Periodic acceptor excitation spectroscopy of single molecules

Doose S, Heilemann M, Michalet X, Weiss S, Kapanidis AN. Periodic acceptor excitation spectroscopy of single molecules. EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS. 2007;36(6):669-674.Alternating-laser excitation (ALEX) spectroscopy has recently been added to the single-molecule spectroscopy toolkit. ALEX monitors interaction and stoichiometry of biomolecules, reports on biomolecular structure by measuring accurate Forster resonance energy transfer (FRET) efficiencies, and allows sorting of subpopulations on the basis of stoichiometry and FRET. Here, we demonstrate that a simple combination of one continuous-wave donor-excitation laser and one directly modulated acceptor-excitation laser (Periodic Acceptor eXcitation) is sufficient to recapitulate the capabilities of ALEX while minimizing the cost and complexity associated with use of modulation techniques

Emergent Properties and Functions of Nanoconfined Nucleic Acid Architectures

6siThe facile ability of DNA to self-assemble has enabled the creation of complex architectures with diverse functions on surfaces or in solution. This approach provides a powerful design tool for the development of nanoscale devices with transformative applications in multiple areas, including the detection of complex biomolecules, drug delivery, and in situ biomolecular synthesis. However, little is known of the effect of confinement on the function of complex nucleic acid architectures, which exhibit unanticipated behaviors that presumably reflect high-level molecular crowding. In this chapter, we review selected recent studies that describe the application and atypical behaviors of nanoconfined nucleic acids, in particular with respect to hybridization, denaturation, conformation, stability, and enzyme accessibility. We argue that the novel behavior of dense nucleic acid arrays naturally emerge as a result of immobilization and reduction in spatial degrees of freedom. We summarize by emphasizing the need for basic physical–chemical studies of dense nucleic acid architectures, involving an interplay of experimental and theoretical approaches, in order to effectively guide the successful technological development of nucleic acid nanodevices.reservedmixedNicholson, Allen W.; Redhu, Shiv K.; Stopar, Alex; Coral, Lucia; Carnevale, Vincenzo; Castronovo, MatteoNicholson, Allen W.; Redhu, Shiv K.; Stopar, Alex; Coral, Lucia; Carnevale, Vincenzo; Castronovo, Matte