Covalent Organic Frameworks for Biomedical Applications

Covalent organic frameworks (COFs) are porous organic polymeric materials that are composed of organic elements and linked together by the thermodynamically stable covalent bonds. The applications of COFs in energy sector and drug delivery are afforded because of the desirable properties of COFs, such as high stability, low density, large surface area, multidimensionality, porosity, and high-ordered crystalline structure expanded. In this review COFs are reviewed, from the perspective of different types of reported COFs, different methods for their synthesis, and their potential applications in the biomedical field. The main goal of this review is to introduce COFs as a biomaterial and to identify specific advantages of different types of COFs that can be exploited for specialized biomedical applications, such as immune engineering.

TiO2 nanowires as an effective sensing platform for rapid fluorescence detection of single-stranded DNA and double-stranded DNA

Numerous nanomaterials have been utilized for novel biosensors with sensitivity and selectivity in the last decades due to their intrinsic unique properties. Herein, a facile fluorescence method for nucleic acid detection was developed by employing TiO₂ nanowires (NWs) as the sensing platform. The quenching effect of TiO₂ NWs to fluorophore-labelled single-stranded DNA (ssDNA) was found to be more significant than that to fluorophore-labelled double-stranded DNA (dsDNA) or triplex DNA probes. More importantly, the whole quenching process was also fast since it just took about ten minutes to reach the equilibrium. Based on the different affinities of TiO₂ NWs to ssDNA, dsDNA and triplex DNA probes, the sequence-specific nucleic acids were detected with sensitivity and specificity. Further investigation has demonstrated that the quenching efficiency of TiO₂ NWs to long ssDNA was apparently superior than that to short ssDNA. Moreover, the fluorescence from various ssDNA probes labelled with a wide spectrum of fluorescent dyes could also be quenched by TiO₂ NWs. These inspiring results reveal that TiO₂ NWs could be an excellent universal nanoquencher used in the next-generation biosensors.

Microbead-Based Platform for Multiplex Detection of DNA and Protein

We present a novel microbead-based detection platform as a simple and universal strategy for simultaneous determination of multiple biomolecules. This platform is composed of streptavidin coated uniform-sized polystyrene microbeads, dye and biotin-labeled ssDNA or aptamer probes, and quencher-labeled complementary sequences. By this method, upon target binding to the probes, quencher strand dissociation is triggered, which results in fluorescence reactivation of the microbead linked probes. The fluorescence variation is readily monitored by flow cytometry and with a high sensitivity. Explicitly, this microbead-based detection platform shows a high sensitivity for target DNA with a detection limit as low as 0.20 nM, alongside good selectivity from one-base mismatched DNA. This novel platform also shows good selectivity and high sensitivity for protein detection when aptamer is used as a probe. The detection limit for lysozyme is as low as 8.56 nM. Moreover, simultaneous detection of multiple targets has been achieved via incorporating different dye-labeled probes on the microbeads concurrently. We have also applied this developed strategy to the detection of target DNA in human serum. This strategy can be easily extended to other targets through simple probe and quencher variation.

Revealing and Resolving the Restrained Enzymatic Cleavage of DNA Self-Assembled Monolayers on Gold: Electrochemical Quantitation and ESI-MS Confirmation

Herein, we report a combined electrochemical and ESI-MS study of the enzymatic hydrolysis efficiency of DNA self-assembled monolayers (SAMs) on gold, platform systems for understanding nucleic acid surface chemistry, and for constructing DNA-based biosensors. Our electrochemical approach is based on the comparison of the amounts of surface-tethered DNA nucleotides before and after exonuclease I (Exo I) incubation using electrostatically bound [Ru(NH₃)₆]³⁺ as redox indicators. It is surprising to reveal that the hydrolysis efficiency of ssDNA SAMs does not depend on the packing density and base sequence, and that the cleavage ends with surface-bound shorter strands (9-13 mers). The ex-situ ESI-MS observations confirmed that the hydrolysis products for ssDNA SAMs (from 24 to 56 mers) are dominated with 10-15 mer fragments, in contrast to the complete digestion in solution. Such surface-restrained hydrolysis behavior is due to the steric hindrance of the underneath electrode to the Exo I/DNA binding, which is essential for the occurrence of Exo I-catalyzed processive cleavage. More importantly, we have shown that the hydrolysis efficiency of ssDNA SAMs can be remarkably improved by adopting long alkyl linkers (locating DNA strands further away from the substrates).

Fluorescence-Tuned Polyhedral Oligomeric Silsesquioxane-Based Porous Polymers

Two series of new polyhedral oligomeric silsesquioxane (POSS)-based fluorescent hybrid porous polymers, HPP-1 and HPP-2, have been prepared by the Heck reaction of octavinylsilsesquioxane with 2,2',7,7'-tetrabromo-9,9'-spirobifluorene and 1,3,6,8-tetrabromopyrene, respectively. Three sets of reaction conditions were employed to assess their effect on fluorescence. These materials exhibit tunable fluorescence from nearly no fluorescence to bright fluorescence both in the solid state and dispersed in ethanol under UV light irradiation by simply altering the reaction conditions. We speculated that the difference may be attributable to the fluorescence quenching induced by Et3 N, P(o-CH3 Ph)3 , and their hydrogen bromide salts employed in the reactions. This finding could give valuable suggestions for the construction of porous polymers with tunable/controllable fluorescence, especially those prepared by Heck and Sonogashira reactions in which these quenchers are used as organic bases or co-catalysts. In addition, the porosities can also be tuned, but different trends in porosity have been found in these two series of polymers, which suggests that various factors should be carefully considered in the preparation of porous polymers with tunable/controllable porosity. Furthermore, HPP-1 c showed moderate CO2 uptake and fluorescence that was efficiently quenched by nitroaromatic explosives, thereby indicating that these materials could be utilized as solid absorbents for the capture and storage of CO2 and as sensing agents for the detection of explosives.

Aptamer-mediated universal enzyme assay based on target-triggered DNA polymerase activity

We herein describe an innovative method for a universal fluorescence turn-on enzyme assay, which relies on the target enzyme-triggered DNA polymerase activity. In the first target recognition step, the target enzyme is designed to destabilize detection probe derived from an aptamer specific to DNA polymerase containing the overhang sequence and the complementary blocker DNA, which consequently leads to the recovery of DNA polymerase activity inhibited by the detection probe. This target-triggered polymerase activity is monitored in the second signal transduction step based on primer extension reaction coupled with TaqMan probe. Utilizing this design principle, we have successfully detected the activities of two model enzymes, exonuclease I and uracil DNA glycosylase with high sensitivity and selectivity. Since this strategy is composed of separated target recognition and signal transduction modules, it could be universally employed for the sensitive determination of numerous different target enzymes by simply redesigning the overhang sequence of detection probe, while keeping TaqMan probe-based signal transduction module as a universal signaling tool.