Single-Molecule Photoactivation FRET: A General and Easy-To-Implement Approach To Break the Concentration Barrier

Single-molecule fluorescence resonance energy transfer (sm-FRET) has become a widely used tool to reveal dynamic processes and molecule mechanisms hidden under ensemble measurements. However, the upper limit of fluorescent species used in sm-FRET is still orders of magnitude lower than the association affinity of many biological processes under physiological conditions. Herein, we introduce single-molecule photoactivation FRET (sm-PAFRET), a general approach to break the concentration barrier by using photoactivatable fluorophores as donors. We demonstrate sm-PAFRET by capturing transient FRET states and revealing new reaction pathways during translation using μm fluorophore labeled species, which is 2–3 orders of magnitude higher than commonly used in sm-FRET measurements. sm-PAFRET serves as an easy-to-implement tool to lift the concentration barrier and discover new molecular dynamic processes and mechanisms under physiological concentrations.     

Discovering DNA methylation patterns for long non-coding RNAs associated with cancer subtypes

Despite growing evidence demonstrates that the long non-coding ribonucleic acids (lncRNAs) are critical modulators for cancers, the knowledge about the DNA methylation patterns of lncRNAs is quite limited. We develop a systematic analysis pipeline to discover DNA methylation patterns for lncRNAs across multiple cancer subtypes from probe, gene and network levels. By using The Cancer Genome Atlas (TCGA) breast cancer methylation data, the pipeline discovers various DNA methylation patterns for lncRNAs across four major subtypes such as luminal A, luminal B, her2-enriched as well as basal-like. On the probe and gene level, we find that both differentially methylated probes and lncRNAs are subtype specific, while the lncRNAs are not as specific as probes. On the network level, the pipeline constructs differential co-methylation lncRNA network for each subtype. Then, it identifies both subtype specific and common lncRNA modules by simultaneously analyzing multiple networks. We show that the lncRNAs in subtype specific and common modules differ greatly in terms of topological structure, sequence conservation as well as expression. Furthermore, the subtype specific lncRNA modules serve as biomarkers to improve significantly the accuracy of breast cancer subtypes prediction. Finally, the common lncRNA modules associate with survival time of patients, which is critical for cancer therapy.     

Ultrafast Fluorescence Spectroscopy via Upconversion and Its Applications in Biophysics

In this review, the experimental set-up and functional characteristics of single-wavelength and broad-band femtosecond upconversion spectrophotofluorometers developed in our laboratory are described. We discuss applications of this technique to biophysical problems, such as ultrafast fluorescence quenching and solvation dynamics of tryptophan, peptides, proteins, reduced nicotinamide adenine dinucleotide (NADH), and nucleic acids. In the tryptophan dynamics field, especially for proteins, two types of solvation dynamics on different time scales have been well explored: ~1 ps for bulk water, and tens of picoseconds for “biological water”, a term that combines effects of water and macromolecule dynamics. In addition, some proteins also show quasi-static self-quenching (QSSQ) phenomena. Interestingly, in our more recent work, we also find that similar mixtures of quenching and solvation dynamics occur for the metabolic cofactor NADH. In this review, we add a brief overview of the emerging development of fluorescent RNA aptamers and their potential application to live cell imaging, while noting how ultrafast measurement may speed their optimization.     

Aptamer Laden Liquid Crystals Biosensing Platform for the Detection of HIV-1 Glycoprotein-120

We report a label-free and simple approach for the detection of glycoprotein-120 (gp-120) using an aptamer-based liquid crystals (LCs) biosensing platform. The LCs are supported on the surface of a modified glass slide with a suitable amount of B40t77 aptamer, allowing the LCs to be homeotropically aligned. A pronounced topological change was observed on the surface due to a specific interaction between B40t77 and gp-120, which led to the disruption of the homeotropic alignment of LCs. This results in a dark-to-bright transition observed under a polarized optical microscope. With the developed biosensing platform, it was possible to not only identify gp-120, but obtained results were analyzed quantitatively through image analysis. The detection limit of the proposed biosensing platform was investigated to be 0.2 µg/mL of gp-120. Regarding selectivity of the developed platform, no response could be detected when gp-120 was replaced by other proteins, such as bovine serum albumin (BSA), hepatitis A virus capsid protein 1 (Hep A VP1) and immunoglobulin G protein (IgG). Due to attributes such as label-free, high specificity and no need for instrumental read-out, the presented biosensing platform provides the potential to develop a working device for the quick detection of HIV-1 gp-120.     

Enhancements of the Gaussian network model in describing nucleotide residue fluctuations for RNA

Gaussian network model (GNM) is an efficient method to investigate the structural dynamics of biomolecules. However, the application of GNM on RNAs is not as good as that on proteins, and there is still room to improve the model. In this study, two novel approaches, named the weighted GNM (wGNM) and the force-constant-decayed GNM (fcdGNM), were proposed to enhance the performance of ENM in investigating the structural dynamics of RNAs. In wGNM, the force constant for each spring is weighted by the number of interacting heavy atom pairs between two nucleotides. In fcdGNM, all the pairwise nucleotides were connected by springs and the force constant decayed exponentially with the separate distance of the nucleotide pairs. The performance of these two proposed models was evaluated by using a non-redundant RNA structure database composed of 51 RNA molecules. The calculation results show that both the proposed models outperform the conventional GNM in reproducing the experimental B-factors of RNA structures. Compared with the conventional GNM, the Pearson correlation coefficient between the predicted and experimental B-factors was improved by 9.85% and 6.76% for wGNM and fcdGNM, respectively. Our studies provide two candidate methods for better revealing the dynamical properties encoded in RNA structures.     

Mirror-Image Oligonucleotides: History and Emerging Applications

As chiral molecules, naturally occurring d -oligonucleotides have enantiomers, l -DNA and l -RNA, which are comprised of l -(deoxy)ribose sugars. These mirror-image oligonucleotides have the same physical and chemical properties as that of their native d -counterparts, yet are highly orthogonal to the stereospecific environment of biology. Consequently, l -oligonucleotides are resistant to nuclease degradation and many of the off-target interactions that plague traditional d -oligonucleotide-based technologies; thus making them ideal for biomedical applications. Despite a flurry of interest during the early 1990s, the inability of d - and l -oligonucleotides to form contiguous Watson–Crick base pairs with each other has ultimately led to the perception that l -oligonucleotides have only limited utility. Recently, however, scientists have begun to uncover novel strategies to harness the bio-orthogonality of l -oligonucleotides, while overcoming (and even exploiting) their inability to Watson–Crick base pair with the natural polymer. Herein, a brief history of l -oligonucleotide research is presented and emerging l -oligonucleotide-based technologies, as well as their applications in research and therapy, are presented.