Deepak K. Prusty

A Fluorogenic Reaction Based on Heavy-Atom Removal for Ultrasensitive DNA Detection

Fluorogenic reactions have recently emerged as a powerful tool for detection, diagnostics, and biosensing applications in a chemical and biological context. However, conventional fluorogenic systems reported to date rely on energy- or photoinduced electron transfer within the probes. Our communication demonstrates a conceptually new approach for generating a strong fluorescence signal through chemical bond formation mediated by a heavy-atom removal process. This method has favorable photophysical properties such as exceptional quantum yield and very low limits of fluorogenic DNA detection.

Light-Triggered Sequence-Specific Cargo Release from DNA Block Copolymer–Lipid Vesicles†

Nanocontainers have gained much importance because of their versatile properties and broad application potential in the fields of chemistry,1 biophysics,2 and nanomedicine.2b, 3 Lipid vesicles have proven to be a particularly effective class of nanocontainers, able to encapsulate and protect diverse small molecules, such as ions and drugs,4 as well as larger biomacromolecules, such as proteins or DNA.2a, 5 Moreover, the engineering of lipid vesicles has sufficiently advanced to a level which enables functionalization and manipulation of their surfaces with specific ligands to improve their poor chemical and physical specificity. For example, proteins (including antibodies),5a, 6 carbohydrates,7 and vitamins2a, 8 have all been used as targeting units anchored to the liposome surfaces to direct these nanocontainers to the site of action. More recently, single-stranded DNA covalently attached to cholesterol or lipid moieties has been incorporated into vesicle bilayers in order to exploit the specific recognition ability of oligonucleotides (ODNs) by hybridization with their complementary strands. These DNA hybrids have been shown to be critical building blocks in the construction of novel self-assembled supravesicular structures in which vesicles were linked by double-stranded ODNs,9 or utilized to induce programmed fusion.10 Moreover, DNA–lipids have been used to construct hybridization-sensitive nanocontainers,11 to improve liposome marking,12 to mimic cellular systems,13 and for multiplexed DNA detection.14 As demonstrated by the numerous examples above, the decoration of vesicles with DNA amphiphiles has resulted in significant advances in the functionality of these containers; the bilayer barrier itself remains a significant hindrance to the release of cargo, however. There have been several successful attempts to liberate cargo molecules from vesicles. One possibility is the generation of pores in the lipid bilayer through the incorporation of natural or synthetic ion channels.15 Another approach, which entails enzymes, makes use of selective lipases for cargo release.16 A promising alternative is the design of “smart” liposomes that are able to release cargo through physicochemical responses to external stimuli (such as nanoparticle incorporation into the membrane, or changes in pH or temperature).17 Furthermore, photosensitizers that generate singlet oxygen (1O2) upon light irradiation have been incorporated into the bilayer or the vesicle interior to mediate cargo release.18 Nevertheless, the liberation of cargo molecules from such functionalized nanocontainers is unfortunately not selective for mixed populations of vesicles and further work is needed to increase the specificity of these container systems. Herein, we report a powerful new approach for selective cargo release from lipid vesicles that is based on amphiphilic DNA block copolymers (DBCs) and the hybridization of photosensitizer units (Scheme 1). It was demonstrated that this new class of nucleic acid amphiphiles, DBCs, can be stably anchored in the phospholipid membrane of liposomes (step 1). The protruding ODN was functionalized with ODN-photosensitizer conjugates through Watson–Crick base pairing (step 2) and after light irradiation (step 3) selective cargo release was achieved (step 4) depending on the DNA code on the surface of the vesicles. DBCs, as used here for cargo release, consist of a single-stranded ODN covalently bound to an organic polymer block. The combination of highly specific DNA interactions with the hydrophobic properties of the polymer block make DBCs ideally suited to diverse nanoscience applications, for example, as gene and drug delivery systems, or as building blocks in nanoelectronic devices.19 Herein, we introduce a new application for DBCs: as a functionalization and release reagent for liposomes. DNA-b-polypropyleneoxide (DNA-b-PPO) was selected because of its amphiphilic nature, which leads the hydrophobic polymer segments to interact with the internal region of the lipid bilayer while the hydrophilic nucleotides remain on the liposome surface free to bind with the complementary DNA sequences. Additional features of DNA-b-PPO include its fully automated synthesis,20 the known ability of PPO to insert into the hydrophobic part of phospholipid bilayers,15d, 21 and its susceptibility to oxidation.22

Modular Assembly of a Pd Catalyst within a DNA Scaffold for the Amplified Colorimetric and Fluorimetric Detection of Nucleic Acids

Catalytic signal amplification is a powerful tool for the detection of chemical and biological analytes. In chemistry it has been employed in sensing various toxic metal ions (e.g. Pd2+, Pb2+, Cu2+, and Hg2+)[1] as well as small molecules such as carbon monoxide[2] and thiols.[3] In a biological context, catalytic reactions have enabled the highly sensitive detection of scarce analytes. They have been widely utilized, for instance, in the detection and assay of proteins,[4] antibodies,[5] and nucleic acids.[6]

DNA-nanoparticle assemblies go organic: Macroscopic polymeric materials with nanosized features

BackgroundOne of the goals in the field of structural DNA nanotechnology is the use of DNA to build up 2- and 3-D nanostructures. The research in this field is motivated by the remarkable structural features of DNA as well as by its unique and reversible recognition properties. Nucleic acids can be used alone as the skeleton of a broad range of periodic nanopatterns and nanoobjects and in addition, DNA can serve as a linker or template to form DNA-hybrid structures with other materials. This approach can be used for the development of new detection strategies as well as nanoelectronic structures and devices.MethodHere we present a new method for the generation of unprecedented all-organic conjugated-polymer nanoparticle networks guided by DNA, based on a hierarchical self-assembly process. First, microphase separation of amphiphilic block copolymers induced the formation of spherical nanoobjects. As a second ordering concept, DNA base pairing has been employed for the controlled spatial definition of the conjugated-polymer particles within the bulk material. These networks offer the flexibility and the diversity of soft polymeric materials. Thus, simple chemical methodologies could be applied in order to tune the networks electrical, optical and mechanical properties.Results and conclusionsOne- two- and three-dimensional networks have been successfully formed. Common to all morphologies is the integrity of the micelles consisting of DNA block copolymer (DBC), which creates an all-organic engineered network.

Sequence-specific nucleic acid mobility using a reversible block copolymer gel matrix and DNA amphiphiles (lipid-DNA) in capillary and microfluidic electrophoretic separations

Reversible noncovalent but sequence‐dependent attachment of DNA to gels is shown to allow programmable mobility processing of DNA populations. The covalent attachment of DNA oligomers to polyacrylamide gels using acrydite‐modified oligonucleotides has enabled sequence‐specific mobility assays for DNA in gel electrophoresis: sequences binding to the immobilized DNA are delayed in their migration. Such a system has been used for example to construct complex DNA filters facilitating DNA computations. However, these gels are formed irreversibly and the choice of immobilized sequences is made once off during fabrication. In this work, we demonstrate the reversible self‐assembly of gels combined with amphiphilic DNA molecules, which exhibit hydrophobic hydrocarbon chains attached to the nucleobase. This amphiphilic DNA, which we term lipid‐DNA, is synthesized in advance and is blended into a block copolymer gel to induce sequence‐dependent DNA retention during electrophoresis. Furthermore, we demonstrate and characterize the programmable mobility shift of matching DNA in such reversible gels both in thin films and microchannels using microelectrode arrays. Such sequence selective separation may be employed to select nucleic acid sequences of similar length from a mixture via local electronics, a basic functionality that can be employed in novel electronic chemical cell designs and other DNA information‐processing systems.

Efficient Separation of Conjugated Polymers Using a Water Soluble Glycoprotein Matrix: From Fluorescence Materials to Light Emitting Devices

Optically active bio-composite blends of conjugated polymers or oligomers are fabricated by complexing them with bovine submaxilliary mucin (BSM) protein. The BSM matrix is exploited to host hydrophobic extended conjugated π-systems and to prevent undesirable aggregation and render such materials water soluble. This method allows tuning the emission color of solutions and films from the basic colors to the technologically challenging white emission. Furthermore, electrically driven light emitting biological devices are prepared and operated.