Roles of the C-Terminal Amino Acids of Non-Hexameric Helicases: Insights from Escherichia coli UvrD.

Helicases are nucleic acid-unwinding enzymes that are involved in the maintenance of genome integrity. Several parts of the amino acid sequences of helicases are very similar, and these quite well-conserved amino acid sequences are termed "helicase motifs". Previous studies by X-ray crystallography and single-molecule measurements have suggested a common underlying mechanism for their function. These studies indicate the role of the helicase motifs in unwinding nucleic acids. In contrast, the sequence and length of the C-terminal amino acids of helicases are highly variable. In this paper, I review past and recent studies that proposed helicase mechanisms and studies that investigated the roles of the C-terminal amino acids on helicase and dimerization activities, primarily on the non-hexermeric Escherichia coli (E. coli) UvrD helicase. Then, I center on my recent study of single-molecule direct visualization of a UvrD mutant lacking the C-terminal 40 amino acids (UvrDΔ40C) used in studies proposing the monomer helicase model. The study demonstrated that multiple UvrDΔ40C molecules jointly participated in DNA unwinding, presumably by forming an oligomer. Thus, the single-molecule observation addressed how the C-terminal amino acids affect the number of helicases bound to DNA, oligomerization, and unwinding activity, which can be applied to other helicases.

DNA-Unwinding Dynamics of Escherichia coli UvrD Lacking the C-Terminal 40 Amino Acids.

The E. coli UvrD protein is a nonhexameric DNA helicase that belongs to superfamily I and plays a crucial role in both nucleotide excision repair and methyl-directed mismatch repair. Previous data suggested that wild-type UvrD has optimal activity in its oligomeric form. However, crystal structures of the UvrD-DNA complex were only resolved for monomeric UvrD, using a UvrD mutant lacking the C-terminal 40 amino acids (UvrDΔ40C). However, biochemical findings performed using UvrDΔ40C indicated that this mutant failed to dimerize, although its DNA-unwinding activity was comparable to that of wild-type UvrD. Although the C-terminus plays essential roles in nucleic acid binding for many proteins with helicase and dimerization activities, the exact function of the C-terminus is poorly understood. Thus, to understand the function of the C-terminal amino acids of UvrD, we performed single-molecule direct visualization. Photobleaching of dye-labeled UvrDΔ40C molecules revealed that two or three UvrDΔ40C molecules could bind simultaneously to an 18-bp double-stranded DNA with a 20-nucleotide, 3' single-stranded DNA tail in the absence of ATP. Simultaneous visualization of association/dissociation of the mutant with/from DNA and the DNA-unwinding dynamics of the mutant in the presence of ATP demonstrated that, as with wild-type UvrD, two or three UvrDΔ40C molecules were primarily responsible for DNA unwinding. The determined association/dissociation rate constants for the second bound monomer were ∼2.5-fold larger than that of wild-type UvrD. The involvement of multiple UvrDΔ40C molecules in DNA unwinding was also observed under a physiological salt concentration (200 mM NaCl). These results suggest that multiple UvrDΔ40C molecules, which may form an oligomer, play an active role in DNA unwinding in vivo and that deleting the C-terminal 40 residues altered the interaction of the second UvrD monomer with DNA without affecting the interaction with the first bound UvrD monomer.

Binding of hairpin pyrrole and imidazole polyamides to DNA: relationship between torsion angle and association rate constants.

N-methylpyrrole (Py)-N-methylimidazole (Im) polyamides are small organic molecules that bind to DNA with sequence specificity and can be used as synthetic DNA-binding ligands. In this study, five hairpin eight-ring Py-Im polyamides 1-5 with different number of Im rings were synthesized, and their binding behaviour was investigated with surface plasmon resonance assay. It was found that association rate (k(a)) of the Py-Im polyamides with their target DNA decreased with the number of Im in the Py-Im polyamides. The structures of four-ring Py-Im polyamides derived from density functional theory revealed that the dihedral angle of the Py amide carbonyl is 14∼18°, whereas that of the Im is significantly smaller. As the minor groove of DNA has a helical structure, planar Py-Im polyamides need to change their conformation to fit it upon binding to the minor groove. The data explain that an increase in planarity of Py-Im polyamide induced by the incorporation of Im reduces the association rate of Py-Im polyamides. This fundamental knowledge of the binding of Py-Im polyamides to DNA will facilitate the design of hairpin Py-Im polyamides as synthetic DNA-binding modules.

Single-molecule imaging of the oligomer formation of the nonhexameric Escherichia coli UvrD helicase.

Superfamily I helicases are nonhexameric helicases responsible for the unwinding of nucleic acids. However, whether they unwind DNA in the form of monomers or oligomers remains a controversy. In this study, we addressed this question using direct single-molecule fluorescence visualization of Escherichia coli UvrD, a superfamily I DNA helicase. We performed a photobleaching-step analysis of dye-labeled helicases and determined that the helicase is bound to 18-basepair (bp) double-stranded DNA (dsDNA) with a 3' single-stranded DNA (ssDNA) tail (12, 20, or 40 nt) in a dimeric or trimeric form in the absence of ATP. We also discovered through simultaneous visualization of association/dissociation of the helicase with/from DNA and the DNA unwinding dynamics of the helicase in the presence of ATP that these dimeric and trimeric forms are responsible for the unwinding of DNA. We can therefore propose a new kinetic scheme for the helicase-DNA interaction in which not only a dimeric helicase but also a trimeric helicase can unwind DNA. This is, to our knowledge, the first direct single-molecule nonhexameric helicase quantification study, and it strongly supports a model in which an oligomer is the active form of the helicase, which carries important implications for the DNA unwinding mechanism of all superfamily I helicases.

Real-time background-free selective imaging of fluorescent nanodiamonds in vivo.

Recent developments of imaging techniques have enabled fluorescence microscopy to investigate the localization and dynamics of intracellular substances of interest even at the single-molecule level. However, such sensitive detection is often hampered by autofluorescence arising from endogenous molecules. Those unwanted signals are generally reduced by utilizing differences in either wavelength or fluorescence lifetime; nevertheless, extraction of the signal of interest is often insufficient, particularly for in vivo imaging. Here, we describe a potential method for the selective imaging of nitrogen-vacancy centers (NVCs) in nanodiamonds. This method is based on the property of NVCs that the fluorescence intensity sensitively depends on the ground state spin configuration which can be regulated by electron spin magnetic resonance. Because the NVC fluorescence exhibits neither photobleaching nor photoblinking, this protocol allowed us to conduct long-term tracking of a single nanodiamond in both Caenorhabditis elegans and mice, with excellent imaging contrast even in the presence of strong background autofluorescence.

Quantitative and kinetic single-molecule analysis of DNA unwinding by Escherichia coli UvrD helicase.

Helicases are nucleic acid-unwinding enzymes involved in the maintenance of genome integrity. Helicases share several "helicase motifs" that are highly conserved amino acid sequences and are classified into six superfamilies (SFs). The helicase SFs are further grouped into two classes based on their functional units. One class that includes SFs 3-6 functions as a hexamer that can form a ring around DNA. Another class that includes SFs 1 and 2 functions in a non-hexameric form. The high homology in the primary and tertiary structures among SF1 helicases suggests that SF1 helicases have a common underlying mechanism. However, two opposing models for the functional unit, monomer and dimer models, have been proposed to explain DNA unwinding by SF1 helicases. This paper briefly describes the classification of helicase SFs and discusses the structural homology and the two opposing non-hexameric helicase models of SF1 helicases by focusing on Escherichia coli SF1 helicase UvrD, which plays a significant role in both nucleotide-excision repair and methyl-directed mismatch repair. This paper reviews past and recent studies on UvrD, including the author's single-molecule direct visualization of wild-type UvrD and a UvrD mutant lacking the C-terminal 40 amino acids (UvrDΔ40C), the latter of which was used in genetic and biochemical assays that supported the monomer model. The visualization revealed that multiple UvrDΔ40C molecules jointly unwind DNA, presumably in an oligomeric form, similar to wild-type UvrD. Therefore, single-molecule direct visualization of nucleic acid-binding proteins can provide quantitative and kinetic information to reveal their fundamental mechanisms.

Feasibility study of a LED light irradiation device for the treatment of chronic neck with shoulder muscle pain/stiffness.

Neck with shoulder muscle stiffness/pain is a common disorder. Commonly used physical therapy, pharmacotherapy, acupuncture, and moxibustion only temporarily alleviate the disorder in most cases, thus the disorder often recurs. Low power laser therapy is often used for neck and shoulder stiffness/pain and has been effective in clinical trials. In this study, we evaluated the safety and effectiveness of a newly developed self-care device for disorders including neck with shoulder muscle stiffness/pain. The device incorporates light-emitting diodes (LEDs), which are safer than lasers, as its light source. Ten adults with neck with shoulder muscle stiffness/pain were subject to LED irradiation (wavelength 780 nm ± 15 nm, output 750 mW, power density 3.8 W/cm2, energy density 5.7×102 J/cm2) for 3 minutes on the affected shoulder at a standard acupuncture point (GB21, Jianjing). Immediately after irradiation, the subjective symptoms of the neck with shoulder muscle stiffness and pain evaluated by a visual analog scale were improved from 58.3 mm ± 18.7 mm to 45.5 mm ± 21.5 mm and from 45.8 mm ± 23.3 mm to 39.4 mm ± 21.8 mm, respectively. The symptoms further improved after 15 minutes of irradiation. The skin temperature at the irradiated point increased from 34.3°C ± 1.1°C to 41.0°C ± 0.7°C. The increase in skin temperature was observed within approximately 5 cm of the irradiated area. There was no effect on the heart rate variability, a measure of the autonomic nervous system; however, the baroreflex sensitivity was slightly increased. No irradiation-related adverse skin events were observed. Our LED irradiation device was found to be safe, and it improved the subjective symptoms of muscle stiff neck with shoulders.

Fluorescence microscopy for visualizing single-molecule protein dynamics.

BACKGROUND: Single-molecule fluorescence imaging (smFI) has evolved into a valuable method used in biophysical and biochemical studies as it can observe the real-time behavior of individual protein molecules, enabling understanding of their detailed dynamic features. smFI is also closely related to other state-of-the-art microscopic methods, optics, and nanomaterials in that smFI and these technologies have developed synergistically. SCOPE OF REVIEW: This paper provides an overview of the recently developed single-molecule fluorescence microscopy methods, focusing on critical techniques employed in higher-precision measurements in vitro and fluorescent nanodiamond, an emerging promising fluorophore that will improve single-molecule fluorescence microscopy. MAJOR CONCLUSIONS: smFI will continue to improve regarding the photostability of fluorophores and will develop via combination with other techniques based on nanofabrication, single-molecule manipulation, and so on. GENERAL SIGNIFICANCE: Quantitative, high-resolution single-molecule studies will help establish an understanding of protein dynamics and complex biomolecular systems.

Two-year clinical evaluation of one-step self-etch systems in non-carious cervical lesions.

OBJECTIVES: This randomized controlled clinical trial evaluated the 2-year clinical performance of S3 Bond (S3) and G-Bond (GB) in 108 non-carious cervical lesions. METHODS: Twenty-three patients, 12 male and 11 female (mean age: 61.8 years, range: 30-79 years) regularly visiting the Nagasaki University Hospital of Medicine and Dentistry, participated in the study. Each patient received both materials randomly. All restorations (53 restorations for S3 and 55 restorations for GB) were placed by one dentist. The restorations were blindly evaluated by two examiners at baseline, 6 months, 1 and 2 years using modified USPHS criteria. The data were statistically analyzed using the Cochran Q test and Fisher's exact test. RESULTS: One restoration of each material was lost during 2 years. The only minor clinical problem was the integrity of the enamel margin. Slight marginal staining occurred adjacent to 11 restorations of both S3 and GB. There was no significant difference in the clinical performance between S3 and GB for each variable. CONCLUSIONS: Under the protocol used in this study, S3 and GB have demonstrated an acceptable clinical performance up to 2 years.

A gold nano-electrode for single ion channel recordings.

The artificial bilayer single channel recording technique is commonly used to observe the detailed physiological properties of various ion channel proteins. It permits easy control of the solution and membrane lipid composition, and is also compatible with pharmacological screening devices. However, its use is limited due to low measurement efficiency. Here, we developed a novel artificial bilayer single channel recording technique in which solubilized ion channel proteins immobilized on a gold nano-electrode are directly incorporated into a lipid bilayer at the same time as the bilayer is formed at the tip of it on coming in contact with an aqueous-oil interface. Using this technique, we measured the single channel currents of several types of channels including KcsA, MthK, hBK and P2X4. This technique requires only one action to simultaneously form the bilayers and reconstitute the channels into the membranes. This simplicity greatly increases the measurement efficiency and allows the technique to potentially be combined with high-throughput screening devices.

Dynamic polymorphism of actin as activation mechanism for cell motility.

Actin filament dynamics are crucial in cell motility. Actin filaments, and their bundles, networks, and gels assemble and disassemble spontaneously according to thermodynamic rules. These dynamically changing structures of actin are harnessed for some of its functions in cells. The actin systems respond to external signals, forces, or environments by biasing the fluctuation of actin assembly structures. In this study, dynamic conformation of actin molecules was studied by monitoring conformational dynamics of actin molecules at the single molecule level in real time. Actin conformation spontaneously fluctuates between multiple conformational states. Regarding myosin motility, the dynamic equilibrium of actin conformation was interpreted as between states that activates and inhibits the motility. The binding of myosin to actin filaments activates myosin motility by shifting the conformational fluctuation of actin towards the state that activates the motility. Thus, the activation mechanism based on thermal fluctuation is suggested at molecular level as well as at cellular level.

Five-year clinical evaluation of two adhesive systems in non-carious cervical lesions.

OBJECTIVE: This controlled clinical trial evaluated the 5-year clinical performance of a self-etching primer system including selective enamel-etching with phosphoric acid and a one-bottle adhesive system. METHODS: Seventy-two non-carious cervical lesions in 8 patients (4 male and 4 female) with a mean age of 61.3 years (range 45-78) participated in the study. An enamel bevel was placed and dentin lightly ground, and cavities restored with clearfil liner bond II (LB) or single bond (SB) in conjunction with a hybrid resin composite (Clearfil AP-X). In the case of 27 cavities for LB, the enamel was pretreated with 37% phosphoric acid for 10 s. Each patient received both types of restoration, which were distributed on a random basis. All restorations (37 restorations for LB and 35 restorations for SB) were placed by one dentist. The restorations were evaluated blind after 5 years using modified USPHS criteria. The data were statistically analyzed using the Fisher's exact test. RESULTS: All but one restoration (which was replaced by a crown after the 2-year recall) were evaluated after 5 years. 100% retention rates were recorded for both restorative groups. No caries was detected in association with any restorations. The only minor problem was marginal discoloration; superficial and localized marginal discoloration occurred around 18% of the restorations, and mainly at the dentin margin. There were no significant differences in the marginal integrity between the LB and SB groups. CONCLUSIONS: Restorative materials used in this study demonstrated a good clinical effectiveness in the restoration of non-carious cervical lesions for 5 years.

Effect of a caries-detecting solution on the tensile bond strength of four dentin adhesive systems.

This study investigated the effect of a caries-detecting solution on the tensile bond strength (TBS) to sound bovine dentin--which was either rinsed thoroughly of or contaminated with the caries-detecting solution. Caries Detector (1.0% acid red in propylene glycol) was applied on flat dentin surfaces for 10 seconds, rinsed, and dried with syringe air. In another group, Caries Detector was not rinsed but air-dried. Then, the surfaces were treated with one of the following adhesive systems: Clearfil Protect Bond, Clearfil SE Bond, One-Up Bond F, or Single Bond. Furthermore, an ingredient of Caries Detector, either 1.0% acid red aqueous solution or propylene glycol, was applied to evaluate the effect of each component. In the control groups, Caries Detector was not applied to the dentin surfaces. Finally, a resin composite was light-cured and the TBS measured. Fractured specimens and treated dentin surfaces were observed by SEM. Caries Detector did not reduce the tensile bond strength of any adhesive system (p>0.05) when rinsed thoroughly. On the other hand, when dentin surface was contaminated with Caries Detector, TBS decreased significantly with Clearfil SE Bond and Single Bond. As for the ingredients of Caries Detector, the effect of acid red on TBS was not significant, but that of propylene glycol was significant.

A Simple Method for Ion Channel Recordings Using Fine Gold Electrode.

The artificial bilayer single-channel recording technique is commonly used to observe detailed pharmacological properties of various ion channel proteins. It permits easy control of the solution and membrane lipid composition, and is also compatible with pharmacological screening devices. However, its use is limited due to low measurement efficiency. Here, we develop a novel artificial bilayer single-channel recording technique in which bilayers are made and channels are reconstituted into the membranes by contacting a gold electrode to the lipid-solution interface. Using this technique, we measured the single-channel currents of two channel-forming peptides, gramicidin and alamethicin, and a channel-forming protein, α-hemolysin. This technique requires only one action, allowing the technique to potentially be combined with high-throughput screening devices.

Synergistic effect of ATP for RuvA-RuvB-Holliday junction DNA complex formation.

The Escherichia coli RuvB hexameric ring motor proteins, together with RuvAs, promote branch migration of Holliday junction DNA. Zero mode waveguides (ZMWs) constitute of nanosized holes and enable the visualization of a single fluorescent molecule under micromolar order of the molecules, which is applicable to characterize the formation of RuvA-RuvB-Holliday junction DNA complex. In this study, we used ZMWs and counted the number of RuvBs binding to RuvA-Holliday junction DNA complex. Our data demonstrated that different nucleotide analogs increased the amount of Cy5-RuvBs binding to RuvA-Holliday junction DNA complex in the following order: no nucleotide, ADP, ATPγS, and mixture of ADP and ATPγS. These results suggest that not only ATP binding to RuvB but also ATP hydrolysis by RuvB facilitates a stable RuvA-RuvB-Holliday junction DNA complex formation.

Optically Detected Magnetic Resonance of Nanodiamonds In Vivo; Implementation of Selective Imaging and Fast Sampling.

Single-molecule fluorescence measurements of biological samples frequently suffer from background autofluorescence originating from fluorescent materials pre-existing in living samples, and from unstable photo-physical properties of fluorescent labeling molecules. In this study, we first describe our method of selective imaging of nanodiamonds containing nitrogen-vacancy centers, promising fluorescent color centers, by a combination of optically detected magnetic resonance. The resultant images exhibit perfect elimination of extraneous fluorescence in real-time microscope observations. As the practical example applied to an in vivo system, we measured the resonance spectrum of nanodiamonds introduced into the intestine of Caenorhabditis elegans in the clear background and compared the spectral profile over time. The observed evolution strongly suggests that the rotation of the nanodiamond was detected. We also report our recent progress in the development of a spectrometer equipped with an avalanche photo-diode for fast sampling of photons, which can be used while observing the selective image of a field of view in a real-time manner. This apparatus is suitable for exploring dynamics through the measurement of fluctuation in fluorescence intensity caused by a rotating nanodiamond.

Single-molecule imaging of the dynamic interactions between macromolecules.

In recent years, the development of single-molecule detection techniques has allowed the dynamic properties of biomolecules, which are normally obscured in conventional ensemble measurements, to be measured. One of these single-molecule detection techniques allows the measurement of dissociation and association events of individual molecules to be measured. This technique is based on the unique premise that the mobility between molecules that are bound and the mobility between those that are free in solution are different. The binding of ATP at the beginning and its dissociation at the end of the hydrolysis reaction were detected at the single-molecule level in real time. In this study, we extended this technique to image the dynamic interactions between large biomolecules (protein/protein and protein/polysaccharide). The binding and dissociation of fluorescently labeled macromolecules to partner molecules fixed on a glass surface were visualized by total internal reflection fluorescence microscopy. The dynamic interactions between the proteins in two energy conversion systems, that is, signaling proteins and enzyme molecules moving on dextran, have been measured. In these systems, the dynamic interactions were sensitive to the factors determining the chemical reactions. Thus, the dynamic interactions monitored in the single-molecule measurements provided useful information to further the understanding of the underlying mechanisms of energy conversion systems.

The effect of light-curing modes on the microleakage of cervical resin composite restorations.

OBJECTIVE: This study investigated the effect of light-curing modes on the microleakage of cervical resin composite restorations. METHODS: Eighty wedge-shaped cervical cavities, C-factor approximately 1.3, were prepared on the labial surface of bovine incisors. The cavities were treated with a two-step experimental self-etching primer adhesive system containing an antibacterial monomer (ABF), according to the manufacturer's instructions, and filled with a single increment of a hybrid resin composite. The restorations were allocated randomly into four groups of 20: Group 1-the restorations were light-cured for 40 s with a conventional light-curing unit (New Light VL-II); Group 2-the restorations were cured with Candelux using a two-step mode; Group 3-the restorations were cured with Astralis 7 using a ramping mode; Group 4-the restorations were light-cured for 3 s with a plasma arc light-curing unit (Wave Light). Half of the specimens from each group were subjected to thermocycling (5-60 degrees C, 15 s dwell time, 5000 cycles) prior to immersion in 0.5% basic fuchsin. The teeth were sectioned and the degrees of dye penetration were scored. The data were analyzed with either the Kruskal-Wallis test or the Mann-Whitney U-test (p < 0.05) RESULTS: No significant differences were found in the microleakage scores among the light-curing modes used. The restorations tended to display more microleakage when they were subjected to thermocycling, but the differences were not statistically significant. CONCLUSIONS: These findings suggest that light-curing modes may have no effect on the microleakage of cervical cavities with a small C-factor, as is the case in this study.

Effect of low-viscosity resin-based composite on the microleakage of cervical restorations.

PURPOSE: To investigate the effect of a low-viscosity resin-based composite (LVC) liner on the microleakage of cervical resin-based composites bonded with new adhesive systems. METHODS: 180 wedge-shaped cervical cavities on bovine incisors were treated with AQ Bond (all-in-one), ABF (experimental two-step self-etching primer containing antibacterial monomer) or Clearfil SE Bond (two-step self-etching primer) systems according to the manufacturers' instructions. Half of the treated cavities in each adhesive system were lined with an LVC (Protect Liner F) and filled with a hybrid resin-based composite (Clearfil AP-X). Ten specimens from each group were immersed in 0.5% basic fuchsin solution immediately after finishing the restorations. The specimens to be subjected to thermocycling (5-60 degrees C, 15 seconds dwell time, 5,000 cycles) or to flexural load cycling (approximately 0.5 mm labio-lingual displacement at the incisal edge, 10,000 cycles, 1 Hz) prior to immersion in the dye solution were also prepared. The teeth were sectioned through the center of the restorations and the degrees of dye penetration were scored. The data were analyzed with the Mann-Whitney U-test or the Kruskal-Wallis test (P < 0.05). RESULTS: The use of the LVC liner significantly improved marginal sealing of AQ Bond. However, the LVC liner could not prevent the deterioration in the marginal integrity caused by thermocycling or flexural load cycling. In the case of ABF, the use of the LVC liner showed a trend toward less microleakage. For Clearfil SE Bond, the LVC liner prevented the deterioration in the marginal seal caused by thermocycling.

Microleakage of cervical cavities restored with flowable composites.

PURPOSE: To investigate the microleakage of cervical cavities restored with flowable composites in conjunction with an all-in-one adhesive system (AQ Bond) and an experimental two-step self-etching primer system (ABF) after thermocycling or flexural load cycling. METHODS: 180 wedge-shaped cervical cavities on the labial surfaces of bovine incisors were treated with AQ Bond or ABF according to the manufacturers' instructions. The treated cavities were filled with one of three flowable composites (AElite Flo, Metafil Flo or Protect Liner F). Ten of 30 specimens for each group were immersed in 0.5% basic fuchsin solution immediately after finishing of the restorations. Specimens to be subjected to thermocycling (5-60 degrees C, 15 seconds dwell time, 5000 cycles) or to flexural load cycling (approximately 0.5 mm labio-lingual displacement at the incisal edge, 10,000 cycles, 1 Hz) prior to immersion in the dye were also prepared. After 24-hour storage in the dye solution, the teeth were sectioned longitudinally through the center of the restorations, and the degrees of dye penetration scored. The microleakage scores of a hybrid composite (Clearfil AP-X) obtained from our previous study were used for comparison. The data were analyzed with the Kruskal-Wallis test and the Mann-Whitney U-test (P < 0.05). RESULTS: No significant differences in the microleakage patterns and scores were found among the flowable composites. On the other hand, significant differences in the microleakage patterns and scores were observed between the flowable and the hybrid composites. Thermocycling caused deterioration of marginal integrity, and the flowable composites showed more microleakage than the hybrid composite. In contrast, flexural load cycling did not cause deterioration of the marginal integrity when the cavities were filled with the flowable composites. Statistical analysis also revealed that the adhesive systems played a large role in the microleakage patterns.