Structural Dynamics Role of AGG Interruptions in Inhibition CGG Repeat Expansion Associated with Fragile X Syndrome.

Abnormal expansion of trinucleotide CGG repeats is responsible for Fragile X syndrome. AGG interruptions in CGG repeat tracts were found in most healthy individuals, suggesting a crucial role in preventing disease-prone repeat expansion. Previous biophysics studies emphasize a difference in the secondary structure affected by AGG interruptions. However, the mechanism of how AGG interruptions impede repeat expansion remains elusive. We utilized single-molecule fluorescence resonance energy transfer spectroscopy to investigate the structural dynamics of CGG repeats and their AGG-interrupted variants. Tandem CGG repeats fold into a stem-loop hairpin structure with the capability to undergo a conformational rearrangement to modulate the length of the overhang. However, this conformational rearrangement is much more retarded when two AGG interruptions are present. Considering the significance of hairpin slippage in repeat expansion, we present a molecular basis suggesting that the internal loop created by two AGG interruptions acts as a barrier, obstructing the hairpin slippage reconfiguration. This impediment potentially plays a crucial role in curbing abnormal expansion, thereby contributing to the genomic stability.

An environmentally sensitive molecular rotor as a NIR fluorescent probe for the detection of islet amyloid polypeptide.

The deposits of human islet amyloid polypeptide (IAPP), also called amylin, in the pancreas have been postulated to be a factor of pancreatic ß-cell dysfunction and is one of the common pathological hallmarks of type II diabetes mellitus (T2DM). Therefore, it is imperative to gain an in-depth understanding of the formation of these aggregates. In this study, we demonstrate a rationally-designed strategy of an environmentally sensitive near-infrared (NIR) molecular rotor utilizing thioflavin T (ThT) as a scaffold for IAPP deposits. We extended the π delocalized system not only to improve the viscosity sensitivity but also to prolong the emission wavelength to the NIR region. A naphthalene moiety was also introduced to adjust the sensitivity of our designed probes to differentiate the binding microenvironment polarity of different targeted proteins. As a result, a novel NIR fluorogenic probe toward IAPP aggregates, namely AmySP-4-Nap-Ene, was first developed. When attached to different protein aggregates, this probe exhibited distinct fluorescence emission profiles. In a comparison with ThT, the fluorescence emission of non-ionic AmySP-4-Nap-Ene exhibits a significant difference between the presence of non-fibrillar and fibrillar IAPP and displays a higher binding affinity toward IAPP fibrils. Further, the AmySP-4-Nap-Ene can be utilized to monitor IAPP accumulating process and image fibrils both in vitro and in living cells.

Mononuclear Manganese(III) Superoxo Complexes: Synthesis, Characterization, and Reactivity.

Metal-superoxo species are typically proposed as key intermediates in the catalytic cycle of dioxygen activation by metalloenzymes involving different transition metal cofactors. In this regard, while a series of Fe-, Co-, and Ni-superoxo complexes have been reported to date, well-defined Mn-superoxo complexes remain rather rare. Herein, we report two mononuclear MnIII-superoxo species, Mn(BDPP)(O2•-) (2, H2BDPP = 2,6-bis((2-(S)-diphenylhydroxylmethyl-1-pyrrolidinyl)methyl)pyridine) and Mn(BDPBrP)(O2•-) (2', H2BDPBrP = 2,6-bis((2-(S)-di(4-bromo)phenylhydroxyl-methyl-1-pyrrolidinyl)methyl)pyridine), synthesized by bubbling O2 into solutions of their MnII precursors, Mn(BDPP) (1) and Mn(BDPBrP) (1'), at -80 °C. A combined spectroscopic (resonance Raman and electron paramagnetic resonance (EPR) spectroscopy) and computational study evidence that both complexes contain a high-spin MnIII center (SMn = 2) antiferromagnetically coupled to a superoxo radical ligand (SOO• = 1/2), yielding an overall S = 3/2 ground state. Complexes 2 and 2' were shown to be capable of abstracting a H atom from 2,2,6,6-tetramethyl-1-hydroxypiperidine (TEMPO-H) to form MnIII-hydroperoxo species, Mn(BDPP)(OOH) (5) and Mn(BDPBrP)(OOH) (5'). Complexes 5 and 5' can be independently prepared by the reactions of the isolated MnIII-aqua complexes, [Mn(BDPP)(H2O)]OTf (6) and [Mn(BDPBrP)(H2O)]OTf (6'), with H2O2 in the presence of NEt3. The parallel-mode EPR measurements established a high-spin S = 2 ground state for 5 and 5'.

Long-Range Hairpin Slippage Reconfiguration Dynamics in Trinucleotide Repeat Sequences.

Trinucleotide repeat (TNR) sequences, which are responsible for several neurodegenerative genetic diseases, fold into hairpins that interfere with the protein machinery in replication or repair, thus leading to dynamic mutation -abnormal expansions of the genome. Despite their high thermodynamic stability, these hairpins can undergo configurational rearrangements, which may be crucial for continuous dynamic mutation. Here, we used CTG repeats as a model system to study their structural dynamics at the single-molecule level. A unique dynamic two-state configuration interchange was discovered over a wide range of odd-numbered CTG repeat sequences. Employing repeat-number-dependent kinetic analysis, we proposed a bulge translocation model, which is driven by the local instability and can be extended reasonably to longer (pathologically relevant) hairpins, implying the potential role in error accumulation in repeat expansion.

Determination of Gold Ions in Human Urine Using Genetically Engineered Microorganisms on a Paper Device.

This paper presents a whole-cell biosensor that operates in conjunction with a smartphone-based fluorescence diagnostic system on a paper device to monitor the concentration of gold ions in human urine. The heavy metal-tolerant bacteria Cupriavidus metallidurans was genetically engineered for use as a chassis in a red fluorescent protein (RFP)-based microbial sensor. The biosensor is highly sensitive to gold ions, with a detection limit of 110 nM. The proposed smartphone-based analysis system provides a user-friendly approach to design tools of personal health monitoring for reporting the presence of gold ions in human urine.

Parity-dependent hairpin configurations of repetitive DNA sequence promote slippage associated with DNA expansion.

Repetitive DNA sequences are ubiquitous in life, and changes in the number of repeats often have various physiological and pathological implications. DNA repeats are capable of interchanging between different noncanonical and canonical conformations in a dynamic fashion, causing configurational slippage that often leads to repeat expansion associated with neurological diseases. In this report, we used single-molecule spectroscopy together with biophysical analyses to demonstrate the parity-dependent hairpin structural polymorphism of TGGAA repeat DNA. We found that the DNA adopted two configurations depending on the repeat number parity (even or odd). Transitions between these two configurations were also observed for longer repeats. In addition, the ability to modulate this transition was found to be enhanced by divalent ions. Based on the atomic structure, we propose a local seeding model where the kinked GGA motifs in the stem region of TGGAA repeat DNA act as hot spots to facilitate the transition between the two configurations, which may give rise to disease-associated repeat expansion.

Direct observation of the primary bond-twisting dynamics of stilbene anion radical.

The anion radicals of stilbenes in the collisionless isolated phase were synthesized by electron attachment, and their dynamics were observed in real time on the femtosecond time scale. The observed coherent vibrational motion (approximately 42 cm(-1)) and the primary bond-twisting dynamics (approximately 650 fs) for the D2 state are on a vastly different time scale from that reported (approximately 10 ns) in solution.

Dynamics of electrons in ammonia cages: the discovery system of solvation.

Two centuries ago solvated electrons were discovered in liquid ammonia and a century later the concept of the solvent cage was introduced. Here, we report a real time study of the dynamics of size-selected clusters, n=20 to 60, of electrons in ammonia, and, for comparison, that of electrons in water cages. Unlike the water case, the observed dynamics for ammonia indicates the formation, through a 100 fs temperature jump, of a solvent collective motion in a 500 fs relaxation process. The agreement of the experimental results-obtained for a well-defined n, gated electron kinetic energy, and time delay-with molecular dynamics theory suggests the critical and different role of the kinetic energy and the librational motions involved in solvation.

Primary steps of the photoactive yellow protein: isolated chromophore dynamics and protein directed function.

The cycle of the photoactive yellow protein (PYP) has been extensively studied, but the dynamics of the isolated chromophore responsible for transduction is unknown. Here, we present real-time observation of the dynamics of the negatively charged chromophore and detection of intermediates along the path of trans-to-cis isomerization using femtosecond mass selection/electron detachment techniques. The results show that the role of the protein environment is not in the first step of double-bond twisting (barrier crossing) but in directing efficient conversion to the cis-structure and in impeding radical formation within the protein.

Electrons in finite-sized water cavities: hydration dynamics observed in real time.

We directly observed the hydration dynamics of an excess electron in the finite-sized water clusters of (H2O)n- with n = 15, 20, 25, 30, and 35. We initiated the solvent motion by exciting the hydrated electron in the cluster. By resolving the binding energy of the excess electron in real time with femtosecond resolution, we captured the ultrafast dynamics of the electron in the presolvated ("wet") and hydrated states and obtained, as a function of cluster size, the subsequent relaxation times. The solvation time (300 femtoseconds) after the internal conversion [140 femtoseconds for (H2O)35-] was similar to that of bulk water, indicating the dominant role of the local water structure in the dynamics of hydration. In contrast, the relaxation in other nuclear coordinates was on a much longer time scale (2 to 10 picoseconds) and depended critically on cluster size.