Designed DNA molecules: principles and applications of molecular nanotechnology

Control of DNA hybridization by photoswitchable molecular glue

Hybridization of DNA is one of the most intriguing events in molecular recognition and is essential for living matter to inherit life beyond generations. In addition to the function of DNA as genetic material, DNA hybridization is a key to control the function of DNA-based materials in nanoscience. Since the hybridization of two single stranded DNAs is a thermodynamically favorable process, dissociation of the once formed DNA duplex is normally unattainable under isothermal conditions. As the progress of DNA-based nanoscience, methodology to control the DNA hybridization process has become increasingly important. Besides many reports using the chemically modified DNA for the regulation of hybridization, we focused our attention on the use of a small ligand as the molecular glue for the DNA. In 2001, we reported the first designed molecule that strongly and specifically bound to the mismatched base pairs in double stranded DNA. Further studies on the mismatch binding molecules provided us a key discovery of a novel mode of the binding of a mismatch binding ligand that induced the base flipping. With these findings we proposed the concept of molecular glue for DNA for the unidirectional control of DNA hybridization and, eventually photoswitchable molecular glue for DNA, which enabled the bidirectional control of hybridization under photoirradiation. In this tutorial review, we describe in detail how we integrated the mismatch binding ligand into photoswitchable molecular glue for DNA, and the application and perspective in DNA-based nanoscience.

Tail-labelling of DNA probes using modified deoxynucleotide triphosphates and terminal deoxynucleotidyl transferase. Application in electrochemical DNA hybridization and protein-DNA binding assays

A simple approach to DNA tail-labelling using terminal deoxynucleotidyl transferase and modified deoxynucleoside triphosphates is presented. Amino- and nitrophenyl-modified dNTPs were found to be good substrates for this enzyme giving 3'-end stretches of different lengths depending on the nucleotide and concentration. 3-Nitrophenyl-7-deazaG was selected as the most useful label because its dNTP was efficiently incorporated by the transferase to form long tail-labels at any oligonucleotide. Accumulation of many nitrophenyl tags per oligonucleotide resulted in a considerable enhancement of voltammetric signals due to the nitro group reduction, thus improving the sensitivity of electrochemical detection of the tail-labelled probes. We demonstrate a perfect discrimination between complementary and non-complementary target DNAs sequences by tail-labelled hybridization probes as well as the ability of tumour suppressor p53 protein to recognize a specific binding site within tail-labelled DNA substrates, making the methodology useful in electrochemical DNA hybridization and DNA-protein interaction assays.

Cooperative melting in caged dimers with only two DNA duplexes

Small molecule-DNA hybrids with only two parallel DNA duplexes (rSMDH2) displayed sharper melting profiles compared to unmodified DNA duplexes, consistent with predictions from neighboring-duplex theory. Using adjusted thermodynamic parameters obtained from a coarse-grain dynamic simulation, the experimental data fit well to an analytical model.

Novel DNA materials and their applications

The last two decades have witnessed the exponential development of DNA as a generic material instead of just a genetic material. The biological function, nanoscale geometry, biocompatibility, biodegradability, and molecular recognition capacity of DNA make it a promising candidate for the construction of novel functional nanomaterials. As a result, DNA has been recognized as one of the most appealing and versatile nanomaterial building blocks. Scientists have used DNA in this way to construct various amazing nanostructures, such as ordered lattices, origami, supramolecular assemblies, and even three-dimensional objects. In addition, DNA has been utilized as a guide and template to direct the assembly of other nanomaterials including nanowires, free-standing membranes, and crystals. Furthermore, DNA can also be used as structural components to construct bulk materials such as DNA hydrogels, demonstrating its ability to behave as a unique polymer. Overall, these novel DNA materials have found applications in various areas in the biomedical field in general, and nanomedicine in particular. In this review, we summarize the development of DNA assemblies, describe the innovative progress of multifunctional and bulk DNA materials, and highlight some real-world nanomedical applications of these DNA materials. We also show our insights throughout this article for the future direction of DNA materials.

Polymerase-directed synthesis of C5-ethynyl locked nucleic acids

Modified nucleic acids have considerable potential in nanobiotechnology for the development of nanomedicines and new materials. Locked nucleic acid (LNA) is one of the most prominent nucleic acid analogues reported so far and we herein for the first time report the enzymatic incorporation of LNA-U and C5-ethynyl LNA-U nucleotides into oligonucleotides. Phusion High Fidelity and KOD DNA polymerases efficiently incorporated LNA-U and C5-ethynyl LNA-U nucleotides into a DNA strand and T7 RNA polymerase successfully accepted the LNA-U nucleoside 5'-triphosphate as substrate for RNA transcripts.

Theoretical description of a DNA-linked nanoparticle self-assembly

Nanoparticles tethered with DNA strands are promising building blocks for bottom-up nanotechnology, and a theoretical understanding is important for future development. Here we build on approaches developed in polymer physics to provide theoretical descriptions for the equilibrium clustering and dynamics, as well as the self-assembly kinetics of DNA-linked nanoparticles. Striking agreement is observed between the theory and molecular modeling of DNA-tethered nanoparticles.

CANADA: designing nucleic acid sequences for nanobiotechnology applications

The design of nucleic acid sequences for a highly specific and efficient hybridization is a crucial step in DNA computing and DNA-based nanotechnology applications. The CANADA package contains software tools for designing DNA sequences that meet these and other requirements, as well as for analyzing and handling sequences. CANADA is freely available, including a detailed manual and example input files, at http://ls11-www.cs.uni-dortmund.de/molcomp/downloads.

DNA-based nano-sized systems for pharmaceutical and biomedical applications

DNA is one of the most important components for all living organisms and many species, including humans, use DNA to store and transmit genetic information to new generations. Recent advances in the handling of DNA have made it possible to use DNA as a building block of nano-sized materials with precisely designed architectures. Although various approaches have been proposed to obtain DNA assemblies with designed architecture in the nano- to micrometer range, there is little information about their interaction with biological components, including target molecules. Understanding the interaction between DNA assemblies and the body is highly important for successful pharmaceutical and biomedical applications. Here, we first review the basic aspects of externally administered DNA molecules, including the stability, permeability and delivery issues. Then, we discuss the unique responses observed in the interaction of structured DNA assemblies and cells expressing Toll-like receptor-9, the receptor responsible for the recognition of unmethylated CpG dinucleotides that are abundant in the DNA of invading pathogens, such as bacteria and viruses.

Valency dependence of polymorphism and polyamorphism in DNA-functionalized nanoparticles

Nanoparticles (NP) functionalized with single-stranded DNA (ssDNA) offer a route to custom-designed, self-assembled nanomaterials with potentially unusual properties. The bonding selectivity of DNA guarantees one-to-one binding to form double-stranded DNA (dsDNA), and an appropriate base sequence results in head-to-tail binding linking NP into networks. We explore the phase behavior and structure of a model for NP functionalized with between 3 and 6 short ssDNA through simulations of a coarse-grained molecular model, allowing us to examine both the role of the number of attached strands (valency) and their relative orientations. The NP assemble into networks where the number of NP links is controlled by the number of attached strands. The large length scale of the DNA links relative to the core NP size opens the possibility for the formation of interpenetrating networks that give rise to multiple thermodynamically distinct states. We find that the 3-functionalized NP have only a single phase transition between a dilute solution of NPs and an assembled network state. 4-Functionalized NP (with tetrahedral symmetry) exhibit four amorphous phases, or polyamorphism, each higher density phase consisting of an additional interpenetrating network. The two investigated geometries of 5-functionalized NP both exhibit two phase transitions and three amorphous phases. Like the 4-functionalized NP, the highest density phase consists of interpenetrating networks, demonstrating that regular symmetry is not a prerequisite for interpenetration to produce thermodynamically distinct phases. The width of the coexistence regions for all phase transitions increases with increasing functionality. Finally, for 6-functionalized NP with octahedral symmetry, the possibility of observing disordered phases with significantly bonded particles is preempted by the formation of ordered crystal phases. Interestingly, the extreme softness of the potential combined with the directional interaction allows for the formation of (at least) six distinct crystalline structures (i.e., polymorphism) consisting of up to six interpenetrating simple cubic lattices.

Synthesis of nucleoside and nucleotide conjugates of bile acids, and polymerase construction of bile acid-functionalized DNA

Aqueous Sonogashira cross-coupling reactions of 5-iodopyrimidine or 7-iodo-7-deazaadenine nucleosides with bile acid-derived terminal acetylenes linked via an ester or amide tether gave the corresponding bile acid-nucleoside conjugates. Analogous reactions of halogenated nucleoside triphosphates gave directly bile acid-modified dNTPs. Enzymatic incorporation of these modified nucleotides to DNA was successfully performed using Phusion polymerase for primer extension. One of the dNTPs (dCTP bearing cholic acid) was also efficient for PCR amplification.

Cleavage of adenine-modified functionalized DNA by type II restriction endonucleases

A set of 6 base-modified 2'-deoxyadenosine derivatives was incorporated to diverse DNA sequences by primer extension using Vent (exo-) polymerase and the influence of the modification on cleavage by diverse restriction endonucleases was studied. While 8-substituted (Br or methyl) adenine derivatives were well tolerated by the restriction enzymes and the corresponding sequences were cleaved, the presence of 7-substituted 7-deazaadenine in the recognition sequence resulted in blocking of cleavage by some enzymes depending on the nature and size of the 7-substituent. All sequences with modifications outside of the recognition sequence were perfectly cleaved by all the restriction enzymes. The results are useful both for protection of some sequences from cleavage and for manipulation of functionalized DNA by restriction cleavage.

HYDROGELS FROM SOFT CONTACT LENSES AND IMPLANTS TO SELF-ASSEMBLED NANOMATERIALS

Hydrogels were the first biomaterials designed for clinical use. Their discovery and applications as soft contact lenses and implants are presented. This early hydrogel research served as a foundation for the expansion of biomedical polymers research into new directions: design of stimuli sensitive hydrogels that abruptly change their properties upon application of an external stimulus (pH, temperature, solvent, electrical field, biorecognition) and hydrogels as carriers for the delivery of drugs, peptides, and proteins. Finally, pathways to self-assembly of block and graft copolymers into hydrogels of precise 3D structures are introduced.

Photophysical characterization of oligopyrene modules for DNA-based nanosystems

The photophysics of free pyrenedicarboxamide (Py-DCA) in solution as well as of single-stranded and double-stranded oligonucleotides (ss and ds ONs) containing 1-7 pyrene building blocks per strand were studied by steady-state and time-resolved fluorescence spectroscopy. It was found that the fluorescence quantum yield Phi(F) of free Py-DCA chromophore in solution is rather high (Phi(F) = 0.44). However, after incorporation of the chromophore into a ss ON the monomeric chromophore fluorescence is quenched more than 40-fold due to electron-transfer reactions with ON bases. An increase of the number n of neighboring pyrenes in an ON results in Phi(F) growth up to 0.25 at n = 6. Starting from n = 2, all fluorescence belongs mainly to excimer formed by pyrene chromophores. Sections composed of multiple pyrenes may be considered as robust functional entities that may serve as independent modules in DNA-based, functional nano-architectures.

Retrieval efficiency of DNA-based databases of digital signals

Using DNA to store digital signals, or data in general, offers significant advantages when compared to other media. The DNA molecule, especially in its double-stranded form, is very stable, compact, and inexpensive. In the past, we have shown that DNA can be used to store and retrieve digital signals encoded and stored in DNA. We have also shown that DNA hybridization can be used as a similarity criterion for retrieving digital signals encoded and stored in a DNA database. Retrieval is achieved through hybridization of "query" and "data" DNA molecules. In this paper, we present a mathematical framework to simulate single-query and parallel-query scenarios, and to estimate hybridization efficiency. Our framework allows for exact numerical solutions as well as closed-form approximations under certain conditions. Similarly to the digital domain, we define a DNA SNR measure to assess the performance of the DNA-based retrieval scheme in terms of database size and source statistics. With approximations, we show that the SNR of any finite-sized DNA-based database is upper bounded by the SNR of an infinitely large DNA-based database that has the same source distribution. Computer simulations are presented to validate our results.

Applied chemistry of natural DNA

Recently, natural DNA has emerged as an appealing biomacromolecule for functional materials. It is abundant and renewable, and possesses the well known double helix structure that promises many unique properties difficult to find in other polymers. Natural DNA has been applied in electronic, optical and biomaterials, as a catalyst for enantioselective reactions, and as a material for cleaning the environment. Most of the applications are based on combining DNA with other chemicals or nanoparticles by electrostatic binding, intercalation or groove binding. In this critical review article, recent developments in utilizing natural DNA are reviewed by focusing on three basic properties of DNA: the electrostatic property as a polyelectrolyte, selective affinity for small molecules, and biocompatibility (128 references).

Novel strategies for the site-specific covalent labelling of nucleic acids

To broaden the scope of applications in DNA nano- and biotechnology, material science, diagnostics and molecular recognition the functionalization of DNA is of utmost importance. In the last decade many new methods have been developed to achieve this goal. Apart from the direct chemical synthesis of modified DNA by automated phosphoramidite chemistry incorporation of labelled triphosphates and the post-synthetic labelling approach evolved as valuable methods. New bioorthogonal reactions as Diels-Alder, click and Staudinger ligations pushed forward the post-synthetic approach as new insights into DNA polymerase substrate specificity allowed generation and amplification of labelled DNA strands. These novel developments are summarized herein.

Synthesis of 8-bromo-, 8-methyl- and 8-phenyl-dATP and their polymerase incorporation into DNA

dATP derivatives bearing Br, Me or Ph groups in position 8 were prepared and tested as substrates for DNA polymerases to show that 8-Br-dATP and 8-Me-dATP were efficiently incorporated, while 8-Ph-dATP was a poor substrate due to its bulky Ph group.

Hierarchies of networked phases induced by multiple liquid-liquid critical points

Nanoparticles and colloids functionalized by four single strands of DNA can be thought of as designed analogs to tetrahedral network-forming atoms and molecules, with a difference that the attached DNA strands allow for control of the length scale of bonding relative to the core size. We explore the behavior of an experimentally realized model for nanoparticles functionalized by four single strands of DNA (a tetramer), and show that this single-component model exhibits a rich phase diagram with at least three critical points and four thermodynamically distinct amorphous phases. We demonstrate that the additional critical points are part of the Ising universality class, like the ordinary liquid-gas critical point. The dense phases consist of a hierarchy of interpenetrating networks, reminiscent of a woven cloth. Thus, bonding specificity of DNA provides an effective route to generate new nano-networked materials with polyamorphic behavior. The concept of network interpenetration helps to explain the generation of multiple liquid phases in single-component systems, suggested to occur in some atomic and molecular network-forming fluids, including water and silica.

Cross-coupling reactions of nucleoside triphosphates followed by polymerase incorporation. Construction and applications of base-functionalized nucleic acids

Construction of functionalized nucleic acids (DNA or RNA) via polymerase incorporation of modified nucleoside triphosphates is reviewed and selected applications of the modified nucleic acids are highlighted. The classical multistep approach for the synthesis of modified NTPs by triphosphorylation of modified nucleosides is compared to the novel approach consisting of direct aqueous cross-coupling reactions of unprotected halogenated nucleoside triphosphates. The combination of cross-coupling of NTPs with polymerase incorporation gives an efficient and straightforward two-step synthesis of modified nucleic acids. Primer extension using biotinylated templates followed by separation using streptavidine-coated magnetic beads and DNA duplex denaturation is used for preparation of modified single stranded oligonucleotides. Examples of using this approach for electrochemical DNA labelling and bioanalytical applications are given.

Electrical protein detection in cell lysates using high-density peptide-aptamer microarrays

BACKGROUND

The dissection of biological pathways and of the molecular basis of disease requires devices to analyze simultaneously a staggering number of protein isoforms in a given cell under given conditions. Such devices face significant challenges, including the identification of probe molecules specific for each protein isoform, protein immobilization techniques with micrometer or submicrometer resolution, and the development of a sensing mechanism capable of very high-density, highly multiplexed detection.

RESULTS

We present a novel strategy that offers practical solutions to these challenges, featuring peptide aptamers as artificial protein detectors arrayed on gold electrodes with feature sizes one order of magnitude smaller than existing formats. We describe a method to immobilize specific peptide aptamers on individual electrodes at the micrometer scale, together with a robust and label-free electronic sensing system. As a proving proof of principle experiment, we demonstrate the specific recognition of cyclin-dependent protein kinases in whole-cell lysates using arrays of ten electrodes functionalized with individual peptide aptamers, with no measurable cross-talk between electrodes. The sensitivity is within the clinically relevant range and can detect proteins against the high, whole-cell lysate background.

CONCLUSION

The use of peptide aptamers selected in vivo to recognize specific protein isoforms, the ability to functionalize each microelectrode individually, the electronic nature and scalability of the label-free detection and the scalability of the array fabrication combine to yield the potential for highly multiplexed devices with increasingly small detection areas and higher sensitivities that may ultimately allow the simultaneous monitoring of tens or hundreds of thousands of protein isoforms.

Synthesis of highly modified DNA by a combination of PCR with alkyne-bearing triphosphates and click chemistry

We report the combination of "click chemistry" with PCR by using alkyne-modified triphosphates for efficient and homogeneous labeling of DNA. A series of modified PCR products of different lengths (300, 900, and 2000 base pairs) were prepared by using a variety of alkyne- and azide-containing triphosphates and different polymerases. After intensive screening of real-time PCR methods, protocols were developed that allow the amplification of genes by using these modified triphosphates with similar efficiency to that of standard PCR. The click reaction on the highly modified PCR fragments provided conversion rates above 90 % and resulted in the functionalization of hundreds of alkynes on large DNA fragments with superb selectivity and efficiency.

Enhanced immunostimulatory activity of oligodeoxynucleotides by Y-shape formation

DNA containing unmethylated CpG dinucleotides (CpG DNA) is a potent activator of innate and acquired immune responses. Although the sequence-specific immunostimulatory activity of CpG DNA has been extensively explored, little information is available about the importance of the stereochemical properties of CpG DNA. In this study, Y-shaped oligodeoxynucleotides (Y-ODNs) were prepared using three ODNs with the halves of each ODN being partially complementary to a half of the other two ODNs. Y-ODN induced greater amounts of tumour necrosis factor-alpha and interleukin-6 from RAW264.7 macrophage-like cells than did conventional single-stranded ODN (ssODN) or double-stranded ODN (dsODN). The Y-ODN was less stable in serum than dsODN, but greater amounts of Y-ODN were taken up by macrophage-like cells compared with dsODN. A newly designed Y-ODN containing three potent CpG motifs generated significantly higher levels of cytokines compared with dsODN containing the identical sequences. These results indicate that the Y-shaped form of ODN is a novel, reproducible and reliable approach to enhancing the immunostimulatory activity of ODNs.

Synthesis of modified DNA by PCR with alkyne-bearing purines followed by a click reaction

Alkyne-bearing deazapurine triphosphates were prepared and successfully incorporated into DNA using the polymerase chain reaction (PCR). The obtained alkyne-labeled DNA was successfully used in a click reaction with galactose azide.

Towards biomedical applications for nucleic acid nanodevices

DNA and RNA can be used to construct artificial nanodevices with strong potential for future biomedical applications. DNA nanodevices can function as biosensors, which detect and report the presence of proteins and naturally occurring nucleic acids, such as mRNA or microRNAs. Complex sensors can be realized by supporting DNA devices with DNA-based information processing. Artificial DNA-based reaction networks can be created that amplify molecular signals or evaluate logical functions to report the simultaneous presence of several disease-related molecules. Other applications for DNA nanodevices are found in controlled release and drug delivery. DNA can be used to build nanocontainers for drugs or switchable hydrogels, which can trap and release compounds. For in vivo applications of DNA nanodevices, techniques for efficient packaging and delivery have been developed and the first examples of intracellular RNA-based nanodevices have already been demonstrated.

Hydrogel biomaterials: a smart future?

Hydrogels were the first biomaterials developed for human use. The state-of-the-art and potential for the future are discussed. Recently, new designs have produced mechanically strong synthetic hydrogels. Protein-based hydrogels and hybrid hydrogels containing protein domains present a novel advance; such biomaterials may self-assemble from block or graft copolymers containing biorecognition domains. One of the domains, the coiled coil, ubiquitously found in nature, has been used as an example to demonstrate the developments in the design of smart hydrogels. The application potential of synthetic, protein based, DNA based, and hybrid hydrogels bodes well for the future of this class of biomaterials.

Self-assembling layers created by membrane proteins on gold

Membrane systems are based on several types of organization. First, amphiphilic lipids are able to create monolayer and bilayer structures which may be flat, vesicular or micellar. Into these structures membrane proteins can be inserted which use the membrane to provide signals for lateral and orientational organization. Furthermore, the proteins are the product of highly specific self-assembly otherwise known as folding, which mostly places individual atoms at precise places in three dimensions. These structures all have dimensions in the nanoscale, except for the size of membrane planes which may extend for millimetres in large liposomes or centimetres on planar surfaces such as monolayers at the air/water interface. Membrane systems can be assembled on to surfaces to create supported bilayers and these have uses in biosensors and in electrical measurements using modified ion channels. The supported systems also allow for measurements using spectroscopy, surface plasmon resonance and atomic force microscopy. By combining the roles of lipids and proteins, highly ordered and specific structures can be self-assembled in aqueous solution at the nanoscale.

Self-assembling DNA dendrimers: a numerical study

DNA is increasingly used as a specific linker to template nanostructured materials. We present a molecular dynamics simulation study of a simple DNA-dendrimer model designed to capture the basic characteristics of the biological interactions, where selectivity and strong cooperativity play an important role. Exploring a large set of densities and temperatures, we follow the progressive formation of a percolating large-scale network whose connectivity can be described by random percolation theory. We identify the relative regions of network formation and kinetic arrest versus phase separation and show that the location of the two-phase region can be interpreted in the same framework as reduced valency models. This correspondence provides guidelines for designing stable, equilibrium self-assembled low-density networks. Finally, we demonstrate a relation between bonding and dynamics, by showing that the temperature dependence of the diffusion constant is controlled by the number of fully unbonded dendrimers.

Dynamic force microscopy imaging of plasmid DNA and viral RNA

Plasmid DNA and viral RNA were imaged in a liquid environment by dynamic force microscopy (DFM) and fine structures of DNA with heights of 1.82+/-0.66 nm were obtained in topographical images. In simultaneously acquired phase images, DNA could be imaged with better contrast at lower imaging forces. By splitting the cantilever oscillation signal into lower and upper parts, the contribution of the adhesion between tip and sample to the topographical images was eliminated, resulting in better signal-to-noise ratio. DFM of the single stranded RNA genome of a human rhinovirus showed loops protruding from a condensed RNA core, 20-50 nm in height. The mechanical rigidity of the RNA was determined by single molecule pulling experiments. From fitting RNA stretching curves to the Worm-Like-Chain (WLC) model a persistence length of 1.0+/-0.17 nm was obtained.

DNA meets synthetic polymers--highly versatile hybrid materials

The combination of synthetic polymers and DNA has provided biologists, chemists and materials scientists with a fascinating new hybrid material. The challenges in preparing these molecular chimeras were overcome by different synthetic strategies that rely on coupling the nucleic acid moiety and the organic polymer in solution or on solid supports. The morphologies and functions of the bioorganic block copolymers can be controlled by the nature of the synthetic polymer segment as well as by the sequence composition and length of the DNA. Recent developments have expanded the scope and applications of these hybrid materials in a number of different areas including biology and medicine, as well as bio- and nanotechnology. Their usage ranges from gene delivery through to DNA detection to programmable nano-containers for DNA-templated organic reactions.

Identification of tunnels in proteins, nucleic acids, inorganic materials and molecular ensembles

The knowledge of the access paths connecting interior of molecular systems with surrounding environment is important for the understanding of structurefunction relationships and engineering of molecules for biotechnological applications. CAVER is a computer program developed for calculations of tunnels, channels or pores in the biomolecules, inorganic materials and molecular ensembles. The algorithm performs a skeleton search based on a reciprocal distance function grid. The algorithm is implemented in the stand-alone version, web version and as plug-in for PyMol. CAVER is available from the website http://loschmidt.chemi.muni.cz/caver.