A DNA pentaplex incorporating nucleobase quintets

Special Issue "Bioinformatics of Unusual DNA and RNA Structures"

Nucleic acids are not only static carriers of genetic information but also play vital roles in controlling cellular lifecycles through their fascinating structural diversity [...].

Guidelines for G-quadruplexes: I. In vitro characterization

Besides the well-known DNA double-helix, non-canonical nucleic acid structures regulate crucial biological activities. Among these oddities, guanine-rich DNA sequences can form unusual four-stranded secondary structures called G-quadruplexes (G4s). G4-prone sequences have been found in the genomes of most species, and G4s play important roles in essential processes such as transcription, replication, genome integrity and epigenetic regulation. Here, we present a short overview of G-quadruplexes followed by a detailed description of the biophysical and biochemical methods used to characterize G4s in vitro. The principles, experimental details and possible shortcomings of each method are discussed to provide a comprehensive view of the techniques used to study these structures. We aim to provide a set of guidelines for standardizing research on G-quadruplexes; these guidelines are not meant to be a dogmatic set of rules, but should rather provide useful information on the methods currently used to study these fascinating motifs.

Rethinking nucleic acids from their origins to their applications

Reviewed are three decades of synthetic biology research in our laboratory that has generated alternatives to standard DNA and RNA as possible informational systems to support Darwinian evolution, and therefore life, and to understand their natural history, on Earth and throughout the cosmos. From this, we have learned that: • the core structure of nucleic acids appears to be a natural outcome of non-biological chemical processes probably in constrained, intermittently irrigated, sub-aerial aquifers on the surfaces of rocky planets like Earth and/or Mars approximately 4.36 ± 0.05 billion years ago; • however, this core is not unique. Synthetic biology has generated many different molecular systems able to support the evolution of molecular information; • these alternatives to standard DNA and RNA support biotechnology, including DNA synthesis, human diagnostics, biomedical research and medicine; • in particular, they support laboratory in vitro evolution (LIVE) with performance to generate catalysts at least 104-105 fold better than standard DNA libraries, enhancing access to receptors and catalysts on demand. Coupling nanostructures to the products of LIVE with expanded DNA offers new approaches for disease therapy; and • nevertheless, a polyelectrolyte structure and size regular building blocks are required for any informational polymer to support Darwinian evolution. These features serve as universal and agnostic biosignatures, useful for seeking life throughout the Solar System. This article is part of the theme issue 'Reactivity and mechanism in chemical and synthetic biology'.

Ion-mediated control of structural integrity and reconfigurability of DNA nanostructures

Nucleic acid-based biomolecular self-assembly enables the creation of versatile functional architectures. Electrostatic screening of the negative charges of nucleic acids is essential for their folding and stability; thus, ions play a critical role in nucleic acid self-assembly in both biology and nanotechnology. However, the ion-DNA interplay and the resulting ion-specific structural integrity and responsiveness of DNA constructs are underexploited. Here, we harness a wide range of mono- and divalent ions to control the structural features of DNA origami constructs. Using atomic force microscopy and Förster resonance energy transfer (FRET) spectroscopy down to the single-molecule level, we report on the global and local structural performance and responsiveness of DNA origami constructs following self-assembly, upon post-assembly ion exchange and post-assembly ion-mediated reconfiguration. We determined the conditions for highly efficient DNA origami folding in the presence of several mono- (Li⁺, Na⁺, K⁺, Cs⁺) and divalent (Ca²⁺, Sr²⁺, Ba²⁺) ions, expanding the range where DNA origami structures can be exploited for custom-specific applications. We then manipulated fully folded constructs by exposing them to unfavorable ionic conditions that led to the emergence of substantial disintegrity but not to unfolding. Moreover, we found that poorly assembled nanostructures at low ion concentrations undergo substantial self-repair upon ion addition in the absence of free staple strands. This reconfigurability occurs in an ion type- and concentration-specific manner. Our findings provide a fundamental understanding of the ion-mediated structural responsiveness of DNA origami at the nanoscale enabling applications under a wide range of ionic conditions.

Isoguanine (2-Hydroxyadenine) and 2-Aminoadenine Nucleosides with an 8-Aza-7-deazapurine Skeleton: Synthesis, Functionalization with Fluorescent and Clickable Side Chains, and Impact of 7-Substituents on Physical Properties

7-Functionalized 8-aza-7-deaza-2'-deoxyisoguanine and 8-aza-7-deaza-2-aminoadenine 2'-deoxyribonucleosides decorated with fluorescent pyrene or benzofuran sensor tags or clickable side chains with terminal triple bonds were synthesized. 8-Aza-7-deaza-7-iodo-2-amino-2'-deoxyadenosine was used as the central intermediate and was accessible by an improved two-step glycosylation/amination protocol. Functionalization of position-7 was performed either on 8-aza-7-deaza-7-iodo-2-amino-2'-deoxyadenosine followed by selective deamination of the 2-amino group or on 7-iodinated 8-aza-7-deaza-2'-deoxyisoguanosine. Sonogashira and Suzuki-Miyaura cross-coupling reactions were employed for this purpose. Octadiynyl side chains were selected as linkers for click reactions with azido pyrenes. K_Taut values calculated from H₂O/dioxane mixtures revealed that side chains have a significant influence on the tautomeric equilibrium. Photophysical properties (fluorescence, solvatochromism, and quantum yields) of the new 8-aza-7-deazapurine nucleosides with fluorescent side chains were determined. Remarkably, a strong excimer fluorescence in H₂O was observed for pyrene dye conjugates of 8-aza-7-deazaisoguanine and 2-aminoadenine nucleosides with a long linker. In other solvents including methanol, excimer fluorescence was negligible. The 2-aminoadenine and isoguanine nucleosides with the 8-aza-7-deazapurine skeleton expand the class of nucleosides applicable to fluorescence detection with respect to diagnostic and therapeutic purposes.

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.

Engineering polymerases for applications in synthetic biology

DNA polymerases play a central role in biology by transferring genetic information from one generation to the next during cell division. Harnessing the power of these enzymes in the laboratory has fueled an increase in biomedical applications that involve the synthesis, amplification, and sequencing of DNA. However, the high substrate specificity exhibited by most naturally occurring DNA polymerases often precludes their use in practical applications that require modified substrates. Moving beyond natural genetic polymers requires sophisticated enzyme-engineering technologies that can be used to direct the evolution of engineered polymerases that function with tailor-made activities. Such efforts are expected to uniquely drive emerging applications in synthetic biology by enabling the synthesis, replication, and evolution of synthetic genetic polymers with new physicochemical properties.

The development of isoguanosine: from discovery, synthesis, and modification to supramolecular structures and potential applications

First systematical review of isoguanosine, an unnatural base, as an isomer of guanosine shows significant differences in diverse properties.

DNA Quadruple Helices in Nanotechnology

DNA has played an early and powerful role in the development of bottom-up nanotechnologies, not least because of DNA's precise, predictable, and controllable properties of assembly on the nanometer scale. Watson-Crick complementarity has been used to build complex 2D and 3D architectures and design a number of nanometer-scale systems for molecular computing, transport, motors, and biosensing applications. Most of such devices are built with classical B-DNA helices and involve classical A-T/U and G-C base pairs. However, in addition to the above components underlying the iconic double helix, a number of alternative pairing schemes of nucleobases are known. This review focuses on two of these noncanonical classes of DNA helices: G-quadruplexes and the i-motif. The unique properties of these two classes of DNA helix have been utilized toward some remarkable constructions and applications: G-wires; nanostructures such as DNA origami; reconfigurable structures and nanodevices; the formation and utilization of hemin-utilizing DNAzymes, capable of generating varied outputs from biosensing nanostructures; composite nanostructures made up of DNA as well as inorganic materials; and the construction of nanocarriers that show promise for the therapeutics of diseases.

Guidelines for the assembly of hydrogen-bonded macrocycles

This article highlights selected examples on the synthesis of hydrogen-bonded macrocycles from ditopic molecules and analyze the main factors, often interrelated, that influence the equilibrium between ring and chain species.

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.

In What Ways Do Synthetic Nucleotides and Natural Base Lesions Alter the Structural Stability of G-Quadruplex Nucleic Acids?

Synthetic analogs of natural nucleotides have long been utilized for structural studies of canonical and noncanonical nucleic acids, including the extensively investigated polymorphic G-quadruplexes (GQs). Dependence on the sequence and nucleotide modifications of the folding landscape of GQs has been reviewed by several recent studies. Here, an overview is compiled on the thermodynamic stability of the modified GQ folds and on how the stereochemical preferences of more than 70 synthetic and natural derivatives of nucleotides substituting for natural ones determine the stability as well as the conformation. Groups of nucleotide analogs only stabilize or only destabilize the GQ, while the majority of analogs alter the GQ stability in both ways. This depends on the preferred syn or anti N-glycosidic linkage of the modified building blocks, the position of substitution, and the folding architecture of the native GQ. Natural base lesions and epigenetic modifications of GQs explored so far also stabilize or destabilize the GQ assemblies. Learning the effect of synthetic nucleotide analogs on the stability of GQs can assist in engineering a required stable GQ topology, and exploring the in vitro action of the single and clustered natural base damage on GQ architectures may provide indications for the cellular events.

Synthesis of 8-Substituted 2'-Deoxyisoguanosines via Unprotected 8-Brominated 2-Amino-2'-deoxyadenosine

A variety of applications of 8-alkynylated nucleosides has prompted the synthesis of new purine analogues. Bromination of unprotected 2-amino-2'-deoxyadenosine with Br₂ /AcOH/AcONa gives 2-amino-8-bromo-2'-deoxyadenosine (87%). The brominated derivative is converted to 8-alkynylated 2-amino-2'-deoxyadenosines by palladium-catalyzed Sonogashira cross-coupling reaction via microwave assistance (81 - 95%). The resulting compounds are further transformed to 8-alkynylated 2'-deoxyisoguanosines (52 - 70%). The physical properties of new compounds are investigated.

8-Aza-2'-deoxyisoguanosine Forms Fluorescent Hydrogels whereas 8-Aza-2'-deoxyguanosine Assembles into Nucleoside Nanotubes

Fluorescent hydrogels have attracted attention for applications in tissue engineering, drug delivery or as molecular machines. This study describes a nucleoside hydrogel formed by 8-aza-2'-deoxyisoguanosine (z⁸ isoG_d ). The new hydrogel is the first guanosine gel that has intrinsic fluorescence. It has long-term stability and a higher thermal stability (T_gel =77 °C) than gels of 2'-deoxyisoguanosine (T_gel =67 °C) and 2'-deoxyguanosine (T_gel =50 °C). Furthermore, the minimum gel concentration is lower at 0.3 mg per 100 μL for z⁸ isoG_d compared to 0.7 mg for 2'-deoxyisoguanosine. Scanning electron microscopy images show that the z⁸ isoG_d gel forms dense bundles of fibers. The related nucleoside 8-aza-2'-deoxyguanosine does not form a hydrogel but forms nanotube-like structures in the solid state. The fluorescence of the z⁸ isoG_d hydrogel responds to external stimuli such as the addition of alkali metal ions, pH change, heat, and UV irradiation. In binary mixtures with nucleoside shape mimics such as 7-deaza-2'-deoxyisoguanosine, the z⁸ isoG_d hydrogel disintegrates.

A parallel stranded G-quadruplex composed of threose nucleic acid (TNA)

G-rich sequences can adopt four-stranded helical structures, called G-quadruplexes, that self-assemble around monovalent cations like sodium (Na⁺ ) and potassium (K⁺ ). Whether similar structures can be formed from xeno-nucleic acid (XNA) polymers with a shorter backbone repeat unit is an unanswered question with significant implications on the fold space of functional XNA polymers. Here, we examine the potential for TNA (α-l-threofuranosyl nucleic acid) to adopt a four-stranded helical structure based on a planar G-quartet motif. Using native polyacrylamide gel electrophoresis (PAGE), circular dichroism (CD) and solution-state nuclear magnetic resonance (NMR) spectroscopy, we show that despite a backbone repeat unit that is one atom shorter than the backbone repeat unit found in DNA and RNA, TNA can self-assemble into stable G-quadruplex structures that are similar in thermal stability to equivalent DNA structures. However, unlike DNA, TNA does not appear to discriminate between Na⁺ and K⁺ ions, as G-quadruplex structures form equally well in the presence of either ion. Together, these findings demonstrate that despite a shorter backbone repeat unit, TNA is capable of self-assembling into stable G-quadruplex structures.

Reprogramming the assembly of unmodified DNA with a small molecule

The ability of DNA to store and encode information arises from base pairing of the four-letter nucleobase code to form a double helix. Expanding this DNA 'alphabet' by synthetic incorporation of new bases can introduce new functionalities and enable the formation of novel nucleic acid structures. However, reprogramming the self-assembly of existing nucleobases presents an alternative route to expand the structural space and functionality of nucleic acids. Here we report the discovery that a small molecule, cyanuric acid, with three thymine-like faces, reprogrammes the assembly of unmodified poly(adenine) (poly(A)) into stable, long and abundant fibres with a unique internal structure. Poly(A) DNA, RNA and peptide nucleic acid (PNA) all form these assemblies. Our studies are consistent with the association of adenine and cyanuric acid units into a hexameric rosette, which brings together poly(A) triplexes with a subsequent cooperative polymerization. Fundamentally, this study shows that small hydrogen-bonding molecules can be used to induce the assembly of nucleic acids in water, which leads to new structures from inexpensive and readily available materials.

Molecular and supramolecular chemistry of rosette nanotubes

Synthetic strategies used to tune the properties of a class of supramolecular 1D nanostructures, the rosette nanotubes, are reviewed herein.

The structural diversity of artificial genetic polymers

Synthetic genetics is a subdiscipline of synthetic biology that aims to develop artificial genetic polymers (also referred to as xeno-nucleic acids or XNAs) that can replicate in vitro and eventually in model cellular organisms. This field of science combines organic chemistry with polymerase engineering to create alternative forms of DNA that can store genetic information and evolve in response to external stimuli. Practitioners of synthetic genetics postulate that XNA could be used to safeguard synthetic biology organisms by storing genetic information in orthogonal chromosomes. XNA polymers are also under active investigation as a source of nuclease resistant affinity reagents (aptamers) and catalysts (xenozymes) with practical applications in disease diagnosis and treatment. In this review, we provide a structural perspective on known antiparallel duplex structures in which at least one strand of the Watson-Crick duplex is composed entirely of XNA. Currently, only a handful of XNA structures have been archived in the Protein Data Bank as compared to the more than 100 000 structures that are now available. Given the growing interest in xenobiology projects, we chose to compare the structural features of XNA polymers and discuss their potential to access new regions of nucleic acid fold space.

Heme activation by DNA: isoguanine pentaplexes, but not quadruplexes, bind heme and enhance its oxidative activity

Guanine-rich, single-stranded, DNAs and RNAs are able to fold to form G-quadruplexes that are held together by guanine base quartets. G-quadruplexes are known to bind ferric heme [Fe(III)-protoporphyrin IX] and to strongly activate such bound hemes toward peroxidase (1-electron oxidation) as well as oxygenase/peroxygenase (2-electron oxidation) activities. However, much remains unknown about how such activation is effected. Herein, we investigated whether G-quadruplexes were strictly required for heme activation or whether related multi-stranded DNA/RNA structures such as isoguanine (iG) quadruplexes and pentaplexes could also bind and activate heme. We found that iG-pentaplexes did indeed bind and activate heme comparably to G-quadruplexes; however, iG-quadruplexes did neither. Earlier structural and computational studies had suggested that while the geometry of backbone-unconstrained iG-quintets templated by cations such as Na(+) or NH4 (+) was planar, that of iG-quartets deviated from planarity. We hypothesize that the binding as well as activation of heme by DNA or RNA is strongly supported by the planarity of the nucleobase quartet or quintet that interacts directly with the heme.

18-crown-6-sodium cholate complex: thermochemistry, structure, and stability

18-Crown-6, one of the most relevant crown ethers, and sodium cholate, a steroidal surfactant classified as a natural bile salt, are components of a novel, synthesized coordination complex: 18-crown-6-sodium cholate (18C6·NaCh). Like crown ethers, bile salts act as building blocks in supramolecular chemistry to design new functionalized materials with a desired structure and properties. In order to obtain thermal behavior of this 1:1 coordination complex, thermogravimetry and differential thermal analysis were used, as well as microscopic observations and differential scanning calorimetry. Temperature dependent infrared (IR) spectroscopy gave a detailed view into phase transitions. The structures during thermal treatment were observed with powder X-ray diffraction, and molecular models of the phases were made. Hard, glassy, colorless compound 18C6·NaCh goes through crystalline-crystalline polymorphic phase transitions at higher temperatures. The room temperature phase is indexed to a triclinic lattice, while in the high temperature phases molecules take randomly one of the two different configurations in the unit cell, resulting in the 2-fold symmetry. The formation of cholesteric liquid crystalline phase occurs simultaneously with partial decomposition, followed by the isotropization with simultaneous and complete decomposition at much higher temperature, as obtained by IR. The results provide valuable information about the relationship between molecular structure, thermal properties, and stability of the complex, indicating the importance of an appropriate choice of cation, amphiphilic, and crown ether unit in order to synthesize compounds with desired behavior.

Temperature-dependent IR spectroscopic and structural study of 18-crown-6 chelating ligand in the complexation with sodium surfactant salts and potassium picrate

18-crown-6 ether (18C6) complexes with the following anionic surfactants: sodium n-dodecylsulfate (18C6-NaDS), sodium 4-(1-pentylheptyl)benzenesulfonate (18C6-NaDBS); and potassium picrate (18C6-KP) were synthesized and studied in terms of their thermal and structural properties. Physico-chemical properties of new solid 1:1 coordination complexes were characterized by infrared (IR) spectroscopy, thermogravimetry and differential thermal analysis, differential scanning calorimetry, X-ray diffraction and microscopic observations. The strength of coordination between Na(+) and oxygen atoms of 18C6 ligand does not depend on anionic part of the surfactant, as established by thermodynamical parameters obtained by temperature-dependent IR spectroscopy. Each of these complexes exhibit different kinds of endothermic transitions in heating scan. Diffraction maxima obtained by SAXS and WAXS, refer the behavior of the compounds 18C6-NaDS and 18C6-NaDBS as smectic liquid crystalline. Distortion of 18C6-NaDS and 18C6-KP complexes occurs in two steps. Temperature of the decomplexation of solid crystal complex 18C6-KP is considerably higher than of mesophase complexes, 18C6-NaDS, and 18C6-NaDBS. The structural and liquid crystalline properties of novel 18-crown-ether complexes are function of anionic molecule geometry, type of chosen cation (Na(+), K(+)), as well as architecture of self-organized aggregates. A good combination of crown ether unit and amphiphile may provide a possibility for preparing new functionalized materials, opening the research field of ion complexation and of host-guest type behavior.

Guanosine and isoguanosine derivatives for supramolecular devices

Guanosine (G) and isoguanosine (isoG) derivatives can self-assemble, yielding supramolecules that have found broad applications in diverse fields.

Photonic DNA-chromophore nanowire networks: harnessing multiple supramolecular assembly modes

Photonic DNA nanostructures are typically prepared by the assembly of multiple sequences of long DNA strands that are conjugated covalently to various dye molecules. Herein we introduce a noncovalent method for the construction of porphyrin-containing DNA nanowires and their networks that uses the programmed assembly of a single, very short, oligodeoxyribonucleotide sequence. Specifically, our strategy exploits a number of supramolecular binding modalities (including DNA base-pairing, metal-ion coordination, and β-cyclodextrin-adamantane derived host-guest interactions) for simultaneous nanowire assembly and porphyrin incorporation. Furthermore, we also show that the resultant DNA-porphyrin assembly can be further functionalized with a complementary "off-the-shelf" DNA binding dye resulting in photonic structures with broadband absorption and energy transfer capabilities.

Mechanism of the deamination reaction of isoguanine: a theoretical investigation

Mechanisms of the deamination reactions of isoguanine with H2O, OH(-), and OH(-)/H2O and of protonated isoguanine (isoGH(+)) with H2O have been investigated by theoretical calculations. Eight pathways, paths A-H, have been explored and the thermodynamic properties (ΔE, ΔH, and ΔG), activation energies, enthalpies, and Gibbs energies of activation were calculated for each reaction investigated. Compared with the deamination reaction of isoguanine or protonated isoguanine (isoGH(+)) with water, the deamination reaction of isoguanine with OH(-) shows a lower Gibbs energy of activation at the rate-determining step, indicating that the deamination reaction of isoguanine is favorably to take place for the deprotonated form isoG(-) with water. With the assistance of an extra water, the reaction of isoguanine with OH(-)/H2O, pathways F and H, are found to be the most feasible pathways in aqueous solution due to their lowest Gibbs energy of activation of 174.7 and 172.6 kJ mol(-1), respectively, at the B3LYP/6-311++G(d,p) level of theory.

Oligonucleotide-Based Systems for Input-Controlled and Non-Covalently Regulated Protein-Binding

Supramolecular chemists continuously take inspiration from complex biological systems to develop functional molecules involved in molecular recognition and self-assembly. In this regard, "smart" synthetic molecules that emulate allosteric proteins are both exciting and challenging, since many allosteric proteins can be considered as molecular switches that bind to other protein targets in a non-covalent fashion, and importantly, are capable of having their output activity controlled by prior binding to input molecules. This review discusses the foundations and passage toward the development of non-covalently operated oligonucleotide-based systems with protein-binding capacity that can be precisely regulated in an input-controlled manner.

The emerging world of synthetic genetics

For over 20 years, laboratories around the world have been applying the principles of Darwinian evolution to isolate DNA and RNA molecules with specific ligand-binding or catalytic activities. This area of synthetic biology, commonly referred to as in vitro genetics, is made possible by the availability of natural polymerases that can replicate genetic information in the laboratory. Moving beyond natural nucleic acids requires organic chemistry to synthesize unnatural analogues and polymerase engineering to create enzymes that recognize artificial substrates. Progress in both of these areas has led to the emerging field of synthetic genetics, which explores the structural and functional properties of synthetic genetic polymers by in vitro evolution. This review examines recent advances in the Darwinian evolution of artificial genetic polymers and their potential downstream applications in exobiology, molecular medicine, and synthetic biology.

G-quadruplexes incorporating modified constituents: a review

This review summarizes the results of structural studies carried out with analogs of G-quadruplexes built from natural nucleotides. Several dozens of base-, sugar-, and phosphate derivatives of the biological building blocks have been incorporated into more than 50 potentially quadruplex forming DNA and RNA oligonucleotides and the stability and folding topology of the resultant intramolecular, bimolecular and tetramolecular architectures characterized. The TG4T, TG5T, the 15 nucleotide-long thrombin binding aptamer, and the human telomere repeat AG3(TTAG3)3 sequences were modified in most cases, and four guanine analogs can be noted as being particularly useful in structural studies. These are the fluorescent 2-aminopurine, the 8-bromo-, and 8-methylguanines, and the hypoxanthine. The latter three analogs stabilize a given fold in a mixture of structures making possible accurate structural determinations by circular dichroism and nuclear magnetic resonance measurements.

Nucleic acid-based nanoengineering: novel structures for biomedical applications

Nanoengineering exploits the interactions of materials at the nanometre scale to create functional nanostructures. It relies on the precise organization of nanomaterials to achieve unique functionality. There are no interactions more elegant than those governing nucleic acids via Watson-Crick base-pairing rules. The infinite combinations of DNA/RNA base pairs and their remarkable molecular recognition capability can give rise to interesting nanostructures that are only limited by our imagination. Over the past years, creative assembly of nucleic acids has fashioned a plethora of two-dimensional and three-dimensional nanostructures with precisely controlled size, shape and spatial functionalization. These nanostructures have been precisely patterned with molecules, proteins and gold nanoparticles for the observation of chemical reactions at the single molecule level, activation of enzymatic cascade and novel modality of photonic detection, respectively. Recently, they have also been engineered to encapsulate and release bioactive agents in a stimulus-responsive manner for therapeutic applications. The future of nucleic acid-based nanoengineering is bright and exciting. In this review, we will discuss the strategies to control the assembly of nucleic acids and highlight the recent efforts to build functional nucleic acid nanodevices for nanomedicine.

Thymine quintets and their higher order assemblies studied by electrospray ionization mass spectrometry and theoretical calculation

We previously reported that thymine molecules can specifically form a pentameric magic number cluster named as thymine quintet in the presence of K(+) , Rb(+) and Cs(+) . Actually, thymine decamer and doubly charged thymine 15-mer metaclusters can be observed along with thymine quintet in the ESI mass spectra of thymine with the addition of K(+) , Rb(+) and Cs(+) . The product ion spectra of these metaclusters, especially the 15-mer with hetero central ions, indicate that they are higher order assemblies of thymine quintets. The collision-induced dissociation experiments show that the gas-phase stabilities of these metaclusters depend on the size of the central ions, following the order Cs(+) > Rb(+) > K(+) , while K(+) leads to the highest dissociation energy of a thymine quintet. The optimized structures of thymine quintet and decamer were provided by density functional theory calculations, which showed that thymine quintet is bowl-shaped and its tilting angle increases with the size of the central ion. Furthermore, the chirality of thymine quintet was defined for the first time and the resulting different diastereoisomers of thymine decamers were also revealed by the calculation study. Copyright © 2011 John Wiley & Sons, Ltd.

Bifacial nucleoside as a surrogate for both T and A in duplex DNA

A new functional bifacial nucleoside derived from 7-aminopyrimido[4,5-d]pyrimidine-2,4(1H,3H)-dione, a Janus-type nucleobase, has been synthesized and incorporated into DNA oligonucleotides. The nucleobase, having self-complementary H-bonding faces, mimics both T and A and engages in the corresponding Watson-Crick-like base pairs, forming stable duplexes.

Self-assembly of three-dimensional DNA nanostructures and potential biological applications

A current challenge in nanoscience is to achieve controlled organization in three-dimensions, to provide tools for biophysics, molecular sensors, enzymatic cascades, drug delivery, tissue engineering, and device fabrication. DNA displays some of the most predictable and programmable interactions of any molecule, natural or synthetic. As a result, 3D-DNA nanostructures have emerged as promising tools for biology and materials science. In this review, strategies for 3D-DNA assembly are discussed. DNA cages, nanotubes, dendritic networks, and crystals are formed, with deliberate variation of their size, shape, persistence length, and porosities. They can exhibit dynamic character, allowing their selective switching with external stimuli. They can encapsulate and position materials into arbitrarily designed patterns, and show promise for numerous biological and materials applications.