DNA at Aqueous/Solid Interfaces: Chirality-Based Detection via Second Harmonic Generation Activity

Boman, Faith C.; Gibbs, Julianne M.; Heckman, Laurel M.; Stepp, Brian R.; Nguyen, SonBinh T.; Geiger, Franz M.

doi:10.1021/ja808007b

Cited by 36 publications

(81 citation statements)

References 68 publications

(118 reference statements)

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“…Second, the free Mg 2þ in solution acts as an electrolyte that screens the electric field sensed by the bulk water molecules, which lowers the SH signal. Similar effects of counter ions on the SH signals from charged interfaces have been reported in previous experiments (29)(30)(31)(32)(33)(34).…”

Section: Resultssupporting

confidence: 87%

“…Using those spectroscopies, the electronic (29, 31) and vibrational (30, 31) spectra of DNA oligonucleotides at a solid/water interface were obtained. In addition, the kinetics of DNA hybridization and the equilibrium between ion-free and ion-bound DNA have been measured using the SH method (29, 31).Surface-sensitive nonlinear spectroscopies allow one to probe equilibrium properties and time-dependent changes in both the electrical charge of molecules and changes in the structure of molecules that are located at interfaces (29)(30)(31)(32)(33)(34)). An attractive feature using DNA bound to the surface of a microparticle, which can react with free EcoR1 molecules in solution, is that the total surface area that can be irradiated and thereby interrogated is much larger than can be achieved using a planar surface.…”

mentioning

confidence: 99%

“…Significant effort and progress has been made in hybridizing artificial colloidal nano-and micromaterials with naturally occurring biological reagents to build self-assembled superstructured materials (20)(21)(22)(23)(24)(25)(26), and to develop biologically coded probes for protein detection and disease treatment (27,28). The present work builds on these pioneering studies, and on studies of DNA supported on flat surfaces using SH and sum-frequency generation spectroscopies (29)(30)(31). Using those spectroscopies, the electronic (29,31) and vibrational (30, 31) spectra of DNA oligonucleotides at a solid/water interface were obtained.…”

mentioning

confidence: 99%

“…The present work builds on these pioneering studies, and on studies of DNA supported on flat surfaces using SH and sum-frequency generation spectroscopies (29)(30)(31). Using those spectroscopies, the electronic (29,31) and vibrational (30, 31) spectra of DNA oligonucleotides at a solid/water interface were obtained. In addition, the kinetics of DNA hybridization and the equilibrium between ion-free and ion-bound DNA have been measured using the SH method (29,31).…”

mentioning

confidence: 99%

mentioning

confidence: 99%

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Binding and cleavage of DNA with the restriction enzyme EcoR1 using time-resolved second harmonic generation

Doughty

Kazer

Eisenthal

2011

Proc. Natl. Acad. Sci. U.S.A.

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The binding of EcoR1 to a 90-bp DNA duplex attached to colloidal microparticles and the subsequent cleavage by the enzyme was observed in real time and label-free with time-resolved second harmonic (SH) spectroscopy. This method provides a unique way to investigate biomolecular interactions based on its sensitivity to changes in structure and electrical charge on formation of a complex and subsequent dynamics. The binding of EcoR1 to the recognition sequence in DNA appears as a rapid increase in the SH signal, which is attributed to the enzyme-induced change in the DNA conformation, going from a rod-like to a bent shape. In the presence of the cofactor Mg 2 , the subsequent decay in the SH signal was monitored in real time as the following processes occurred: cleavage of DNA, dissociation of the enzyme from the DNA, and diffusion of the 74-bp fragment into the bulk solution leaving the 16-bp fragment attached to the microparticle. The observed decay was dependent on the concentration of Mg 2 , which functions as a cofactor and as an electrolyte. With SH spectroscopy the rehybridization dynamics between the rehybridized microparticle bound and free cleaved DNA fragments was observed in real time and label-free following the cleavage of DNA. Collectively, the experiments reported here establish SH spectroscopy as a powerful method to investigate equilibrium and time-dependent biological processes in a noninvasive and label-free way.cleavage kinetics | DNA-endonuclease | rehybridization kinetics | nonspecific binding T he highly selective binding of proteins to specific nucleotide sequences in DNA is an essential step in many biological processes, including gene regulation, gene expression, and DNA hybridization (1). The family of type II restriction enzymes, which includes EcoR1, have been, and continue to be, of major importance in serving as model systems of protein-DNA interactions. The endonucleases, because of their capability to bind and cleave specific DNA sequences, also play a key role in DNA recombinant and cloning methods (1, 2). The EcoR1-DNA equilibria and reaction dynamics have been probed extensively by a number of established methods, such as, but not limited to: FRET (3-5), gel electrophoresis (6-15), surface plasmon resonance (16), microfluidic trapping (17), two-color cross-correlation spectroscopy (18), and isothermal calorimetry (19).The essential characteristic of the method used here is the application of second harmonic (SH) spectroscopy to selectively probe the interface of a polystyrene carboxylate (PSC) microparticle, to which target DNA molecules have been attached. Significant effort and progress has been made in hybridizing artificial colloidal nano-and micromaterials with naturally occurring biological reagents to build self-assembled superstructured materials (20-26), and to develop biologically coded probes for protein detection and disease treatment (27,28). The present work builds on these pioneering studies, and on studies of DNA supported on flat surfaces using SH and sum-frequ...

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