Nano Biophotonics (eBook)

Science and Technology

Satoshi Kawata, Hiroshi Masuhara, Fumio Tokunaga (Herausgeber)

eBook Download: PDF | EPUB

2007 | 1. Auflage
444 Seiten
Elsevier Science (Verlag)
978-0-08-047135-8 (ISBN)

Infos

This third volume in the series represents the Proceedings of the 3rd International Nanophotonics Symposium, July 6-8, 2006, Icho-Kaikan, Osaka University, Osaka, Japan. Over a two-day symposium, distinguished scientists from around the world convened to discuss the latest progress in this field and the conclusions have been summarised in Nano Biophotonics: Science and Technology. The contents of this book have been compiled by invited lecturers, research members of the relevant projects/program, and some of general participants. The book has 27 chapters which are classified into 4 parts, nano bio-spectroscopy, nano bio-dynamics, nano bio-processing, and nano bio-devices.

* Bridges the gap between conventional photophysics & photochemistry and nanoscience
* Continuing the series that focuses on 'hot' areas of photochemistry, optics, material science and bioscience

Inhalt

Front Cover 1
Nano Biophotonics 4
Copyright Page 5
Table of Contents 14
Preface 6
Organization of the Symposium 7
Participants list 8
Group Photograph of the Symposium 12
Part I: Nano Bio Spectroscopy 18
Chapter 1: Single molecule nano-bioscience: Fluctuations and adaptive biological molecular machines 20
1. SINGLE MOLECULE IMAGING 21
2. IMAGING MOVEMENT AND CHEMICAL REACTION OF MOLECULAR MOTORS 23
3. SINGLE MOLECULE SPECTROSCOPY AND DYNAMIC STRUCTURES OF BIOMOLECULES 24
4. IMAGING SINGLE MOLECULES IN LIVE CELLS 26
5. Single molecule manipulation and mechanical properties of biomolecules 28
6. NON-PROCESSIVE MYOSIN, MUSCLE MYOSIN 30
7. MECHANISM OF MOLECULAR MOTORS: PROCESSIVE KINESIN MOTOR 32
8. PROCESSIVE MYOSIN MOTOR, MYOSIN V AND VI 35
9. CONCLUSIONS 37
REFERENCES 37
Chapter 2: Alternating laser excitation spectroscopy of freely diffusing single molecule: Applications to bimolecular structure, dynamics and interactions 40
1. INTRODUCTION 40
2. THEORETICAL AND THECHNICAL BACKGROUND 42
3. RESULTS AND DISCUSSION 48
4. SUMMERY 58
ACKNOWLEDGEMENTS 58
REFERENCES 58
Chapter 3: Linear and non-linear Raman microspectroscopy and imaging of single living cells: Visualization of life and death at the cellular level 60
1. INTRODUCTION 60
2. IN VIVO REAL-TIME PURSUIT OF THE CELL ACTIVITY OF SINGLE LIVING FISSION YEAST CELLS BY TIME- AND SPACE-RESOLVED RAMAN MICROSPECTROSCOPY 61
3. IN VIVO TIME-RESOLVED RAMAN IMAGING OF A SPONTANEOUS DEATH PROCESS OF A SINGLE BUDDING YEAST CELL 65
4. NON-LINEAR RAMAN MICROSPECTROSCOPY AND IMAGING OF SINGLE LIVING CELLS 67
5. CONCLUSIONS 72
ACKNOWLEDGEMENTS 72
REFERENCES 72
Chapter 4: Raman, CARS and near-field Raman-CARS microscopy for cellular and molecular imaging 74
1. INTRODUCTION 74
2. SLIT-SCANNING RAMAN MICROSCOPY FOR CELLULAR IMAGING 75
3. TIP-ENHANCED RAMAN SPECTROSCOPY 77
3. TERS ANALYSIS OF DNA-BASED ADENINE MOLECULES 78
4. TIP ENHANCED NONLINEAR OPTICAL SPECTROSCOPY 81
REFERENCES 87
Chapter 5: Enhanced photothermal spectroscopy for observing chemical reactions in biological cells 90
1. SENSITIVE DETECTION OF NONFLUORESCENT BIOMOLECULES 90
2. PHOTOTHERMAL SIGNAL ENHANCEMENT 92
3. ULTRAVIOLET-EXCITATION MICROSCOPIC THERMAL LENS MEASUREMENTS 96
4. MICROSCOPIC THERMAL LENS MEASUREMENTS WITH A MODE-LOCKED LASER 102
5. SUMMARY 107
ACKNOWLEGEMENTS 107
REFERENCES 107
Chapter 6: Probing conformational dynamics in biopolymers by contact-induced fluorescence quenching 110
1. INTRODUCTION 110
2. SELECTIVE FLUORESCENCE QUENCHING OF ORGANIC FLUOROPHORES BY PHOTOINDUCED ELECTRON TRANSFER REACTIONS 111
3. MONITORING POLYMER DYNAMICS USING PET-PROBES 116
4. MONITORING PROTEIN FOLDING USING PET-PROBES 120
5. DESIGN AND DIAGNOSTIC APPLICATIONS OF PET-PROBES 122
6. CONCLUSION AND OUTLOOK 128
REFERENCES 129
Chapter 7: Second harmonic generation imaging microscopy of fibrillar structures 132
1. INTRODUCTION 132
2. EXPERIMENTAL METHODS 134
3. RESULTS AND DISCUSSION 135
4. SUMMARY 146
ACKOWLEDGMENT 146
REFERENCES 146
Part II: Nano Bio Dynamics 148
Chapter 8: Imaging of enzyme catalysis by wide field microscopy 150
ABSTRACT 150
1. INTRODUCTION 150
2. EXPERIMENTAL SECTION 152
3. RESULTS AND DISCUSSION 153
4. CONCLUSIONS 157
ACKNOWLEDGMENTS 157
REFERENCES 158
Chapter 9: Interferometric detection and tracking of nanoparticles 160
1. INTRODUCTION 160
2. DETECTION OF GOLD NANOPARTICLES 162
3. DETECTION OF DIELECTRIC OBJECTS 171
4. TRACKING OF GOLD NANOPARTICLES 172
5. CONCLUSION 174
ACKNOWLEDGEMENT 174
REFERENCES 175
Chapter 10: Interaction between metal-free porphine and surface Ag atoms through temporal fluctuation of surface-enhanced resonance Raman scattering 178
1. INTRODUCTION 178
2. EXPERIMENTAL 180
3. RESULTS 180
4. DISCUSSION 185
5. CONCLUSIONS 189
ACKNOWLEDGMENTS 190
REFERENCES 190
Chapter 11: General importance of anomalous diffusion in biological inhomogeneous systems 192
1. INTRODUCTION 192
2. GENERAL DESCRIPTION OF ANOMALOUS DIFFUSION 193
3. RELATIONSHIP OF THE OBSERVED DIFFUSION COEFFICIENT (DOBS) WITH THE SAMPLING FUNCTIONS OF EACH EXPERIMENTAL METHOD 196
4. DIFFERENTIATION OF MSD AND ANOMALOUS DIFFUSION COEFFICIENT 198
5. EXAMPLES OF DIFFUSIOMETRY FOR INHOMOGENEOUS SYSTEM WITH ANOMALOUS DIFFUSION 199
6. GENERAL IMPORTANCE OF ANOMALOUS DIFFUSION IN MATERIAL TRANSPORTS IN EXTRACELLULAR MATRICES (ECM) 202
7. CONCLUSIONS 204
ACKNOWLEDGEMENTS 204
REFERENCES 204
Chapter 12: Two-color picosecond time-resolved infrared super-resolution microscopy 206
1. INTRODUCTION 206
2. EXPERIMENTAL 208
3. RESULTS AND DISCUSSION 210
4. CONCLUSION 211
ACKNOWLEDGMENT 212
REFERENCES 212
Chapter 13: Molecular motion under the trapping potential of optical tweezers 214
1. INTRODUCTION 214
2. EXPERIMENTAL 215
3. DATA ANALYSIS OF FLUORESCENCE CORRELATION SIGNALS 216
4. EFFECT OF NEAR INFRARED LASER IRRADIATION ON TRANSLATIONAL MOTION OF MOLECULES IN SOLUTION 219
5. SUMMARY 221
ACKNOWLEDGMENT 222
REFERENCES 222
Chapter 14: Nanoscale fluid motion via molecular pores and polymer actuators 224
1. ABSTRACT 224
2. INTRODUCTION 225
3. METHODS 226
4. RESULTS 230
5. DISCUSSION 236
ACKNOWLEGEMENTS 239
REFERENCES 239
Part III: Nano Bio Processing 242
Chapter 15 Femtosecond nonlinear processing in solution: From crystallization to manipulation and patterning 244
1. INTRODUCTION 244
2. CRYSTAL GROWTH TRIGGERED BY FEMTOSECOND LASER ABLATION 245
3. FEMTOSECOND LASER-INDUCED CRYSTALLIZATION OF PROTEINS AND MOLECULES 247
4. MANIPULATION OF SINGLE BEADS BY FEMTOSECOND LASER-INDUCED BUBBLING 250
5. PATTERNING OF PROTEIN CUBES AND BIO CELLS IN SOLUTION BY FEMTOSECOND LASER-INDUCED SHOCKWAVE AND BUBBLING 252
6. FEMTOSECOND LASER-INDUCED INJECTION OF NANO PARTICLES INTO SINGLE BIO CELLS 254
7. FEMTOSECOND NONLINEAR PROCESSES AND MECHANICAL EFFECTS 256
ACKNOWLEDGEMENTS 259
REFERENCES 259
Chapter 16: Single living cell processing in water medium using focused femtosecond laser-induced shockwave and cavitation bubble 262
1. INTRODUCTION 262
2. SAMPLE AND MICROSCOPE 263
3. SHOCKWAVE AND CAVITATION BUBBLE GENERATION PROCESSES 264
4. MOTIONS OF SINGLE ANIMAL CELL CULTURED ON A SUBSTRATE 265
5. REGENERATION PROCESS OF CELL MONITORED BY TOTAL INTERNAL REFLECTION FLUORESCENECE IMAGING 267
6. DIRECT CUTTING OF SINGLE ACTIN STRESS FIBRE 269
7. CONCLUSION 270
ACKNOWLEDGEMENTS 271
REFERENCES 271
Chapter 17: Subcellular effects of femtosecond laser irradiation 272
1. INTRODUCTION 272
2. CELL-LEVEL EFFECTS INDUCED BY LASER IRRADIATION 274
3. CONCLUSION 288
REFERENCES 288
Chapter 18 Femtosecond laser nanosurgery of biological cells and tissues 290
1. INTRODUCTION 290
2. PLASMA FORMATION 290
3. IRRADIANCE AND FREE ELECTRON DISTRIBUTION WITHIN THE FOCAL VOLUME 291
4. CHEMICAL EFFECTS OF LOW-DENSITY PLASMAS 292
5. THERMAL EFFECTS 293
6. THERMOELASTIC STRESS EVOLUTION 295
7. BUBBLE FORMATION 296
8. EXPERIMENTAL DETERMINATION OF BREAKDOWN THRESHOLD AND BUBBLE SIZE 299
9. IMPLICATIONS FOR LASER EFFECTS ON CELLS AND TISSUES 302
REFERENCES 303
Chapter 19: Femtosecond laser nanomachining of silicon wafers and two-photon nanolithography for stem cell research 304
1. INTRODUCTION 304
2. MATERIALS AND METHODS 305
3. RESULTS 308
4. CONCLUSIONS 310
ACKNOWLEDGEMENTS 313
REFERENCES 313
Chapter 20: Gold nanorods: application to bioscience and medicine 314
1. INTRODUCTION OF GOLD NANORODS 314
2. BIOCOMPARTIBLE GOLD NANORODS 318
3. BIODISTRIBUTION OF GOLD NANORODS 322
4. CONCLUSION 323
REFERENCES 323
Part IV: Nano Bio Devices 326
Chapter 21: Protein modules: Functional proteins incorporated in viral polyhedra 328
1. INTRODUCTION 328
2. EXPERIMENTAL 331
3. IMMOBILIZATION OF EGFP AND CDMP1 PROTEINS 334
4. EVALUATION OF PROTEINS IN POLYHEDRA BY TIME-RESOLVED FLUORESCENCE 336
5. CONCLUDING REMARKS 339
ACKNOWLEDGEMENT 340
REFERENCES 340
Chapter 22: Immobilization of protein molecules into insect viral occlusion body and its application 342
1. CYTOPLASMIC POLYHEDROSIS VIRUS 342
2. IMMOBILIZATION OF PROTEIN MOLECULES INTO POLYHEDRA 344
3. PROTEIN MICROARRAYS 345
4. SCAFFOLD FOR CELL PROLIFERATION 346
REFERENCES 348
Chapter 23: All-optical switching in rhodopsin proteins 350
1. INTRODUCTION 350
2. THEORETICAL MODEL 354
3. ALL-OPTICAL SWITCHING WITH CW PUMP BEAMS 356
4. ALL-OPTICAL SWITCHING WITH PULSED PUMP BEAM 360
CONCLUSION 367
REFERENCES 370
Chapter 24: A photoisomerization study on photoactive yellow protein model chromophores from solution to crystalline phases 374
1. INTRODUCTION 374
2. PYP MODEL CHROMOPHORES 376
3. DENATURED PYP 381
4. PHOTOISOMERIZATION OF PCT IN CRYSTALLINE STATE 382
5. CONCLUSION AND PERSPECTIVE 386
ACKNOWLEDGEMENTS 387
REFERENCES 387
Chapter 25: Defect mode and laser action in cholesteric liquid crystal 390
1. INTRODUCTION 390
2. PHOTONIC BAND GAP AND BAND EDGE LASING IN CHOLESTERIC LIQUID CRYSTAL 392
3. TWIST DEFECT MODE IN CHOLESTERIC LIQUID CRYSTAL 394
4. CHIRAL DEFECT MODE INDUCED BY PARTIAL DEFORMATION OF HELIX 396
5. TUNABLE DEFECT MODE LASING IN A PERIODIC STRUCTURE CONTAINING LC LAYER AS A DEFECT 397
6. SUMMARY 401
ACKNOWLEDGEMENTS 402
REFERENCES 402
Chapter 26: Integrated photonic devices using semiconductor quantum-well structures 404
1. INTRODUCTION 404
2. AREA-SELECTIVE QUANTUM-WELL DISORDERING 405
3. GRATING COMPONENTS FOR SEMICONDUCTOR INTEGRATED PHOTONIC DEVICES 407
4. DBR LASERS USING CURVED SURFACE GRATING 410
5. MONOLITHIC MOPA WITH INTEGRATED OUTCOUPLER 415
6. TUNABLE EXTENDED-CAVITY LASER 420
7. GRATING-COUPLED SURFACE-EMITTING LASER 423
8. CONCLUSION 425
REFERENCES 425
Chapter 27: Process control and new developments in crystal growth from solution: oxide, organic, protein and nitride 428
1. INTRODUCTION 428
2. GROWTH OF HIGH QUALITY CSLIB6O10 CRYSTAL 429
3. GROWTH OF HIGH QUALITY PROTEIN CRYSTALS 431
4. NA FLUX LPE GROWTH OF BULK GAN CRYSTAL 437
5. CONCLUSIONS 440
ACKNOWLEDGMENTS 441
REFERENCES 441
Author Index 444

Textauszug

Chapter 1

Single molecule nano-bioscience: Fluctuations and adaptive biological molecular machines

Toshio Yanagida1,2; Jun Kozuka1,2; Takuya Okada1,2; Yuichi Taniguchi1,2; Mitsuhiro Iwaki1,2; Yoshiharu Ishii1    1 Soft nano-machine Project, CREST, JST
2 Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871 Japan

Biomolecules assemble to form molecular machines such as molecular motors, cell signal processors, DNA transcription processors and protein synthesizers. The molecular machines react and behave in response to their surroundings with great flexibility. This flexibility is essential for biological organisms and biological systems. The underlying mechanism of molecular machines is not as simple as that expected from an analogy with man-made machines. Given that molecular machines are only nanometers in size and have a flexible structure, they are very prone to thermal agitation. In addition, the input energy level is not much different from average thermal energy level, kBT. Molecular machines can use this thermal noise with a high efficiency of energy conversion for their functions. This is sharp contrast to man-made machines that operate at energies much higher than thermal noise.

In recent years, single molecule detection techniques have attracted great deal of attention in the field of life science [1,2]. Observing and manipulating biomolecules allows their dynamic behaviors to be directly revealed as has been demonstrated for motor proteins. Reactions of biological molecules are generally stochastic. Therefore in ensemble measurements, dynamic behaviors of individual molecules are averaged and hidden. In biosystems such as live cells, biomolecules work in complicated heterogeneous systems, involving various types of molecules. It is difficult to qualitatively detect dynamic behaviors of proteins of interest in such systems using ensemble averaged measurements. The single molecule detection techniques are expected to overcome these difficulties and have already been successfully applied to study the dynamic properties of biological molecules such as motor proteins, enzymes, RNA polymerase and cell signaling proteins. The dynamic behavior of biomolecules revealed using single molecule detection techniques will be a breakthrough for understanding the mechanism of function of biomolecules.

1 SINGLE MOLECULE IMAGING

The single molecule detection techniques are based on the two key techniques of single molecule imaging and single molecule manipulation. Light microscopy is a method that allows us to image biomolecules as they work in an active manner in biomolecular assemblies and cells. To visualize single molecules of nanometer size, fluorescent probes must be attached. In order to visualize faint fluorescence from single molecules, it is critical to increase S/N ratio by reducing the background. Local illumination is used to reduce the background noises contributed from fluorescent molecules in solution. We have developed total internal reflection fluorescence (TIRF) microscopy, in which only surface between solution and slide glass is illuminated (Figure 1A)[3]. The TIRF microscopy is advantageous for observation of behavior of biomolecules; that is, movement of individual molecules on the glass surface and the changes occurred in molecules immobilized on the glass surface are allowed to be visualized.

Fig. 1 Total internal reflection microscopy and single molecule imaging. (A) Evanescent field is generated near the surface between glass and water when a laser is total internally reflected. Individual spots arise from single fluorescence molecules attached to protein myosin. (B) Time trajectory of fluorescence intensity from single molecules. Arrow indicates photobleaching. The fluorescence intensity drops to a base line all of sudden. (C) Fluorescence intensity profile of a single spot in one-dimension. The fluorescence intensity distribute over a range of the wavelength of light. (D) Visualization of movement of single molecular motors myosin on actin filaments immobilized on the glass surface. The movement of single myosin molecules can be detected as movement of fluorescence spots. (E) Visualization of the turnover of the hydrolysis of ATP by detecting the association of Cy3-ATP and dissociation of Cy3-ADP. The turnover is seen as fluorescence turn-on and off at the position of myosin immobilized on the glass surface.

Fluorescence from single molecules is imaged as spots. Fluorescence signals are accumulation of photons emitted from single fluorescent molecules. Since photon detection is stochastic, the fluorescence intensity (total number of photons emitted) fluctuates. After emission of large number of photons, fluorescent molecules cease to emit photons all of sudden and do not emit them again (Figure 1B). This photobleaching is explained by irreversible photochemical reaction of the molecules. The number of photons that single molecules emit until the photobleaching characterizes the fluorophores. In the case of TMR or Cy3 which is used for single molecule measurements, the photobleaching occurs after a molecule emits approximately 100 thousand to 1 million photons. The sudden drop of the fluorescence due to the photobleaching is characteristic of single molecules and this is utilized as a test on whether the fluorescence spots observed come from single molecules or more. Fluorescent spots from single molecules of the order of nm in size spread to several hundreds nm due to diffraction of light (Figure 1C). It would be possible that several molecules exist in a small area 100 nm × 100 nm and that several molecules form an aggregate. It is difficult to distinguish overlapped spots in the images. From the observation of the photobleaching process it is possible to discriminate individual spots from an overlapped spot. The fluorescence from a single fluorophore drops in a single step and two molecules in two steps. Together with the fluorescence intensity, the number of fluorescent

A single molecule fluorescence imaging microscope, which was first built based on an inverted microscope was prism type [3]. Epi- and prism type TIRF microscopy were switched by moving a mirror. For TIRF microscopy, a 60° dispersion prism was placed on a quartz slide glass with a gap filled with fluorescence–less pure glycerol. Incident angle was adjusted in order for incident beam to be totally internally reflected on the interface between the slide glass and buffer solution. Objective lens type TIRF microscopy is a method to generate evanescent field using an objective lens with large numerical aperture (NA) instead of a prism [4]. Epi- and TIRF fluorescence microscopy can be switched by shifting the position of the laser between the edge and center of the objective lens by moving the mirror. The illumination area does not change while the illumination method changes. The objective type TIRF microscopy allows us to change sample without changing the optical system. Also it provides large free space above the specimen where the prism is placed for a prism type TIRF microscope. It enables us to do other operations such as laser trap experiments at the same time [5]. Another advantage is the thickness between slide glass and cover glass. For objective TIRF microscopy, the illumination and detection is done on the same side, whereas, for prism type TIRF microscopy, the evanescent field is generated on the other side of the detection. The thickness of the specimens is limited for prism type TIRF microscopy. Thick sample space allows us to place bulky specimen such as cells [6].

2 IMAGING MOVEMENT AND CHEMICAL REACTION OF MOLECULAR MOTORS

The movement of molecular motors is visualized by tracing the position of fluorescently labeled protein molecules on the counterparts immobilized on the glass surface (Figure 1D). The movement of linear motors such as kinesin and unconventional myosin has been detected using fluorescently labeled or GFP tagged molecules [7]. The fluorescent spots arisen from single kinesin molecules move along fluorescent lines of microtubules immobilized on the surface in the presence of ATP. Kinesin moves processively or for long distance without dissociation. Unconventional myosin V and VI are also processive motors along actin filaments but the direction of the movement is opposite. The movement of both kinesin and unconventional myosin appears smooth with essentially constant velocity of several μm/sec. However, the movement no longer appears smooth when the spatial resolution is improved to a few nm. The stepwise movements of kinesin and unconventional myosin V and VI are clearly observed in the imaging under the condition where the movement is very slow at low concentration of ATP [8].

In addition to active movement, diffusive movement of molecular motors has been observed. In contrast to the stepwise movement of double-headed kinesin, single-headed kinesin such as unconventional KIF1A exhibits Brownian movement on microtubules in the presence of ATP [9]. Unconventional KIF1A is a naturally single headed motor protein in the kinesin family. The additional electrostatic interaction with microtubules is thought to prevent dissociation of kinesin from microtubules during movement. Similar Brownian movement of single headed kinesin has been reported using truncated conventional kinesin [10]. In...

Produkt-Details

• Erscheint lt. Verlag: 16.2.2007
• Sprache: englisch
• Themenwelt: Naturwissenschaften ► Chemie ► Analytische Chemie
• Themenwelt: Naturwissenschaften ► Chemie ► Physikalische Chemie
• Themenwelt: Naturwissenschaften ► Physik / Astronomie ► Angewandte Physik
• Themenwelt: Technik
• ISBN-10: 0-08-047135-8 / 0080471358
• ISBN-13: 978-0-08-047135-8 / 9780080471358