<p> Bax is a pro-apoptotic protein believed to permeabilize mitochondria during apoptosis. The mechanism Bax uses is not well understood. In this work, we use fluorescence techniques to shed light on how tBid activates Bax and we examine the topology of the pore-forming domain of Bax. </p> <p> The manner in which tBid promotes apoptosis via Bax activation is not known. Study of tBid and Bax interaction using a new FRET pair showed that the proteins only interacted in the presence ofmembranes. The Bax pore was shown to have a variable size distribution. A fluorescence technique of simultaneously measuring pore formation, Bax insertion and FRET showed that tBid interaction with Bax occurred before all the Bax inserted or formed pores in the liposomes. A chronological order is proposed for Bax pore formation. tBid first binds to liposomes. tBid proceeds to interact with Bax, and Bax inserts into the membrane. After insertion, Bax oligomerizes and forms small pores. More Bax is recruited and the pores become larger. </p> <p> The two central hairpin helices of Bax, helices 5 and 6, are known as the pore-forming domain. We used cysteine scanning with the environment sensitive fluoroprobe NBD to gain insight into the topology of these helices. Fluorescence intensity changes and emission blue shifts showed that residues in these helices undergo conformational reorganization during pore formation. In the activated oligomeric conformation, fluorescence lifetimes showed that helix 5 was more inaccessible to water than helix 6. Cobalt, a cationic NBD quencher, effectively quenched residues in the pore-forming domain, consistent with a pore that is lined with anionic lipid head groups. Quenching with nitroxide groups at various lipid depths showed that residues on helix 6 were most quenched by a shallow quencher, while residues on helix 5 were quenched by deeper quenchers. Compared to beta sheet pore-forming proteins, the data obtained suggests that Bax and possibly other alpha helical pore-forming proteins form a lipidic pore in a dynamic environment. Combined together, the data suggest a model for Bax in which helix 5 spans the bilayer, and helix 6 is buried just below the lipid headgroups of a toroidal pore. </p> / Thesis / Master of Science (MSc)

Fluorescent nucleic acid base analogues (FBAs) are an important class of molecule used to study the structure and dynamics of DNA and RNA. These base analogues are molecules with structures that resemble one of the natural bases but which, unlike the natural bases, have high fluorescence quantum yields. 2-Aminopurine (2AP) has long been the most widely used fluorescent base analogue and is one of the few base analogues commercially available. One problem with 2AP is that it undergoes significant quenching when incorporated into DNA: the quantum yield decreases 100 fold from that of the free base, thus becoming too low for use in, for example, single molecule studies. A secondary problem is that the 305 nm absorption peak requires excitation in the UV. A variety of new fluorescent base analogues are being produced, with a view to remedying the deficiencies of 2AP and expanding the current range of use. The first part of this thesis explores the one-photon photophysical properties of several of these novel FBAs. The first of these novel FBAs is the 6-aza-uridine family. These compounds, analogues of uridine, have large Stokes shifts and their absorption and emission spectra are red-shifted in comparison to 2AP; their quantum yields as free bases have been shown to exceed that of 2AP and their environmental sensitivity has been demonstrated. Time-resolved measurements reported in this thesis indicate the presence of multiple emitting species. A density functional theory (DFT) study has been carried out to rationalise these emitting species as rotational isomers. Similar fluorescence lifetime measurements were made on a second class of FBAs, the quadracyclic adenine analogues, qANs; these results also indicated the presence of multiple emitting species. Experimental results show that these FBAs undergo excited-state proton transfer. The final FBA studied in this thesis is pentacyclic adenine, pA. This FBA showed some of the most promising characteristics of all the analogues investigated, such as a high quantum yield in both polar and non-polar solvents. A time-resolved investigation into pA-containing oligonucleotides indicated that in an oligonucleotide pA adopts multiple stacked conformations and its behaviour is highly sequence dependent. Several of these aforementioned fluorescent base analogues have absorption spectra in a region that makes them accessible to two-photon (2P) excitation with a Ti:Sapphire laser. In biological systems, multiphoton excitation has several advantages over one-photon excitation. By avoiding the use of ultraviolet light there is reduced phototoxicity. Out of focus photobleaching and autofluorescence are also minimised which leads to a higher signal-to-background ratio and allows deeper tissue penetration to be achieved. Fluorescent base analogues tend to have small Stokes shifts; this is another problem that can be overcome by using two-photon excitation. To be of potential use in multiphoton microscopy, a FBA must have a high two-photon absorption cross-section and a high two-photon brightness. Previously, the highest two- photon brightness measured for a fluorescent base analogue was less than 2 GM. Amongst the base analogues investigated here, are several that have higher two-photon brightness than ever reported for FBAs; these include pA which is shown to have the highest 2P brightness of a FBA in an oligonucleotide, 1.3 GM, and a member of the 6-azauridine family which as a free base has a 2P brightness of 18 GM. Detection of individual molecules represents the ultimate level of sensitivity and enables details about a molecular system that would otherwise be concealed using conventional ensemble techniques to be revealed. With the improved 2P brightness of the molecules measured in this thesis, it has become feasible to detect single FBA molecules using 2P excitation. To maximise the chance of detection, ultrafast, shaped laser pulses have been used as the excitation source. For the first time, the signal has been high enough and the molecule of interest sufficiently photostable such that 2P fluorescence correlation spectroscopy of a fluorescent base analogue in an oligonucleotide could be measured. In summary, this thesis reports the fluorescence lifetimes and two-photon cross-sections of a series of novel fluorescent base analogues, as well as fluorescence correlation spectroscopy measurements of the most promising candidates.