STUDY OF RNA-MEDIATED FLUORESCING COLLOIDAL CdSe NANOSTRUCTURES – ENHANCED PHOTOPHYSICS AND MORPHOLOGICAL TRANSFORMATION INDUCED BY CONFORMATIONAL CHANGE IN RNA

Abstract

Over the last three decades there has been a formidable growth in the areas of nanoscience and nanotechnology. An understanding and progress in these fields have merged different scientific and technological disciplines boosting interdisciplinary research for designing advanced/smart materials. There are two approaches for the synthesis of nanomaterials - the top down and the bottom-up. The top down approach utilizes the physical methods, while in the bottom-up strategy chemical methods have been employed for their synthesis. Among various wet chemical methods, colloidal approach provides an interesting methodology to grow nanostructures of varied size and shape with greater flexibility and reproducibility desired for tunable physicochemical properties. Semiconducting nanomaterials are among the most widely investigated nanosystems because of their extensive usage in diverse fields of technology and biomedical. The nanotechnological protocols have further revolutionized these areas, which assist in their bandgap engineering and tailoring of size/shape and dimensionalities. Such materials have been extensively explored for designing efficient devices needed in the domain of optoelectronics, photovoltaic solar cells and biomedical. The II-VI semiconductors with a band gap energy lying in the visible range have been drawing increasing attention for their utilization in the field of visible light induced photocatalysis, photophysics and sensing. Colloidal CdSe nanoparticles with distinctive features such as large molar extinction coefficient and fairly high tunable absorption cross section (0.2 - 10 × 10-15 cm2 for varied size ranging from 1 to 4 nm) and band gap lying in the visible region, makes it as an important semiconductor for its usage in solar cells, optoelectronics, photodetector, lasers and display technology. The greener synthesis of quantized colloidal particles has been realized by making use of environmentally benign template(s) and precursor(s) with hydrophilic functional groups so as to solubilize them in aqueous medium, addressing the global concerns for safety and health. Lately, the synthesis of nanomaterials by interfacing them with the natural biomolecules like proteins, enzymes, lipids, and nucleic acids is emerging as a convenient tool to design newer materials of varied dimensionalities ii and large functionalities. Besides, such molecules also provide the biocompatibility to the inorganic core to produce nanohybrids. The resulting building block(s) could also be explored for designing different nanoarchitectures with varied dimensionalities (0D, 1D, 2D and 3D) in the process of self-assembly. Among the above listed natural biopolymers, RNA is known to have distinctive advantages over others for designing new nanostructures because of its single strandedness, structural and physicochemical features. Besides, it also provides them the multifunctionalities, biocompatibility and enhances their solubility in aqueous medium. The surface of CdSe QDs is often modified by employing suitable surfactant/template for their thermodynamic stabilization. The present thesis work explores a new one pot “greener” synthetic protocol for producing the fluorescent colloidal CdSe nanostructures of varied morphologies employing biocompatible capping agent, RNA in aqueous medium. The functionalities of RNA have been explored to control both the nucleation and growth of these nanostructures in the process of self-assembly. The photophysics of these nanostructures have also been examined thoroughly under varied experimental conditions. The entire work presented in this thesis has been divided into six chapters. A brief account of the contents of these chapters has been furnished below: The first chapter presents a brief introduction of nanotechnology and different types of nanosystems. It includes the importance and application of semiconductor based nanosystems and furnishes an overview of their general optical and photophysical behavior. Among II-VI semiconductors, some distinctive features of CdSe based nanosystems have been highlighted. Different approaches employed for the synthesis of colloidal CdSe nanostructures and enhancement of their photophysical behavior have been discussed. The aim and objective of the present work have also been outlined in this chapter. The second chapter describes the experimental details covering the used reagents, apparatus, instruments and techniques. It also included a brief description of some of the sophisticated instruments employed for the characterization of the as synthesized nanostructures in terms of their structure, morphology/size/shape/dimensionality, optical, photophysical and electrical properties. A brief account of the methodologies used for iii preparing the samples for characterization along with the different formulae needed for data analyses have also been provided. It also includes the general procedure adopted for the synthesis of RNA-CdSe nanostructures. The third chapter has been divided into two sections - Section A and Section B. The Section A reports the synthesis of fluorescing RNA-mediated colloidal Cd2+/CdSe nanostructures in aqueous medium under mild experimental conditions. XRD, XPS, SAED, HRTEM and Raman analyses show the formation of CdSe in the hexagonal phase. It initially produced CdSe QDs (4 nm), but the presence of excess Cd2+ induced the folding of RNA upon aging to produce encapsulated CdSe nanoneedles having the dimension (average length × width at tip × width at the centre) of 42.2 × 4.2 × 6.8 nm, which upon further aging results in their stacking. These nanostructures fluoresce in the visible range with a fluorescence quantum efficiency and the average fluorescence lifetime (<τ>) of about 22% and 106 ns respectively. The transformation of QDs into nanoneedles in the self-assembly is also evidenced by about four fold increase in the rotational correlation time from 17.7 ns for the fresh sample to 68.0 ns, which is associated with an increase in the <τ> from 106 to 116 ns. The folding of RNA has been evidenced by CD, IR, 1H and 31P NMR spectroscopy. It possibly results in the transformation of RNA from its B- to A- form involving the puckering of ribose, thereby causing a change in its conformation from C2'-endo into thermodynamically stable C3'-endo. In section B, the surface properties, I-V characteristics and sensing features of the above synthesized RNA- Cd2+/CdSe nanostructures have been analyzed. The observed morphological transformation has been further investigated by designing the adsorption of rhodamine B on their surface by estimating the surface area for both nanosystems. I-V measurements with the drop-cast film, prepared from both the fresh and aged nanostructures, demonstrated the rectifying behavior with a significant increase in the current upon illumination to that observed in the dark. It supported the dynamics of charge carriers observed for the colloidal CdSe solution. These nanostructures showed efficient and effective sensing of Hg2+ ions in the presence of other heavy metal ions (Pb2+, Ni2+, Co2+, Cu2+ and Mn2+) at 1 nM. The mechanism of these processes has also been analyzed. The fourth chapter has also been splitted into two sections. Section A reports the synthesis of Zn2+/Cd2+ bound RNA-mediated CdSe nanostructures. A typical stoichiometric ratio of Zn2+ : Cd2+ = 1 : 2 containing relatively lower Zn2+ ions (1.5 × 10-4 mol dm-3) induces iv the puckering of sugar moiety of RNA bound to the surface of CdSe to bring an effective conformational change from its B to thermodynamically stable A form as has been revealed by IR, NMR and CD spectroscopy. In the early stages it controls the nucleation of CdSe QDs without forming an additional ZnSe phase. In the self-assembly these QDs get encapsulated in RNA strand to produce flute-like nanoarchitectures via porous buildingblocks. The average size of the freshly prepared CdSe QDs reduces from 3.5 to about 1 nm upon aging. The addition of Zn2+ ions regularly increase the blue-shifted band edge fluorescence and fluorescence lifetime to induce intense white-light-emission via yellow emission during the self-assembly. In this process Zn2+/Cd2+ ions bound to folded RNA effectively passivate the CdSe surface through non-covalent interactions as well as by entering of Zn2+ ions into the octahedral voids to enhance the fluorescence quantum efficiency to 64 ± 2%. In section B, the surface properties, electrical behavior and sensing features of the above synthesized Zn2+/Cd2+ bound RNA-mediated CdSe nanostructures have been examined. The surface analysis demonstrated the highest surface area for these nanosystems among all the above synthesized materials. I-V plots of drop-cast thin film for fresh CdSe sample exhibit the symmetric nature, which become asymmetric for the self-assembled sample. This system is found to be selective for Cu2+ ions. These ions could be estimated at ≤ 10 nM in the presence of certain interfering bivalent metal ions except Hg2+ (Mn2+, Ni2+, Pb2+ and Co2+). The fifth chapter has been divided into two sections. Section A reports the synthesis of colloidal CdSe nanostructures mediated by RNA in the presence of 1,3-diaminopropane (DAP) and excess Cd2+. The presence of DAP which initially forms a chains of QDs in metastable state induces their growth along (100) plane to produce thermodynamically more stable honey-comb like porous morphology in the process of self-assembly. This transformation is evidenced by AFM and TEM analyses, and by an increase in the rotational time constant from 14.7 to 31.5 ns. The DAP initially binds nucleotide(s) of RNA through alcoholic group of sugar and PO2 - to produce QDs, which eventually causes a change in the conformation of RNA from B to thermodynamically more stable A-form involving prominently the binding of excess Cd2+ on RNA strand with DAP to its different moieties such as guanine, cytosine, uracil, –OH group of sugar, and PO2 -, as was evidenced by IR, 1H NMR, 31P NMR, XPS and CD spectroscopy. These interactions cause the passivation of CdSe surface associated with enhanced fluorescence efficiency (0.36 ± 0.02) and v fluorescence lifetime (121 ns) by trapping of charge carriers into different heterojunctions formed by Cd2+-amine interaction. Section B reports the surface area determination, analysis of I-V and sensing behavior of as synthesized nanostructures. Their surface behavior has been analyzed by the adsorption of RhB on these nanostructure. I–V studies shows the rectifying behavior from which ILight/IDark under forward bias condition have been computed to be 10 and 12.5, respectively. These nanostructures could selectively detect Hg2+ ions at ≥ 0.5 nM, as was estimated by monitoring the quenching of fluorescence. The mechanism of quenching has been analyzed thoroughly. The sixth chapter presents the summary and conclusions arrived from the third, fourth and fifth chapters. It also provided a comparision of results on different aspects of different CdSe nanostructures prepared under different exerimental conditions and a comparison with the previous reports. Some future prospectives of the present work have also been pointed out.