for melamine detection based on melamine-thymine recognition. SYBR Green I was utilized as a reporter for this method as it did not require any modification or expensive equipment. In the absence of melamine, polythymine DNA was digested by Exo I, which caused a decrease in the fluorescence signal. In the presence of melamine, the polythymine DNA was able to fold into a double chain structure, however this was done with the help of T-melamine-T mismatches to prevent degradation. Then, the SYBR Green I combined with the double-stranded DNA to result in an intense fluorescence signal. The limit of detection in this method was 1.58 μM, which satisfied the FDA standards. This method also had a good linear relationship within the range of 10–200 μM. In addition, this new method has a good selectivity to distinguish melamine from the component of milk. As a result, we developed a simple and highly selectivity method for melamine detection.

ATP-Driven Temporal Control over Structure Switching of Polymeric Micelles

An adenosine triphosphate (ATP)-fueled micellar system in the out-of-equilibrium state was constructed based on 4,5-diamino-1,3,5-triazine (DAT)-containing block copolymer. The block copolymer self-assembled into spherical micelles in equilibrium steady state at pH higher than its p K_a. The pendant DAT residues in protonated form acted as ATP catchers via hydrogen bonding and electrostatic interactions. Activated by ATP fuel, the polymeric micelles spontaneously disrupted into small aggregates of ATP/polymer hybrid complexes. The consumption of ATP energy via the enzymatic hydrolysis led to dissociation of the complexes and reversible formation of polymeric micelles. A transient self-assembly cycle, in which the assembly underwent autonomous division-fusion motion, was created using ATP fuel and enzyme; the switching of assembly structure was sustained by continuous supply of ATP fuel. This DAT-containing block copolymer have good biocompatibility, and drug-loaded micelles display ATP-responsive release behavior. It is expected that this ATP-fueled supramolecular assembly system will provide a functional platform for biomimic chemistry and therapeutic applications.

Bifacial Nucleobases for Hexaplex Formation in Aqueous Solution

Although DNA can form triplex and quadruplex structures through hydrogen bonds, design and preparation of structures with more than five strands is difficult even when artificial nucleic acids are used. Herein we report a hexaplex formed by oligomers of artificial nucleic acids bearing bifacial molecules on d-threoninol. Aminopyrimidine and cyanuric acid derivatives were selected as bases because they have complementary hydrogen bonding patterns. The complex formed by aminopyrimidine and cyanuric acid decamers melted with large hysteresis. Hexaplex formation was indicated by gel electrophoresis, size exclusion chromatography and atomic force microscopy imaging, and proven directly through native mass spectrometry. CD measurements and molecular dynamics simulations indicated that the hexaplex adopts a helical structure. The hexaplex formation was highly dependent on pH and the presence of divalent cations. The hexaplex was stable in aqueous solution, and its unique structure and properties may lead to novel nanostructures, molecular assemblies, metal sensors, and ion channels.

Design of Bivalent Nucleic Acid Ligands for Recognition of RNA-Repeated Expansion Associated with Huntington's Disease

We report the development of a new class of nucleic acid ligands that is comprised of Janus bases and the MPγPNA backbone and is capable of binding rCAG repeats in a sequence-specific and selective manner via, inference, bivalent H-bonding interactions. Individually, the interactions between ligands and RNA are weak and transient. However, upon the installation of a C-terminal thioester and an N-terminal cystine and the reduction of disulfide bond, they undergo template-directed native chemical ligation to form concatenated oligomeric products that bind tightly to the RNA template. In the absence of an RNA target, they self-deactivate by undergoing an intramolecular reaction to form cyclic products, rendering them inactive for further binding. The work has implications for the design of ultrashort nucleic acid ligands for targeting rCAG-repeat expansion associated with Huntington's disease and a number of other related neuromuscular and neurodegenerative disorders.

Synthesis, molecular docking, ctDNA interaction, DFT calculation and evaluation of antiproliferative and anti-Toxoplasma gondii activities of 2,4-diaminotriazine-thiazole derivatives

Synthesis, characterization, and investigation of antiproliferative activities against human cancer cell lines (MV4-11, MCF-7, and A549) and Toxoplasma gondii parasite of twelve novel 2,4-diaminotriazine-thiazoles are presented. The toxicity of the compounds was studied at three different cell types, normal mouse fibroblast (Balb/3T3), mouse fibroblast (L929), and human VERO cells. The structures of novel compounds were determined using ¹H and ¹³C NMR, FAB(+)-MS, and elemental analyses. Among the derivatives, 4a–k showed very high activity against MV4-11 cell line with IC₅₀ values between 1.13 and 3.21 µg/ml. Additionally, the cytotoxic activity of compounds 4a–k against normal mouse fibroblast Balb/3T3 cells is about 20–100 times lower than against cancer cell lines. According to our results, compounds 4a, 4b, 4d, and 4i have very strong activity against human breast carcinoma MCF-7, with IC₅₀ values from 3.18 to 4.28 µg/ml. Moreover, diaminotriazines 4a–l showed significant anti-Toxoplasma gondii activity, with IC₅₀ values 9–68 times lower than those observed for sulfadiazine. Molecular docking studies indicated DNA-binding site of hTopoI and hTopoII as possible anticancer targets and purine nucleoside phosphorylase as possible anti-toxoplasmosis target. Our UV–Vis spectroscopic results indicate also that diaminotriazine-thiazoles tends to interact with DNA by intercalation. Additionally, the structure and the interaction and binding energies of a model complex formed by compound 4a and two thymine molecules are investigated using quantum mechanical methods.

Shape selective bifacial recognition of double helical DNA

An impressive array of antigene approaches has been developed for recognition of double helical DNA over the past three decades; however, few have exploited the 'Watson-Crick' base-pairing rules for establishing sequence-specific recognition. One approach employs peptide nucleic acid as a molecular reagent and strand invasion as a binding mode. However, even with integration of the latest conformationally-preorganized backbone design, such an approach is generally confined to sub-physiological conditions due to the lack of binding energy. Here we report the use of a class of shape-selective, bifacial nucleic acid recognition elements, namely Janus bases, for targeting double helical DNA or RNA. Binding occurs in a highly sequence-specific manner under physiologically relevant conditions. The work may provide a foundation for the design of oligonucleotides for targeting the secondary and tertiary structures of nucleic acid biopolymers.