Ensemble-based measurements of kinetic isotope effects (KIEs) have advanced physical understanding of enzyme-catalyzed reactions, but controversies remain. KIEs are used as reporters of rate-limiting H-transfer steps, quantum mechanical tunnelling, dynamics and multiple reactive states. Single molecule (SM) enzymatic KIEs could provide new information on the physical basis of enzyme catalysis. Here, single pair fluorescence energy transfer (spFRET) was used to measure SM enzymatic KIEs on the H-transfer catalyzed by the enzyme pentaerythritol tetranitrate reductase. We evaluated a range of methods for extracting the SM KIE from single molecule spFRET time traces. The SM KIE enabled separation of contributions from nonenzymatic protein and fluorophore processes and H-transfer reactions. Our work demonstrates SM KIE analysis as a new method for deconvolving reaction chemistry from intrinsic dynamics.

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Five isomorphic fluorescent uridine mimics have been subjected to two-photon (2P) excitation analysis to investigate their potential applicability as non-perturbing probes for the single-molecule detection of nucleic acids. We find that small structural differences can cause major changes in the two-photon excitation probability, with the 2P cross sections varying by over one order of magnitude. Two of the probes, both furan-modified uridine analogs, have the highest 2P cross sections (3.8 GM and 7.6 GM) reported for nucleobase analogs, using a conventional Ti:sapphire laser for excitation at 690 nm; they also have the lowest emission quantum yields. In contrast, the analogs with the highest reported quantum yields have the lowest 2P cross sections. The structure-photophysical property relationship presented here is a first step towards the rational design of emissive nucleobase analogs with controlled 2P characteristics. The results demonstrate the potential for major improvements through judicious structural modifications.

We demonstrate that pulse shaping of a broadband Ti:sapphire laser can result in almost an order of magnitude increase in the sensitivity and signal to background ratio (SBR) of multiphoton total internal reflection fluorescence (TIRF) microscopy. We produced transform-limited pulses of 15 fs duration at the sample, and observed a 8-fold enhancement in the fluorescence of CdSe/ZnS quantum dots via two-photon objective-type TIRF excitation. There was a concomitant 6-fold increase of the SBR upon compression of the pulse duration. Enhancement of non-linear evanescent imaging has recently been demonstrated using surface-plasmons [Opt. Express 17, 5987 (2009)] and structured substrates [Opt. Express 18, 23218 (2010)]. Our approach of ultrafast pulse shaping could be used alone or combined with these new methods to offer significant gains in image quality.

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