In the last decade the use of nanomaterials has been having a great impact in biosensing. In particular, the unique properties of noble metal nanoparticles have allowed for the development of new biosensing platforms with enhanced capabilities in the specific detection of bioanalytes. Noble metal nanoparticles show unique physicochemical properties (such as ease of functionalization via simple chemistry and high surface-to-volume ratios) that allied with their unique spectral and optical properties have prompted the development of a plethora of biosensing platforms. Additionally, they also provide an additional or enhanced layer of application for commonly used techniques, such as fluorescence, infrared and Raman spectroscopy. Herein we review the use of noble metal nanoparticles for biosensing strategies--from synthesis and functionalization to integration in molecular diagnostics platforms, with special focus on those that have made their way into the diagnostics laboratory.
Light has always fascinated mankind and since the beginning of recorded history it has been both a subject of research and a tool for investigation of other phenomena. Today, with the advent of nanotechnology, the use of light has reached its own dimension where light-matter interactions take place at wavelength and subwavelength scales and where the physical/chemical nature of nanostructures controls the interactions. This is the field of nanophotonics which allows for the exploration and manipulation of light in and around nanostructures, single molecules, and molecular complexes. What is more is the use of nanophotonics in biomolecular interactions—nanobiophotonics—has prompt for a plethora of molecular diagnostics and therapeutics making use of the remarkable nanoscale properties. In this paper, we shall focus on the uses of nanobiophotonics for molecular diagnostics involving specific sequence characterization of nucleic acids and for gene delivery systems of relevance for therapy strategies. The use of nanobiophotonics for the combined diagnostics/therapeutics (theranostics) will also be addressed, with particular focus on those systems enabling the development of safer, more efficient, and specific platforms. Finally, the translation of nanophotonics for theranostics into the clinical setting will be discussed.
Restriction enzymes are the bread and butter of Molecular Biology. Nonetheless, how restriction enzymes recognize and cleave their target is not always clear. When developing a method for the enzymatic production of oligonucleotides, we noticed that type II endonucleases BtsCI and BseGI, which recognize the sequence GGATGNN^, perform incomplete digestions of DNA hairpins, with the top strand nick not always occurring correctly. We tested the cutting of synthetic hairpins containing all possible combinations of dinucleotides following the recognition site and our results show that all sequences containing one adenine following GGATG were digested more efficiently. We further show that the same sequence preference is also observable in double stranded DNA at higher Mg2+ concentrations and even in optimal conditions. Kinetic results show that BtsCI has a noteworthy difference in the first-rate constants between different sequences and between the two catalytic domains. An increase in Mg2+ resulted in a drastic decrease in the catalytic activity of the top (sense) strand that wasn’t always accompanied by a nick in the bottom strand (antisense).
This protocol describes the synthesis and detailed calibration of a gold nanoparticle-based nanobeacon \ (Au-nanobeacon) as an innovative theranostic approach for detection and inhibition of sequence-speci c DNA and RNA for in vitro and ex vivo applications.Under hairpin con guration, proximity to gold nanoparticles leads to uorescence quenching; hybridization to a complementary target restores uorescence emission due to the gold nanobeacons' conformational reorganization that causes the uorophore and the AuNP to part from each other.This concept can easily be extended and adapted to assist the in vitro evaluation of silencing potential of a given sequence to be later used for ex vivo gene silencing and RNAi approaches, with the ability to monitor real-time gene delivery action.The time range for the entire protocol is ~8 days, including synthesis, functionalization and calibration of Aunanobeacons, RNAi and gene silencing assays.
We propose an experimental-based tool for dealing with fluorescence modulation close to nanoparticles for application in studies of fluorophores in the vicinity of gold nanoparticles (AuNPs), typically addressed via theoretical models. We performed a photophysical characterization of fluorophores in the vicinity of AuNPs, showing that correct Φ(F) determination suffers from a local pH effect, and address the observed radiative enhancement. Our approach is based on the experimental assurance that the reference fluorophores are in the same optical conditions as those of the AuNP-fluorophore conjugates. We demonstrate the relevance for introducing corrections for the inner filter effect and the reabsorption of the emitted light caused by AuNPs. The proposed approach could circumvent the need for theoretical based corrections and allow for more accurate determination of fluorescence emission in the vicinity of gold nanoparticles.