Optical Tweezers for Single Molecule Biology

Molecular machinery on the micro-scale, believed to be the fundamental building blocks of life, involve forces of 1-100 pN and movements of nanometers to micrometers. Micromechanical single-molecule experiments seek to understand the physics of nucleic acids, molecular motors, and other biological systems through direct measurement of forces and displacements. Optical tweezers are a popular choice among several complementary techniques for sensitive force-spectroscopy in the field of single molecule biology. The main objective of this thesis was to design and construct an optical tweezers instrument capable of investigating the physics of molecular motors and mechanisms of protein/nucleic-acid interactions on the single-molecule level. A double-trap optical tweezers instrument incorporating acousto-optic trap-steering, two independent detection channels, and a real-time digital controller was built. A numerical simulation and a theoretical study was performed to assess the signal-to-noise ratio in a constant-force molecular motor stepping experiment. Real-time feedback control of optical tweezers was explored in three studies. Position-clamping was implemented and compared to theoretical models using both proportional and predictive control. A force-clamp was implemented and tested with a DNA-tether in presence of the enzyme lambda exonuclease. The results of the study indicate that the presented models describing signal-to-noise ratio in constant-force experiments and feedback control experiments in optical tweezers agree well with experimental data. The effective trap stiffness can be increased by an order of magnitude using the presented position-clamping method. The force-clamp can be used for constant-force experiments, and the results from a proof-of-principle experiment, in which the enzyme lambda exonuclease converts double-stranded DNA to single-stranded DNA, agree with previous research. The main objective of the thesis was thus achieved. The developed instrument and presented results on feedback control serve as a stepping stone for future contributions to the growing field of single molecule biology.

Studies on follicular growth in the immature rat and hamster: Effect of a single injection of gonadotropin or estrogen on the rate of3H-thymidine incorporation into ovarian DNAin vitro

Initiation of follicular growth by specific hormonal stimuli in ovaries of immature rats and hamsters was studied by determining the rate of incorporation of3H-thymidine into ovarian DNAin vitro. Incorporation was considered as an index of DNA synthesis and cell multiplication. A single injection of pregnant mare serum gonadotropin could thus maximally stimulate by 18 hr3H-thymidine incorporation into DNA of the ovary of immature hamsters. Neutralization of pregnant mare serum gonadotropin by an antiserum to ovine follicle stimulating hormone only during the initial 8–10 hr and not later could inhibit the increase in3H-thymidine incorporationin vitro observed at 18 hr, suggesting that the continued presence of gonadotropin stimulus was not necessary for this response. The other indices of follicular growth monitored such as ovarian weight, serum estradiol and uterine weight showed discernible increase at periods only after the above initial event. A single injection of estrogen (diethyl stilbesterol or estradiol-l7β) could similarly cause 18 hr later, a stimulation in the rate of incorporation of3H-thymidine into DNAin vitro in ovaries of immature rats. The presence of endogenous gonadotropins, however, was obligatory for observing this response to estrogen. Evidence in support of the above was two-fold: (i) administration of antiserum to follicle stimulating hormone or luteinizing hormone along with estrogen completely inhibited the increase in3H-thymidine incorporation into ovarian DNAin vitro; (ii) a radioimmunological measurement revealed following estrogen treatment, the presence of a higher concentration of endogenous follicle stimulating hormone in the ovary. Finally, administration of varying doses of ovine follicle stimulating hormone along with a constant dose of estrogen to immature rats produced a dose-dependent increment in the incorporation of3H-thymidine into ovarian DNAin vitro. These observations suggested the potentiality of this system for developing a sensitive bioassay for follicle stimulating hormone.

Physico-chemical properties of pure and x-ray irradiated single crystals of KAP

Single crystals of potassium hydrogen phthalate (KAP) have been grown by slow evaporation method from aqueous solutions. Thermal analyses indicate that KAP crystals decompose into phthalic anhydride and KOH around 520 K. Electrical properties of single crystals of KAP have been studied along with the effect of X-ray irradiation of the crystals. The electrical transport appears to be associated with tunneling of protons. The irradiated crystal exhibits lower dielectric constant and higher ac conductivity.

The effects of organic environmental toxicants on hard tissue formation in developing tooth : An in vitro study in mice

Dioxins are organic toxicants that are known to impair tooth development, especially dental hard tissue formation. The most toxic dioxin congener is 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Further, clinical studies suggest that maternal smoking during pregnancy can affect child s tooth development. One of the main components of tobacco smoke is the group of non-halogenated polycyclic aromatic hydrocarbons (PAHs), a representative of which is 7,12-dimethylbenz[a]anthracene (DMBA). Tributyltin (TBT), an organic tin compound, has been shown to impair bone mineralization in experimental animals. In addition to exposure to organic toxicants, a well-established cause for enamel hypomineralization is excess fluoride intake. The principal aim of this thesis project was to examine in vitro if, in addition to dioxins, other organic environmental toxicants, like PAHs and organic tin compounds, have adverse effects on tooth development, specifically on formation and mineralization of the major dental hard tissues, the dentin and the enamel. The second aim was to investigate in vitro if fluoride could intensify the manifestation of the detrimental developmental dental effects elicited by TCDD. The study was conducted by culturing mandibular first and second molar tooth germs of E18 NMRI mouse embryos in a Trowell-type organ culture and exposing them to DMBA, TBT, and sodium fluoride (NaF) and/or TCDD at various concentrations during the secretory and mineralization stages of development. Specific methods used were HE-staining for studying cell and tissue morphology, BrdU-staining for cell proliferation, TUNEL-staining for apoptosis, and QPCR, in situ hybridization and immunohistochemistry for the expressions of selected genes associated with mineralization. This thesis work showed that DMBA, TBT, TCDD and NaF interfere with dentin and enamel formation of embryonic mouse tooth in vitro, and that fluoride can potentiate the harmful effect of TCDD. The results suggested that adverse effects of TBT involve altered expression of genes associated with mineralization, and that DMBA and TBT as well as NaF and TCDD together primarily affect dentin mineralization. Since amelogenesis does not start until mineralization of dentin begins, impaired enamel matrix secretion could be a secondary effect. Dioxins, PAHs and organotins are all liposoluble and can be transferred to the infant by breast-feeding. Since doses are usually very low, developmental toxicity on most of the organs is difficult to indentify clinically. However, tooth may act as an indicator of exposure, since the major dental hard tissues, the dentin and the enamel, are not replaced once they have been formed. Thus, disturbed dental hard tissue formation raises the question of more extensive developmental toxicity.

Design of Single-Input-Single-Output Compliant Mechanisms for Practical Applications Using Selection Maps

We present an interactive map-based technique for designing single-input-single-output compliant mechanisms that meet the requirements of practical applications. Our map juxtaposes user-specifications with the attributes of real compliant mechanisms stored in a database so that not only the practical feasibility of the specifications can be discerned quickly but also modifications can be done interactively to the existing compliant mechanisms. The practical utility of the method presented here exceeds that of shape and size optimizations because it accounts for manufacturing considerations, stress limits, and material selection. The premise for the method is the spring-leverage (SL) model, which characterizes the kinematic and elastostatic behavior of compliant mechanisms with only three SL constants. The user-specifications are met interactively using the beam-based 2D models of compliant mechanisms by changing their attributes such as: (i) overall size in two planar orthogonal directions, separately and together, (ii) uniform resizing of the in-plane widths of all the beam elements, (iii) uniform resizing of the out-of-plane thick-nesses of the beam elements, and (iv) the material. We present a design software program with a graphical user interface for interactive design. A case-study that describes the design procedure in detail is also presented while additional case-studies are posted on a website. DOI:10.1115/1.4001877].

X-ray diffraction from single Al6CuLi3 grains showing five-fold symmetry

We present here the detailed results of X-ray diffraction from single quasicrystals of Al6CuLi3. X-ray precession photographs taken down the two-, three- and five-fold axes along with rotation and zero-level Weissenberg photographs are shown. Preliminary analysis of the diffraction data rules out the twin hypothesis.

Ionic conductivity and dielectric measurements in single crystal β---AgI

Ionic conductivity measurements have been made on pure, copper-doped and cadmium-doped single crystals. Dielectric measurements in the frequency range 30Hz–100Hz showed that there was no anomalously to be (0.64 ± 0.02) eV and migration energies for silver ion intersitials and vacancies in the c direction to be (0.41 ± 0.02) eV and (0.50 ± 0.02) eV respectively. ESR measurements have shown that copper exists as Cu+ in these crystals. Dielectric measurements in the frequency range (OHz–100KHz showed that there was no anomalously high value for ε as reported earlier.

Synthesis and characterization of metal substituted AlxCr1-x(acetylacetonate)(3) single-source precursors for their application to MOCVD of thin films

A detailed study, involving the synthesis of a single-source precursor containing two metal ions sharing the same crystallographic site, has been undertaken to elucidate the use of such a single-source precursor in a CVD process for growing thin films of oxides comprising these two metals, ensuring a uniform composition and distribution of metal ions. The substituted complexes Cr1-xAlx(acac)(3), where acac = acetyl-acetonate, have been prepared by a co-synthesis method, and characterized using UV-Vis spectroscopy. TGA/DTA measurements, and single crystal X-ray diffraction at low temperature. All the studied compositions crystallize in the monoclinic space group P2(1)/c with Z = 4 in the unit cell. It was observed that the ratio (Al:Cr) of the site occupancy for the metal ions, obtained from single crystal refinement, is in agreement with the results obtained from complexometric titrations. All the solid state structures have the metal in an octahedral environment forming six-membered chelate rings. M-O acac bond lengths and disorder in the terminal carbon have been studied in detail for these substituted metal-organic complexes. One composition among these was chosen to evaluate their suitability as a single-source precursor in a LPMOCVD process (low-pressure metal-organic chemical vapour deposition) for the deposition of a substituted binary metal oxide thin film. The resulting thin films were characterized by X-ray diffraction, scanning electron microscopy, and infrared spectroscopy. (C) 2010 Elsevier Ltd. All rights reserved.

Impact of energy quantisation in single electron transistor island on hybrid complementary metal oxide semiconductor-single electron transistor integrated circuits

For the first time, the impact of energy quantisation in single electron transistor (SET) island on the performance of hybrid complementary metal oxide semiconductor (CMOS)-SET transistor circuits has been studied. It has been shown through simple analytical models that energy quantisation primarily increases the Coulomb Blockade area and Coulomb Blockade oscillation periodicity of the SET device and thus influences the performance of hybrid CMOS-SET circuits. A novel computer aided design (CAD) framework has been developed for hybrid CMOS-SET co-simulation, which uses Monte Carlo (MC) simulator for SET devices along with conventional SPICE for metal oxide semiconductor devices. Using this co-simulation framework, the effects of energy quantisation have been studied for some hybrid circuits, namely, SETMOS, multiband voltage filter and multiple valued logic circuits. Although energy quantisation immensely deteriorates the performance of the hybrid circuits, it has been shown that the performance degradation because of energy quantisation can be compensated by properly tuning the bias current of the current-biased SET devices within the hybrid CMOS-SET circuits. Although this study is primarily done by exhaustive MC simulation, effort has also been put to develop first-order compact model for SET that includes energy quantisation effects. Finally, it has been demonstrated that one can predict the SET behaviour under energy quantisation with reasonable accuracy by slightly modifying the existing SET compact models that are valid for metallic devices having continuous energy states.

Disorder-driven electronic localization and phase separation in superconducting Fe1+yTe0.5Se0.5 single crystals

We have investigated the influence of Fe excess on the electrical transport and magnetism of Fe1+yTe0.5Se0.5 (y=0.04 and 0.09) single crystals. Both compositions exhibit resistively determined superconducting transitions (T-c) with an onset temperature of about 15 K. From the width of the superconducting transition and the magnitude of the lower critical field H-c1, it is inferred that excess of Fe suppresses superconductivity. The linear and nonlinear responses of the ac susceptibility show that the superconducting state for these compositions is inhomogeneous. A possible origin of this phase separation is a magnetic coupling between Fe excess occupying interstitial sites in the chalcogen planes and those in the Fe-square lattice. The temperature derivative of the resistivity d(rho)/d(T) in the temperature range T-c < T < T-a with T-a being the temperature of a magnetic anomaly, changes from positive to negative with increasing Fe. A log 1/T divergence of the resistivity above T-c in the sample with higher amount of Fe suggests a disorder-driven electronic localization.

X-ray and molecular-dynamics studies on Mycobacterium leprae single-stranded DNA-binding protein and comparison with other eubacterial SSB structures

The crystal structures of two forms of Mycobacterium leprae single-stranded DNA-binding protein (SSB) have been determined at 2.05 and 2.8 A resolution. Comparison of these structures with the structures of other eubacterial SSBs indicates considerable variation in their quaternary association, although the DNA-binding domains in all of them exhibit the same OB-fold. This variation has no linear correlation with sequence variation, but could be related to variation in protein stability. Molecular-dynamics simulations have been carried out on tetrameric molecules derived from the two forms and the prototype Escherichia coli SSB and the individual subunits of both proteins. Together, the X-ray studies and molecular-dynamics simulations yield information on the relatively rigid and flexible regions of the molecule and on the effect of oligomerization on flexibility. The simulations provide insight into the changes in subunit structure on oligomerization. They also provide insight into the stability and time evolution of the hydrogen bonds/water bridges that connect the two pairs of monomers in the tetramer.

A nonhelical, multiple β-turn conformation in a glycine-rich heptapeptide fragment of trichogin A IV containing a single central α-aminoisobutyric acid residue

The conformational properties of the protected seven-residue C-terminal fragment the lipopeptaibol antibiotic Trichogin A IV (Boc-Gly-Gly-Leu-Aib-Gly-Ile-Leu-OMe) has been examined in CDCl3 and (CD3)2SO by 1H-nmr. Evidence for a multiple β-turn conformation [type I′ at Gly(1)-Gly(2), type II at Leu(3)-Aib(4), and a type I′ at Aib(4)-Gly(5)] suggests that Leu(3) has preferred an extended or semiextended conformation over a helical conformation in CDCl3. This structure is thus in contrast to earlier observations of seven-residue peptides containing a single central Aib preferring helical conformations in both solution and crystalline slates. A structural transition to a frayed right-handed helix is absented in (CD3)2SO. These results suggest that nonhelical conformations may be important in Gly-rich peptides containing Aib. Further, the presence of amino acids with contradictory influences on backbone conformational freedom can lead to well-defined conformational transitions even in small peptides