Low temperature assembly of functional 3D DNA-PNA-protein complexes

Triangle-toothed gear occlude-guided universal nanotechnology constructs 3D symmetric DNA polyhedra with high assembly efficiency for precision cancer therapy

Chemotherapy is commonly used to treat malignant tumors. However, conventional chemotherapeutic drugs often cannot distinguish between tumor and healthy cells, resulting in adverse effects and reduced therapeutic efficacy. Therefore, zigzag-shaped gear-occlude-guided cymbal-closing (ZGC) DNA nanotechnology was developed based on the mirror-symmetry principle to efficiently construct symmetric DNA polyhedra. This nanotechnology employed simple mixing steps for efficient sequence design and assembly. A targeting aptamer was installed at a user-defined position using an octahedron as a model structure. Chemotherapeutic drug-loaded polyhedral objects were subsequently delivered into tumor cells. Furthermore, anticancer drug-loaded DNA octahedra were intravenously injected into a HeLa tumor-bearing mouse model. Assembly efficiency was almost 100 %, with no residual building blocks identified. Moreover, this nanotechnology required a few DNA oligonucleotides, even for complex polyhedrons. Symmetric DNA polyhedrons retained their structural integrity for 24 h in complex biological environments, guaranteeing prolonged circulation without drug leakage in the bloodstream and promoting efficient accumulation in tumor tissues. In addition, DNA octahedra were cleared relatively slowly from tumor tissues. Similarly, tumor growth was significantly inhibited in vivo, and a therapeutic outcome comparable to that of conventional gene-chemo combination therapy was observed. Moreover, no systemic toxicity was detected. These findings indicate the potential application of ZGC DNA nanotechnology in precision medicine.

Superlarge, Rigidified DNA Tetrahedron with a Y-Shaped Backbone for Organizing Biomolecules Spatially and Maintaining Their Full Bioactivity

A major impediment to the clinical translation of DNA tiling nanostructures is a technical bottleneck for the programmable assembly of DNA architectures with well-defined local geometry due to the inability to achieve both sufficient structural rigidity and a large framework. In this work, a Y-backbone was inserted into each face to construct a superlarge, sufficiently rigidified tetrahedral DNA nanostructure (called RDT) with extremely high efficiency. In RDT, the spatial size increased by 6.86-fold, and the structural rigidity was enhanced at least 4-fold, contributing to an ∼350-fold improvement in the resistance to nucleolytic degradation even without a protective coating. RDT can be mounted onto an artificial lipid-bilayer membrane with molecular-level precision and well-defined spatial orientation that can be validated using the fluorescence resonance energy transfer (FRET) assay. The spatial orientation of Y-shaped backbone-rigidified RDT is unachievable for conventional DNA polyhedrons and ensures a high level of precision in the geometric positioning of diverse biomolecules with an approximately homogeneous environment. In tests of RDT, surface-confined horseradish peroxidase (HRP) exhibited nearly 100% catalytic activity and targeting aptamer-immobilized gold nanoparticles showed 5.3-fold enhanced cellular internalization. Significantly, RDT exhibited a 27.5-fold enhanced structural stability in a bodily environment and did not induce detectable systemic toxicity.

DNA polyhedrons cube, prism, and square pyramid protect the catalytic activity of catalase: A thermodynamics and kinetics study

DNA is widely used as building block material for the construction of polyhedral nanostructures. DNA polyhedrons (DNA prism, cube, and square pyramid) are small 3D wireframed nanostructures with tunable shapes and sizes. Despite substantial progress in synthesis, the study regarding cellular responses to DNA polyhedrons is limited. Herein, the molecular interaction between DNA polyhedrons and the antioxidant enzyme, catalase has been explored. The enzymatic activity of bovine liver catalase (BLC) remains unaltered in the presence of DNA polyhedrons after 1 h of incubation. However, the activity of BLC was protected after 24 h of incubation in the presence of DNA polyhedrons as compared to the natural unfolding. The kinetics study confirmed the protective role of DNA polyhedrons on BLC with lower KM and higher catalytic efficiency. Furthermore, no profound conformational changes of BLC occur in the presence of DNA polyhedrons as observed in spectroscopic studies. From fluorescence quenching data we confirmed the binding between DNA polyhedrons and BLC. The thermodynamic parameters indicate that non-covalent bonds played a major role during the interaction of BLC with DNA polyhedrons. Moreover, the hepatic catalase activity remains unaltered in the presence of DNA polyhedrons. The cytotoxicity assay revealed that DNA polyhedrons were biocompatible in the cellular environment. The protective role of DNA polyhedrons on enzyme activity and the unaltered conformational change of protein ensures the biocompatibility of DNA polyhedrons in the cellular environment.

Self-Assembled Artificial DNA Nanocompartments and Their Bioapplications

Compartmentalization is the strategy evolved by nature to control reactions in space and time. The ability to emulate this strategy through synthetic compartmentalization systems has rapidly evolved in the past years, accompanied by an increasing understanding of the effects of spatial confinement on the thermodynamic and kinetic properties of the guest molecules. DNA nanotechnology has played a pivotal role in this scientific endeavor and is still one of the most promising approaches for the construction of nanocompartments with programmable structural features and nanometer-scaled addressability. In this review, the design approaches, bioapplications, and theoretical frameworks of self-assembled DNA nanocompartments are surveyed. From DNA polyhedral cages to virus-like capsules, the construction principles of such intriguing architectures are illustrated. Various applications of DNA nanocompartments, including their use for programmable enzyme scaffolding, single-molecule studies, biosensing, and as artificial nanofactories, ending with an ample description of DNA nanocages for biomedical purposes, are then reported. Finally, the theoretical hypotheses that make DNA nanocompartments, and nanosystems in general, a topic of great interest in modern science, are described and the progresses that have been done until now in the comprehension of the peculiar phenomena that occur within nanosized environments are summarized.

Synthesis of Protein-Oligonucleotide Conjugates

Nucleic acids and proteins form two of the key classes of functional biomolecules. Through the ability to access specific protein-oligonucleotide conjugates, a broader range of functional molecules becomes accessible which leverages both the programmability and recognition potential of nucleic acids and the structural, chemical and functional diversity of proteins. Herein, we summarize the available conjugation strategies to access such chimeric molecules and highlight some key case study examples within the field to showcase the power and utility of such technology.

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.

Elucidation of the key role of Pt···Pt interactions in the directional self-assembly of platinum(II) complexes

Molecular self-assembly provides a bottom-up platform to design supramolecular functional materials, attracting numerous interests in material sciences. The utilization of platinum(II) complexes as building blocks of supramolecular assemblies opens up the unique noncovalent Pt···Pt interaction as one of the driving forces, imparting the supramolecular materials with rich spectroscopic features. However, the exact role of Pt···Pt interactions in molecular assembly remains elusive. The current study combines experimental and computational techniques to elucidate the role of Pt···Pt interactions in the self-assembly process of a representative amphiphilic platinum(II) complex. This work demonstrates the directional role of Pt···Pt interactions in assisting the molecular assembly in an anisotropic manner, achieving the formation of ordered self-assembled structures.

Here, we report the use of an amphiphilic Pt(II) complex, K[Pt{(O₃SCH₂CH₂CH₂)₂bzimpy}Cl] (PtB), as a model to elucidate the key role of Pt···Pt interactions in directing self-assembly by combining temperature-dependent ultraviolet-visible (UV-Vis) spectroscopy, stopped-flow kinetic experiments, quantum mechanics (QM) calculations, and molecular dynamics (MD) simulations. Interestingly, we found that the self-assembly mechanism of PtB in aqueous solution follows a nucleation-free isodesmic model, as revealed by the temperature-dependent UV-Vis experiments. In contrast, a cooperative growth is found for the self-assembly of PtB in acetone–water (7:1, vol/vol) solution, which is further verified by the stopped-flow experiments, which clearly indicates the existence of a nucleation phase in the acetone–water (7:1, vol/vol) solution. To reveal the underlying reasons and driving forces for these self-assembly processes, we performed QM calculations and show that the Pt···Pt interactions arising from the interaction between the p_z and d_z² orbitals play a crucial role in determining the formation of ordered self-assembled structures. In subsequent oligomer MD simulations, we demonstrate that this directional Pt···Pt interaction can indeed facilitate the formation of linear structures packed in a helix-like fashion. Our results suggest that the self-assembly of PtB in acetone–water (7:1, vol/vol) solution is predominantly driven by the directional noncovalent Pt···Pt interaction, leading to the cooperative growth and the formation of fibrous nanostructures. On the contrary, the self-assembly in aqueous solution forms spherical nanostructures of PtB, which is primarily due to the predominant contribution from the less directional hydrophobic interactions over the directional Pt···Pt and π−π interactions that result in an isodesmic growth.

Structural DNA nanotechnology: Immobile Holliday junctions to artificial robots

DNA nanotechnology marvels the scientific world with its capabilities to design, engineer, and demonstrate nanoscale shapes. This review is a condensed version walking the reader through the structural developments in the field over the past 40 years starting from the basic design rules of the double-stranded building block to the most recent advancements in self-assembled hierarchically achieved structures to date. It builds off from the fundamental motivation of building 3-dimensional (3D) lattice structures of tunable cavities going all the way up to artificial nanorobots fighting cancer. The review starts by covering the most important developments from the fundamental bottom-up approach of building structures, which is the 'tile' based approach covering 1D, 2D, and 3D building blocks, after which, the top-down approach using DNA origami and DNA bricks is also covered. Thereafter, DNA nanostructures assembled using not so commonly used (yet promising) techniques like i-motifs, quadruplexes, and kissing loops are covered. Highlights from the field of dynamic DNA nanostructures have been covered as well, walking the reader through the various approaches used within the field to achieve movement. The article finally concludes by giving the authors a view of what the future of the field might look like while suggesting in parallel new directions that fellow/future DNA nanotechnologists could think about.

Functionalizing Framework Nucleic-Acid-Based Nanostructures for Biomedical Application

Strategies for functionalizing diverse tetrahedral framework nucleic acids (tFNAs) have been extensively explored since the first successful fabrication of tFNA by Turberfield. One-pot annealing of at least four DNA single strands is the most common method to prepare tFNA, as it optimizes the cost, yield, and speed of assembly. Herein, the focus is on four key merits of tFNAs and their potential for biomedical applications. The natural ability of tFNA to scavenge reactive oxygen species, along with remarkable enhancement in cellular endocytosis and tissue permeability based on its appropriate size and geometry, promotes cell-material interactions to direct or probe cell behavior, especially to treat inflammatory and degenerative diseases. Moreover, the structural programmability of tFNA enables the development of static tFNA-based nanomaterials via engineering of functional oligonucleotides or therapeutic molecules, and dynamic tFNAs via attachment of stimuli-responsive DNA apparatuses, leading to potential applications in targeted therapies, tissue regeneration, antitumor strategies, and antibacterial treatment. Although there are impressive performance and significant progress, the challenges and prospects of functionalizing tFNA-based nanostructures are still indicated in this review.

Probing the Formation Kinetics and Thermodynamics with Rationally Designed Analytical Tools Enables One-Pot Synthesis and Purification of a Tetrahedral DNA Nanostructure

The development of robust analytical tools capable of probing the formation kinetics and thermodynamics of DNA nanostructures is a crucial step toward better understanding and manufacturing of diverse DNA-based materials. Herein, we introduce a real-time fluorescence anisotropy assay and rationally designed DNA reaction termination probes (DRTPs) as a set of new tools for exploring the formation mechanisms of DNA nanostructures. We deployed these tools for probing the formation of a classic tetrahedral DNA nanostructure (TDN) as a model system. Our tools revealed that the formation of TDN was dominated by simultaneous hybridization, whereas its undesired side products were caused mainly through step-wise hybridization. An optimal reaction temperature exists that favors the formation of TDN over side products. With insight into the TDN formation mechanism, we further engineered magnetic DRTPs to achieve single-step purification of TDN, enabling 10-fold improvement in the ratio between the targeted TDN and undesired side products without tedious procedures or bulky instruments. Combining the optimal reaction and purification conditions, we finally demonstrated the one-pot synthesis and purification of TDN. The analytical techniques offered in this work may hold potential to find wide applications and inspire new analytical methods for structural DNA nanotechnology.

Functional modulation of cytochrome C upon specific binding to DNA nanoribbons

We discovered that the function of cytochrome C can be modulated by DNA nanoribbons. Meanwhile, the interplay between the DNA nanoribbons and the native cytochrome C and the possible mechanisms are also discussed.

Construction of a reconfigurable DNA nanocage for encapsulating a TMV disk

A new reconfigurable DNA nanocage based on a DNA origami method has been constructed to capture a tobacco mosaic virus (TMV) disk. We used a hairpin to control the transformation of the nanocage and a strand of TMV RNA to attract the TMV disk. Our design could inspire new DNA-protein complex designs.

Redox Engineering of Cytochrome c using DNA Nanostructure-Based Charged Encapsulation and Spatial Control

Three-dimensional (3D) DNA nanostructures facilitate the directed self-assembly of various objects with designed patterns with nanometer scale addressability. Here, we report the enhancement of cytochrome c (cyt c) redox activity by using a designed 3D DNA nanostructure attached to a gold electrode to spatially control the position of cyt c within the tetrahedral framework. Charged encapsulation and spatial control result in the significantly increased redox potential and enhanced electron transfer of this redox protein when compared to cyt c directly adsorbed on the gold surface. Two different protein attachment sites on one double stranded edge of a DNA tetrahedron were used to position cyt c inside and outside of the cage. Cyt c at both binding sites show similar redox potential shift and only slight difference in the electron transfer rate, both orders of magnitude faster than the cases when the protein was directly deposited on the gold electrode, likely due to an effective electron transfer pathway provided by the stabilization effect of the protein created by the DNA framework. This study shows great potential of using structural DNA nanotechnology for spatial control of protein positioning on electrode, which opens new routes to engineer redox proteins and interface microelectronic devices with biological function.

Principles and Applications of Nucleic Acid Strand Displacement Reactions

Dynamic DNA nanotechnology, a subfield of DNA nanotechnology, is concerned with the study and application of nucleic acid strand-displacement reactions. Strand-displacement reactions generally proceed by three-way or four-way branch migration and initially were investigated for their relevance to genetic recombination. Through the use of toeholds, which are single-stranded segments of DNA to which an invader strand can bind to initiate branch migration, the rate with which strand displacement reactions proceed can be varied by more than 6 orders of magnitude. In addition, the use of toeholds enables the construction of enzyme-free DNA reaction networks exhibiting complex dynamical behavior. A demonstration of this was provided in the year 2000, in which strand displacement reactions were employed to drive a DNA-based nanomachine (Yurke, B.; et al. Nature 2000, 406, 605-608). Since then, toehold-mediated strand displacement reactions have been used with ever increasing sophistication and the field of dynamic DNA nanotechnology has grown exponentially. Besides molecular machines, the field has produced enzyme-free catalytic systems, all DNA chemical oscillators and the most complex molecular computers yet devised. Enzyme-free catalytic systems can function as chemical amplifiers and as such have received considerable attention for sensing and detection applications in chemistry and medical diagnostics. Strand-displacement reactions have been combined with other enzymatically driven processes and have also been employed within living cells (Groves, B.; et al. Nat. Nanotechnol. 2015, 11, 287-294). Strand-displacement principles have also been applied in synthetic biology to enable artificial gene regulation and computation in bacteria. Given the enormous progress of dynamic DNA nanotechnology over the past years, the field now seems poised for practical application.

Selective in Situ Assembly of Viral Protein onto DNA Origami

Engineering hybrid protein-DNA assemblies in a controlled manner has attracted particular attention, for their potential applications in biomedicine and nanotechnology due to their intricate folding properties and important physiological roles. Although DNA origami has served as a powerful platform for spatially arranging functional molecules, in situ assembly of proteins onto DNA origami is still challenging, especially in a precisely controlled and facile manner. Here, we demonstrate in situ assembly of tobacco mosaic virus (TMV) coat proteins onto DNA origami to generate programmable assembly of hybrid DNA origami-protein nanoarchitectures. The protein nanotubes of controlled length are precisely anchored on the DNA origami at selected locations using TMV genome-mimicking RNA strands. This study opens a new route to the organization of protein and DNA into sophisticated protein-DNA nanoarchitectures by harnessing the viral encapsidation mechanism and the programmability of DNA origami.

DNA-spheres decorated with magnetic nanocomposites based on terminal transfer reactions for versatile target detection and cellular targeted drug delivery

We present an elegant approach to make a magnetic nanoparticle (MNP) conjugated DNA-sphere (MNP/DNA-SP) which is integrated with disulfide (MNP/DS-SP) or an aptamer (MNP/sgc8-SP) for GSH detection, selective cancer cell recognition, effective drug delivery, and bioimaging.

Supramolecular Protein Assemblies Based on DNA Templates

DNA plays an important role in the process of protein assembly. DNA viruses such as the M13 virus are typical examples in which single DNA genomes behave as templates to induce the assembly of multiple major coat protein (PVIII) monomers. Thus, the design of protein assemblies based on DNA templates attracts much interest in the construction of supramolecular structures and materials. With the development of DNA nanotechnology, precise 1D and 3D protein nanostructures have been designed and constructed by using DNA templates through DNA-protein interactions, protein-ligand interactions, and protein-adapter interactions. These DNA-templated protein assemblies show great potential in catalysis, medicine, light-responsive systems, drug delivery, and signal transduction. Herein, we review the progress on DNA-based protein nanostructures that possess sophisticated nanometer-sized structures with programmable shapes and stimuli-responsive parameters, and we present their great potential in the design of biomaterials and biodevices in the future.

Molecular self-assembly using peptide nucleic acids

Peptide nucleic acids (PNAs) are extensively studied for the control of genetic expression since their design in the 1990s. However, the application of PNAs in nanotechnology is much more recent. PNAs share the specific base-pair recognition characteristic of DNA together with material-like properties of polyamides, both proteins and synthetic polymers, such as Kevlar and Nylon. The first application of PNA was in the form of PNA-amphiphiles, resulting in the formation of either lipid integrated structures, hydrogels or fibrillary assemblies. Heteroduplex DNA-PNA assemblies allow the formation of hybrid structures with higher stability as compared with pure DNA. A systematic screen for minimal PNA building blocks resulted in the identification of guanine-containing di-PNA assemblies and protected guanine-PNA monomer spheres showing unique optical properties. Finally, the co-assembly of PNA with thymine-like three-faced cyanuric acid allowed the assembly of poly-adenine PNA into fibers. In summary, we believe that PNAs represent a new and important family of building blocks which converges the advantages of both DNA- and peptide-nanotechnologies.

Adsorption characteristics of Cytochrome c/DNA complex Langmuir molecular assemblies at the air–water interface: a surface area-normalized isotherm study

We present the formation of a complex molecular network consisting of highly water soluble λ-DNA and a redox protein, Cytochrome c (Cyt c), at the air–water interface by Langmuir–Blodgett technique.

Versatility of peptide nucleic acids (PNAs): role in chemical biology, drug discovery, and origins of life

This review briefly discussed nomenclature, synthesis, chemistry, and biophysical properties of a plethora of PNA derivatives reported since the discovery of aegPNA. Different synthetic methods and structural analogs of PNA synthesized till date were also discussed. An insight was gained into various chemical, physical, and biological properties of PNA which make it preferable over all other classes of modified nucleic acid analogs. Thereafter, various approaches with special attention to the practical constraints, characteristics, and inherent drawbacks leading to the delay in the development of PNA as gene therapeutic drug were outlined. An explicit account of the successful application of PNA in different areas of research such as antisense and antigene strategies, diagnostics, molecular probes, and so forth was described along with the current status of PNA as gene therapeutic drug. Further, the plausibility of the existence of PNA and its role in primordial chemistry, that is, origin of life was explored in an endeavor to comprehend the mystery and open up its deepest secrets ever engaging and challenging the human intellect. We finally concluded it with a discussion on the future prospects of PNA technology in the field of therapeutics, diagnostics, and origin of life.

Purification and assembly of thermostable Cy5 labeled γ-PNAs into a 3D DNA nanocage

PNA is hybrid molecule ideally suited for bridging the functional landscape of polypeptides with the structural diversity that can be engineered with DNA nanostructures. However, PNA can be more challenging to work with in aqueous solvents due to its hydrophobic nature. A solution phase method using strain promoted, copper free click chemistry was developed to conjugate the fluorescent dye Cy5 to 2 bifunctional PNA strands as a first step toward building cyclic PNA-polypeptides that can be arranged within 3D DNA nanoscaffolds. A 3D DNA nanocage was designed with binding sites for the 2 fluorescently labeled PNA strands in close proximity to mimic protein active sites. Denaturing polyacrylamide gel electrophoresis (PAGE) is introduced as an efficient method for purifying charged, dye-labeled PNA conjugates from large excesses of unreacted dye and unreacted, neutral PNA. Elution from the gel in water was monitored by fluorescence and found to be more efficient for the more soluble PNA strand. Native PAGE shows that both PNA strands hybridize to their intended binding sites within the DNA nanocage. Förster resonance energy transfer (FRET) with a Cy3 labeled DNA nanocage was used to determine the dissociation temperature of one PNA-Cy5 conjugate to be near 50°C. Steady-state and time resolved fluorescence was used to investigate the dye orientation and interactions within the various complexes. Bifunctional, thermostable PNA molecules are intriguing candidates for controlling the assembly and orientation of peptides within small DNA nanocages for mimicking protein catalytic sites.

Hybrid photocathodes for solar fuel production: coupling molecular fuel-production catalysts with solid-state light harvesting and conversion technologies

Artificial photosynthesis is described as the great scientific and moral challenge of our time. We imagine a future where a significant portion of our energy is supplied by such technologies. However, many scientific, engineering and policy challenges must be addressed for this realization. Scientific challenges include the development of effective strategies to couple light absorption, electron transfer and catalysis for efficient conversion of light energy to chemical energy as well as the construction and study of structurally diverse assemblies to carry out these processes. In this article, we review recent efforts from our own research to develop a modular approach to interfacing molecular fuel-production catalysts to visible-light-absorbing semiconductors and discuss the role of the interfacing material as a protection layer for the catalysts as well as the underpinning semiconductor. In concluding, we briefly discuss the potential benefits of a globally coordinated project on artificial photosynthesis that interfaces teams of scientists, engineers and policymakers. Further, we offer cautions that such a large interconnected organization should consider. This article is inspired by, and draws largely from, an invited presentation given by the corresponding author at the Royal Society at Chicheley Hall, home of the Kavli Royal Society International Centre, Buckinghamshire on the themed meeting topic: 'Do we need a global project on artificial photosynthesis?'

PNA as a Biosupramolecular Tag for Programmable Assemblies and Reactions

The programmability of oligonucleotide hybridization offers an attractive platform for the design of assemblies with emergent properties or functions. Developments in DNA nanotechnologies have transformed our thinking about the applications of nucleic acids. Progress from designed assemblies to functional outputs will continue to benefit from functionalities added to the nucleic acids that can participate in reactions or interactions beyond hybridization. In that respect, peptide nucleic acids (PNAs) are interesting because they combine the hybridization properties of DNA with the modularity of peptides. In fact, PNAs form more stable duplexes with DNA or RNA than the corresponding natural homoduplexes. The high stability achieved with shorter oligomers (an 8-mer is sufficient for a stable duplex at room temperature) typically results in very high sequence fidelity in the hybridization with negligible impact of the ionic strength of the buffer due to the lack of electrostatic repulsion between the duplex strands. The simple peptidic backbone of PNA has been shown to be tolerant of modifications with substitutions that further enhance the duplex stability while providing opportunities for functionalization. Moreover, the metabolic stability of PNAs facilitates their integration into systems that interface with biology. Over the past decade, there has been a growing interest in using PNAs as biosupramolecular tags to program assemblies and reactions. A series of robust templated reactions have been developed with functionalized PNA. These reactions can be used to translate DNA templates into functional polymers of unprecedented complexity, fluorescent outputs, or bioactive small molecules. Furthermore, cellular nucleic acids (mRNA or miRNA) have been harnessed to promote assemblies and reactions in live cells. The tolerance of PNA synthesis also lends itself to the encoding of small molecules that can be further assembled on the basis of their nucleic acid sequences. It is now well-established that hybridization-based assemblies displaying two or more ligands can interact synergistically with a target biomolecule. These assemblies have now been shown to be functional in vivo. Similarly, PNA-tagged macromolecules have been used to prepare bioactive assemblies and three-dimensional nanostructures. Several technologies based on DNA-templated synthesis of sequence-defined polymers or DNA-templated display of ligands have been shown to be compatible with reiterative cycles of selection/amplification starting with large libraries of DNA templates, bringing the power of in vitro evolution to synthetic molecules and offering the possibility of exploring uncharted molecular diversity space with unprecedented scope and speed.

Self assembled nanocages from DNA–protoporphyrin hybrid molecules

DNA–organic hybrid molecular building blocks are generated by covalent conjugation of the carboxyl groups of protoporphyrin IX with the amine functional groups of modified DNA oligomers.

Study of cytochrome c-DNA interaction--evaluation of binding sites on the redox protein

Artificial assemblies consisting of the cationic cytochrome c (cyt c) and double-stranded DNA are interesting for the field of biohybrid systems because of the high electro-activity of the incorporated redox protein. However, little is known about the interactions between these two biomolecules. Here, the complex of reduced cyt c and a 41 base pair oligonucleotide was characterized in solution as a function of pH and ionic strength. Persistent cyt c-DNA agglomerates were observed by UV-vis and DLS (dynamic light scattering) at pH 5.0 and low ionic strength. The strength of the interaction was attenuated by raising the pH or the ionic strength. At pH 7.0 agglomerates were not formed, allowing interaction analysis by NMR spectroscopy. Using TROSY (transverse relaxation-optimized spectroscopy)-HSQC (heteronuclear single quantum coherence) experiments it was possible to identify the DNA binding site on the cyt c surface. Numerous residues surrounding the exposed heme edge of cyt c were involved in transient binding to DNA under these conditions. This result was supported by SEC (size exclusion chromatography) experiments at pH 7.0 showing that the interaction is sufficient for co-elution of cyt c and DNA.