Deprotonation mechanism of a single-stranded DNA i-motif

An atomistic Molecular Dynamics simulation to study the unfolding and deprotonation mechanism of a single-stranded and fully protonated DNA i-motif.

Regulation of an enzyme cascade reaction by a DNA machine

A strategy for the regulation of enzyme cascade reaction efficiency by a DNA machine in vitro is presented. Two cascade enzymes (GOx and HRP) are attached to the DNA machine, and the enzyme cascade reaction shows much higher efficiency when the two enzymes are brought closer by the DNA machine than when they are distant.

A triggered DNA hydrogel cover to envelop and release single cells

We develop an enzyme-triggered permeable DNA hydrogel cover to envelop and release single cells in microwells. The porous structure of the DNA hydrogel allows nutrients and waste to pass through, leading to a cell viability as high as 98%. The design provides a general method to culture, monitor, and manipulate single cells, and has potential applications in cell patterning and studying cell communication.

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.

Properties of amphiphilic oligonucleotide films at the air/water interface and after film transfer

The self-assembly of amphiphilic hybrid materials containing an oligonucleotide sequence at the air/water interface was investigated by means of pressure-molecular area (Π-A) isotherms. In addition, films were transferred onto solid substrates and imaged using scanning force microscopy. We used oligonucleotide molecules with lipid tails, which consisted of a single stranded oligonucleotide 11 mer containing two hydrophobically modified 5-(dodec-1-ynyl)uracil nucleobases (dU11) at the 5'-end of the oligonucleotide sequence. The air/water interface was used as confinement for the self-assembling process of dU11. Scanning force microscopy of films transferred via Langmuir-Blodgett technique revealed mono-, bi- (Π ≥ 2 mN/m) and multilayer formation (Π ≥ 30 mN/m). The first layer was 1.6 ± 0.1 nm thick. It was oriented with the hydrophilic oligonucleotide moiety facing the hydrophilic substrate while the hydrophobic alkyl chains faced air. In the second layer the oligonucleotide moiety was found to face the air. The second layer was found to cover up to 95% of the sample area. Our measurements indicated that the rearrangement of the molecules into bi- and multiple bilayers happened already at the air/water interface. Similar results were obtained with a second type of oligonucleotide amphiphile, an oligonucleotide block copolymer, which was composed of an oligonucleotide 11 mer covalently attached at the terminus to polypropyleneoxide (PPO).

DNA branch migration reactions through photocontrollable toehold formation

Strand displacement cascades are commonly used to make dynamically assembled structures. Particularly, the concept of "toehold-mediated DNA branch migration reactions" has attracted considerable attention in relation to dynamic DNA nanostructures. However, it is a challenge to obtain and control the formation of pure 1:1 ratio DNA duplexes with toehold structures. Here, for the first time, we report a photocontrolled toehold formation method, which is based on the photocleavage of 2-nitrobenzyl linker-embedded DNA hairpin precursor structures. UV light irradiation (λ ≈ 365 nm) of solutions containing these DNA hairpin structures causes the complete cleavage of the nitrobenzyl linker, and pure 1:1 DNA duplexes with toehold structures are easily formed. Our experimental results indicate that the amount of toehold can be controlled by simply changing the dose of UV irradiation and that the resulting toehold structures can be used for subsequent toehold-mediated DNA branch migration reactions, e.g., DNA hybridization chain reactions. This newly established method will find broad application in the construction of light-powered, controllable, and dynamic DNA nanostructures or large-scale DNA circuits.

Programmed colorimetric logic devices based on DNA-gold nanoparticle interactions

A system including nucleic acid strands and unmodified gold nanopartcles is activated to perform programmed logic functions, using pH and DNA as inputs and the plasmonic-related color change of gold nanoparticles as the output. The complexity of the logic devices can be simply enhanced by appropriate engineering.

Controllable and reproducible construction of a SERS substrate and its sensing applications

A simple method for the preparation of a highly stable and reliable surface-enhanced Raman scattering (SERS) substrate was proposed. The SERS enhancement was demonstrated with good controllability and reproducibility through the controlled formation/deformation of SERS "hotspots" using a reversible DNA nanoswitch. Highly effective DNA detection was achieved using a well-designed sandwich structure.

Study of pH-induced folding and unfolding kinetics of the DNA i-motif by stopped-flow circular dichroism

Using the stopped-flow circular dichroism (SFCD) technique, we investigate the kinetics of the pH-induced folding and unfolding process of the DNA i-motif. The results show that the molecule can fold or unfold on a time scale of 100 ms when the solution pH is changed. It is also found that the folding and unfolding rates strongly depend on the solution pH. On the basis of quantitative data, we propose theoretical models to decipher the folding and unfolding kinetics. Our models suggest that the cooperativity of protons is crucial for both the folding and unfolding process. In the unfolding process, the cooperative neutralization of two protons (out of the total six protons in the i-motif molecule) is the only rate-limiting step. In the folding process, there exists a critical step in which three protons bind cooperatively to the DNA strand. These results offer an in-depth understanding of the folding and unfolding kinetics of the DNA i-motif and may give precise guidance for constructing novel nanodevices based on the DNA i-motif.

Structural modification of siRNA for efficient gene silencing

Small interfering RNA (siRNA) holds a great promise for the future of genomic medicine because of its highly sequence-specific gene silencing and universality in therapeutic target. The medical use of siRNA, however, has been severely hampered by the inherent physico-chemical properties of siRNA itself, such as low charge density, high structural stiffness and rapid enzymatic degradation; therefore, the establishment of efficient and safe siRNA delivery methodology is an essential prerequisite, particularly for systemic administration. For an efficient systemic siRNA delivery, it is a critical issue to obtain small and compact siRNA polyplexes with cationic condensing reagents including cationic polymers, because the size and surface properties of the polyplexes are major determinants for achieving desirable in vivo fate. Unfortunately, synthetic siRNA is not easily condensed with cationic polymers due to its intrinsic rigid structure and low spatial charge density. Accordingly, the loose siRNA polyplexes inevitably expose siRNA to the extracellular environment during systemic circulation, resulting in low therapeutic efficiency and poor biodistribution. In this review, we highlight the innovative approaches to increase the size of siRNA via structural modification of the siRNA itself. The attempts include several methodologies such as hybridization, chemical polymerization, and micro- and nano-structurization of siRNA. Due to its increased charge density and flexibility, the structured siRNA can produce highly condensed and homogenous polyplexes compared to the classical monomeric siRNA. As a result, stable and compact siRNA polyplexes can enhance serum stability and target delivery efficiency in vivo with desirable biodistribution. The review specifically aims to provide the recent progress of structural modification of siRNA. In addition, the article also briefly and concisely explains the improved physico-chemical properties of structured siRNA with respect to stability, condensation ability and gene silencing efficiency.

Reconfigurable three-dimensional DNA nanostructures for the construction of intracellular logic sensors

Right out of the (logic) gate: Logic gates made from 3D DNA nanotetrahedra were constructed that are responsive to various ions, small molecules, and short strands of DNA. By including dynamic sequences in one or more edges of the tetrahedra, a FRET signal can be generated in the manner of AND, OR, XOR, and INH logic gates, as well as a half-adder circuit. These DNA logic gates were also applied to intracellular detection of ATP.

Photon-manipulated drug release from a mesoporous nanocontainer controlled by azobenzene-modified nucleic acid

Herein a photon-manipulated mesoporous release system was constructed based on azobenzene-modified nucleic acids. In this system, the azobenzene-incorporated DNA double strands were immobilized at the pore mouth of mesoporous silica nanoparticles. The photoisomerization of azobenzene induced dehybridization/hybridization switch of complementary DNA, causing uncapping/capping of pore gates of mesoporous silica. This nanoplatform permits holding of guest molecules within the nanopores under visible light but releases them when light wavelength turns to the UV range. These DNA/mesoporous silica hybrid nanostructures were exploited as carriers for the cancer cell chemotherapy drug doxorubicin (DOX) due to its stimuli-responsive property as well as good biocompatibility via MTT assay. It is found that the drug release behavior is light-wavelength-sensitive. Switching of the light from visible to the UV range uncapped the pores, causing the release of DOX from the mesoporous silica nanospheres and an obvious cytotoxic effect on cancer cells. We envision that this photocontrolled drug release system could find potential applications in cancer therapy.

Designed diblock oligonucleotide for the synthesis of spatially isolated and highly hybridizable functionalization of DNA-gold nanoparticle nanoconjugates

Conjugates of DNA and gold nanoparticles (AuNPs) typically exploit the strong Au-S chemistry to self-assemble thiolated oligonucleotides at AuNPs. However, it remains challenging to precisely control the orientation and conformation of surface-tethered oligonucleotides and finely tune the hybridization ability. We herein report a novel strategy for spatially controlled functionalization of AuNPs with designed diblock oligonucleotides that are free of modifications. We have demonstrated that poly adenine (polyA) can serve as an effective anchoring block for preferential binding with the AuNP surface, and the appended recognition block adopts an upright conformation that favors DNA hybridization. The lateral spacing and surface density of DNA on AuNPs can also be systematically modulated by adjusting the length of the polyA block. Significantly, this diblock oligonucleotide strategy results in DNA-AuNPs nanoconjugates with high and tunable hybridization ability, which form the basis of a rapid plasmonic DNA sensor.

Templated synthesis of nylon nucleic acids and characterization by nuclease digestion

Nylon nucleic acids containing oligouridine nucleotides with pendent polyamide linkers and flanked by unmodified heteronucleotide sequences were prepared by DNA templated synthesis. Templation was more efficient than the single-stranded synthesis: Coupling step yields were as high as 99.2%, with up to 7 amide linkages formed in the synthesis of a molecule containing 8 modified nucleotides. Controlled digestion by calf spleen phosphodiesterase enabled the mapping of modified nucleotides in the sequences. A combination of complete degradation of nylon nucleic acids by snake venom phosphodiesterase and dephosphorylation of the resulting nucleotide fragments by bacterial alkaline phosphatase, followed by LCMS analysis, clarified the linear structure of the oligo-amide linkages. The templated synthesis strategy afforded nylon nucleic acids in the target structure and was compatible with the presence heteronucleotides. The complete digestion procedure produced a new species of DNA analogues, nylon ribonucleosides, which display nucleosides attached via a 2'-alkylthio linkage to each diamine and dicarboxylate repeat unit of the original nylon nucleic acids. The binding affinity of a nylon ribonucleoside octamer to the complementary DNA was evaluated by thermal denaturing experiments. The octamer was found to form stable duplexes with an inverse dependence on salt concentration, in contrast to the salt-dependent DNA control.

Reversible regulation of protein binding affinity by a DNA machine

We report a DNA machine that can reversibly regulate target binding affinity on the basis of distance-dependent bivalent binding. It is a tweezer-like DNA machine that can tune the spatial distance between two ligands to construct or destroy the bivalent binding. The DNA machine can strongly bind to the target protein when the ligands are placed at an appropriate distance but releases the target when the bivalent binding is disrupted by enlargement of the distance between the ligands. This "capture-release" cycle could be repeatedly driven by single-stranded DNA without changing the ligands and target protein.

Challenges and opportunities for structural DNA nanotechnology

DNA molecules have been used to build a variety of nanoscale structures and devices over the past 30 years, and potential applications have begun to emerge. But the development of more advanced structures and applications will require a number of issues to be addressed, the most significant of which are the high cost of DNA and the high error rate of self-assembly. Here we examine the technical challenges in the field of structural DNA nanotechnology and outline some of the promising applications that could be developed if these hurdles can be overcome. In particular, we highlight the potential use of DNA nanostructures in molecular and cellular biophysics, as biomimetic systems, in energy transfer and photonics, and in diagnostics and therapeutics for human health.

Stable conformations of a single stranded deprotonated DNA i-motif

We present molecular dynamics simulations of a single stranded deprotonated DNA i-motif in explicit solvent. Our results indicate that hairpin structures are stable equilibrium conformations at 300 K. The entropic preference of these configurations is explained by strong water ordering effects due to the present number of hydrogen bonds. We observe a full unfolding at higher temperatures in good agreement with experimental results.

Chemistry of nucleic acids: impacts in multiple fields

Research in nucleic acids has made major advances in the past decade in multiple fields of science and technology. Here we discuss some of the most important findings in DNA and RNA research in the fields of biology, chemistry, biotechnology, synthetic biology, nanostructures and optical materials, with emphasis on how chemistry has impacted, and is impacted by, these developments. Major challenges ahead include the development of new chemical strategies that allow synthetically modified nucleic acids to enter into, and function in, living systems.

DNA origami: a quantum leap for self-assembly of complex structures

The spatially controlled positioning of functional materials by self-assembly is one of the fundamental visions of nanotechnology. Major steps towards this goal have been achieved using DNA as a programmable building block. This tutorial review will focus on one of the most promising methods: DNA origami. The basic design principles, organization of a variety of functional materials and recent implementation of DNA robotics are discussed together with future challenges and opportunities.

Dynamic DNA nanotechnology using strand-displacement reactions

The specificity and predictability of Watson-Crick base pairing make DNA a powerful and versatile material for engineering at the nanoscale. This has enabled the construction of a diverse and rapidly growing set of DNA nanostructures and nanodevices through the programmed hybridization of complementary strands. Although it had initially focused on the self-assembly of static structures, DNA nanotechnology is now also becoming increasingly attractive for engineering systems with interesting dynamic properties. Various devices, including circuits, catalytic amplifiers, autonomous molecular motors and reconfigurable nanostructures, have recently been rationally designed to use DNA strand-displacement reactions, in which two strands with partial or full complementarity hybridize, displacing in the process one or more pre-hybridized strands. This mechanism allows for the kinetic control of reaction pathways. Here, we review DNA strand-displacement-based devices, and look at how this relatively simple mechanism can lead to a surprising diversity of dynamic behaviour.

DNA as a versatile chemical component for catalysis, encoding, and stereocontrol

DNA (deoxyribonucleic acid) is the genetic material common to all of Earth's organisms. Our biological understanding of DNA is extensive and well-exploited. In recent years, chemists have begun to develop DNA for nonbiological applications in catalysis, encoding, and stereochemical control. This Review summarizes key advances in these three exciting research areas, each of which takes advantage of a different subset of DNA's useful chemical properties.

DNA machines: bipedal walker and stepper

The assembly of a "bipedal walker" and of a "bipedal stepper" using DNA constructs is described. These DNA machines are activated by H(+)/OH(-) and Hg(2+)/cysteine triggers. The bipedal walker is activated on a DNA template consisting of four nucleic acid footholds. The forward "walking" of the DNA on the template track is activated by Hg(2+) ions and H(+) ions, respectively, using the thymine-Hg(2+)-thymine complex or the i-motif structure as the DNA translocation driving forces. The backward "walking" is activated by OH(-) ions and cysteine, triggers that destroy the i-motif or thymine-Hg(2+)-thymine complexes. Similarly, the "bipedal stepper" is activated on a circular DNA template consisting of four tethered footholds. With the Hg(2+)/cysteine and H(+)/OH(-) triggers, clockwise or anticlockwise stepping is demonstrated. The operation of the DNA machines is followed optically by the appropriate labeling of the walker-foothold components with the respective fluorophores/quenchers units.

Analysis of DNA hybridization regarding the conformation of molecular layer with piezoelectric microcantilevers

Lead Zirconate Titanate (PZT)-embedded microcantilevers were fabricated with dimensions of 30 × 90 × 3 μm(3) (width × length × thickness). A thicker PZT layer improved the actuation and enabled long-term data acquisition in common aqueous buffers with a frequency resolution of 20 Hz. A quantitative assay was conducted in the range of 1-20 μM and the resonant frequency was found to increase with the concentration of target DNAs and the probe DNAs were almost saturated at 20 μM. Back-filling with ethyleneglycol-modified alkanethiol was shown to facilitate the hybridization efficiency and stabilize the surface reaction, resulting in a signal enhancement of 40%. We report for the first time how secondary structures in oligonucleotide monolayer change the surface property of a dynamic mode microcantilever and subsequently affect its oscillating behavior. Using fabricated microcantilevers, the real time changes in resonant frequency upon hybridization were measured by utilizing different probe and target sets. The results revealed that the microcantilevers experienced a resonant frequency upshift during the hybridization with complementary DNAs if a dimer structure was present between DNA probes. A resonant frequency downshift was observed for DNA probes that did not contain any complex secondary structures. In addition, the results demonstrate the potential of using these microcantilevers to extract structural information of oligonucleotides.

DNA-SWNT hybrid hydrogel

In this communication, we report the preparation of DNA-SWNT hybrid hydrogel which is pH responsive and strength tunable.

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.