Yu-Ming Chang

Conformational Changes in DNA upon Ligand Binding Monitored by Circular Dichroism

Circular dichroism (CD) spectroscopy is an optical technique that measures the difference in the absorption of left and right circularly polarized light. This technique has been widely employed in the studies of nucleic acids structures and the use of it to monitor conformational polymorphism of DNA has grown tremendously in the past few decades. DNA may undergo conformational changes to B-form, A-form, Z-form, quadruplexes, triplexes and other structures as a result of the binding process to different compounds. Here we review the recent CD spectroscopic studies of the induction of DNA conformational changes by different ligands, which includes metal derivative complex of aureolic family drugs, actinomycin D, neomycin, cisplatin, and polyamine. It is clear that CD spectroscopy is extremely sensitive and relatively inexpensive, as compared with other techniques. These studies show that CD spectroscopy is a powerful technique to monitor DNA conformational changes resulting from drug binding and also shows its potential to be a drug-screening platform in the future.

Energy level alignment, electron injection, and charge recombination characteristics in CdS/CdSe cosensitized TiO2 photoelectrode

The band-edge levels of CdS-, CdSe-, and CdS/CdSe-sensitized TiO2 electrodes were determined by ultraviolet photoelectron spectroscopy (UPS) to explore the reason leading to the high performance of the TiO2/CdS/CdSe electrode. The obtained UPS results show the stepwise energy level in the TiO2/CdS/CdSe electrode, indicating energy level alignment occurrence between CdS and CdSe in the TiO2/CdS/CdSe. Time-resolved photoluminescence and open-circuit photovoltage decay experiments reveal that the photogenerated electrons in the TiO2/CdS/CdSe have higher injection efficiency, but lower recombination rate to the electrolyte, attributable to the stepwise structure of band-edge levels constructed by the effect of the energy level alignment.The band-edge levels of CdS-, CdSe-, and CdS/CdSe-sensitized TiO2 electrodes were determined by ultraviolet photoelectron spectroscopy (UPS) to explore the reason leading to the high performance of the TiO2/CdS/CdSe electrode. The obtained UPS results show the stepwise energy level in the TiO2/CdS/CdSe electrode, indicating energy level alignment occurrence between CdS and CdSe in the TiO2/CdS/CdSe. Time-resolved photoluminescence and open-circuit photovoltage decay experiments reveal that the photogenerated electrons in the TiO2/CdS/CdSe have higher injection efficiency, but lower recombination rate to the electrolyte, attributable to the stepwise structure of band-edge levels constructed by the effect of the energy level alignment.

Structural study of TcaR and its complexes with multiple antibiotics from Staphylococcus epidermidis

TcaR and IcaR are a weak and a strong negative regulator of transcription of the ica locus, respectively, and their presence prevents the poly-N-acetylglucosamine production and biofilm formation in Staphylococcus epidermidis. Although TcaR was shown to interact with the ica promoter, the precise binding region and the mechanism of interaction remained unclear. Here we present the 3D structure of TcaR in its apo form and in complex with salicylate as well as several aminoglycoside and β-lactam antibiotics. A comparison of the native and complex TcaR structures indicates that the mechanism of regulation involves a large conformational change in the DNA-binding lobe. Here, we deduced the consensus binding sequence of two [∼TTNNAA] hexamers embedded in a 16 bp sequence for a TcaR dimer. Six TcaR dimers bind specifically to three approximately 33 bp segments close to the IcaR binding region with varying affinities, and their repressor activity is directly interfered by salicylate and different classes of natural antimicrobial compounds. We also found in this study that the antimicrobial compounds we tested were shown not only to inhibit TcaR–DNA interaction but also to further induce biofilm formation in S. epidermidis in our in vivo assay. The results support a general mechanism for antibiotics in regulating TcaR–DNA interaction and thereby help understand the effect of antibiotic exposure on bacterial antibiotic resistance through biofilm formation.

Micro-Raman spectroscopy of a single freestanding GaN nanorod grown by molecular beam epitaxy

Micro-Raman spectra were measured on a single freestanding GaN nanorod, which was grown by molecular beam epitaxy. A sharp linewidth of E2(high) mode of 2.1cm−1 measured in the x(y,y)x¯ configuration indicates the high crystalline quality of the nanorod. The angle-dependent Raman spectroscopy shows that the integrated intensities of these first-order Raman modes follow the theoretical sinusoidal functions. The forbidden E1(LO) mode that appeared in the x(z,z)x¯ scattering configurations is assigned to the quasi-LO phonon mode. Power-dependent Raman spectroscopy shows redshift with increasing laser power density due to sample heating which is confirmed by Stokes and anti-Stokes measurements. The broadband centered at 708.5cm−1 is ascribed to the surface mode of the nanostructure.

Coherent phonon spectroscopy of GaAs surfaces using time-resolved second-harmonic generation

Abstract The general theory and experimental considerations are presented for a novel all-optical time-domain technique for measuring low frequency vibrational modes of surfaces (phonons or adsorbate vibrational modes). A pump-laser pulse impulsively drives an initial displacement of the surface atoms. The subsequent free-induction decay of the coherent phonon modes of the surface atoms is detected by time-resolved second-harmonic generation (SHG). The spectral features are recovered by fitting the time-domain data to exponentially decaying sinusoids. This all-optical probe has advantages over inelastic particle scattering techniques because it can be applied at buried interfaces. It has signal to noise advantages over linear and spontaneous Raman techniques. This technique is demonstrated by measurement of surface optical phonon spectra on the clean GaAs (110)–relaxed–(1×1), GaAs (100)–(1×6), and GaAs (100)–(4×1) in UHV and of a local monolayer-scale interfacial mode at the buried native-oxide-covered GaAs (100). The chemical sensitivity is demonstrated by in situ oxidation of the GaAs (100)–(4×6). The general mechanism of generating coherent surface phonons is discussed in light of the symmetry selection rules.

The modulation effect of transverse, antibonding, and higher-order longitudinal modes on the two-photon photoluminescence of gold plasmonic nanoantennas.

Plasmonic nanoantennas exhibit various resonant modes with distinct properties. Upon resonant excitation, plasmonic gold nanoantennas can generate strong two-photon photoluminescence (TPPL). The TPPL from gold is broadband and depolarized, and may serve as an ideal local source for the investigation of antenna eigenmodes. In this work, TPPL spectra of three arrays of single-crystalline gold nanoantennas are comprehensively investigated. We carefully compare the TPPL spectra with dark-field scattering spectra and numerically simulated spectra. We show the modulation effect of the transverse resonant mode and the nonfundamental longitudinal mode on the TPPL spectrum. We also demonstrate suppression of TPPL due to the subradiant antibonding modes and study the influence of antenna resonant modes on the overall TPPL yield. Our work provides direct experimental evidence on nanoantenna-mediated near-to-far-field energy coupling and gains insight into the emission spectrum of the TPPL from gold nanoantennas.

Structural basis for the identification of the N-terminal domain of coronavirus nucleocapsid protein as an antiviral target.

Coronaviruses (CoVs) cause numerous diseases, including Middle East respiratory syndrome and severe acute respiratory syndrome, generating significant health-related and economic consequences. CoVs encode the nucleocapsid (N) protein, a major structural protein that plays multiple roles in the virus replication cycle and forms a ribonucleoprotein complex with the viral RNA through the N protein’s N-terminal domain (N-NTD). Using human CoV-OC43 (HCoV-OC43) as a model for CoV, we present the 3D structure of HCoV-OC43 N-NTD complexed with ribonucleoside 5′-monophosphates to identify a distinct ribonucleotide-binding pocket. By targeting this pocket, we identified and developed a new coronavirus N protein inhibitor, N-(6-oxo-5,6-dihydrophenanthridin-2-yl)(N,N-dimethylamino)acetamide hydrochloride (PJ34), using virtual screening; this inhibitor reduced the N protein’s RNA-binding affinity and hindered viral replication. We also determined the crystal structure of the N-NTD–PJ34 complex. On the basis of these findings, we propose guidelines for developing new N protein-based antiviral agents that target CoVs.

Coherent longitudinal optical phonon and plasmon coupling in the near-surface region of InN

Coherent phonon spectroscopy of a high-quality InN epitaxial layer is carried out using time-resolved second-harmonic generation. A coherent longitudinal optical phonon and plasmon coupling mode only at 447cm−1 can be resolved in the spectrum. Its frequency shows no dependence on the photoinjected carrier density up to 1.5×1019cm−3. This phenomenon is attributed to the hybridization of a coherent A1(LO) phonon with the intrinsic cold plasma accumulated in the near-surface region of InN, where the plasma density could reach on the order of 1020cm−3, much higher than the bulk carrier concentration 1×1018cm−3 determined by Hall effect measurement.

Origin of long lifetime of band-edge charge carriers in organic–inorganic lead iodide perovskites

Significance Hybrid organic–inorganic perovskites (HOIPs) are among the most promising materials for next-generation solar cells that combine high efficiency and low cost. The record efficiency of HOIP-based solar cells has reached above 22%, which is comparable to that of silicon solar cells. HOIP solar cells can be manufactured using simple solution processing methods that can be drastically cheaper than the current commercial solar cell technologies. Despite the progress so far, the microscopic mechanism for the high solar cell efficiency in HOIPs is yet to be understood. Our study shows that rotation of organic molecules in HOIPs extends the lifetime of photoexcited charge carriers, leading to the high efficiency. This insight can guide the progress toward improved solar cell performance. Long carrier lifetime is what makes hybrid organic–inorganic perovskites high-performance photovoltaic materials. Several microscopic mechanisms behind the unusually long carrier lifetime have been proposed, such as formation of large polarons, Rashba effect, ferroelectric domains, and photon recycling. Here, we show that the screening of band-edge charge carriers by rotation of organic cation molecules can be a major contribution to the prolonged carrier lifetime. Our results reveal that the band-edge carrier lifetime increases when the system enters from a phase with lower rotational entropy to another phase with higher entropy. These results imply that the recombination of the photoexcited electrons and holes is suppressed by the screening, leading to the formation of polarons and thereby extending the lifetime. Thus, searching for organic–inorganic perovskites with high rotational entropy over a wide range of temperature may be a key to achieve superior solar cell performance.

Correlation of spin and structure in doped bismuth ferrite nanoparticles

The mutiferroic Bi1−xEuxFeO3 nanoparticles with x = 0 to 0.4 are studied by x-ray diffraction (XRD), Raman spectra and electron spin resonance (ESR) with X-band (9.53 GHz), in order to investigate the doping effect on crystalline and spin structures. Both XRD and Raman spectrum reveal a structural transformation at x = 0.15, which is associated with the shortening of Bi—O bond length. These structural data are further related to the variation of ESR peak position and peak area, providing evidence for the enhancement of ferromagnetic coupling as x < 0.3.