Self-Assembly of DNA Origami Heterodimers in High Yields and Analysis of the Involved Mechanisms.

Efficient fabrication of structurally and functionally diverse nanomolecular devices and machines by organizing separately prepared DNA origami building blocks into a larger structure is limited by origami attachment yields. A general method that enables attachment of origami building blocks using 'sticky ends' at very high yields is demonstrated. Two different rectangular origami monomers are purified using agarose gel electrophoresis conducted in solute containing 100 × 10 m NaCl, a treatment that facilitates the dissociation of most of the incorrectly hybridized origami structures that form through blunt-end interactions during the thermal annealing process and removes these structures as well as excess strands that otherwise interfere with the desired heterodimerization reaction.

Study of DNA Origami Dimerization and Dimer Dissociation Dynamics and of the Factors that Limit Dimerization.

Organizing DNA origami building blocks into higher order structures is essential for fabrication of large structurally and functionally diverse devices and molecular machines. Unfortunately, the yields of origami building block attachment reactions are typically not sufficient to allow programed assembly of DNA devices made from more than a few origami building blocks. To investigate possible reasons for these low yields, a detailed single-molecule fluorescence study of the dynamics of rectangular origami dimerization and origami dimer dissociation reactions is conducted.

DNA bipedal motor walking dynamics: an experimental and theoretical study of the dependency on step size.

We present a detailed coarse-grained computer simulation and single molecule fluorescence study of the walking dynamics and mechanism of a DNA bipedal motor striding on a DNA origami. In particular, we study the dependency of the walking efficiency and stepping kinetics on step size. The simulations accurately capture and explain three different experimental observations.

Photon-by-Photon Hidden Markov Model Analysis for Microsecond Single-Molecule FRET Kinetics.

The function of biological macromolecules involves large-scale conformational dynamics spanning multiple time scales, from microseconds to seconds. Such conformational motions, which may involve whole domains or subunits of a protein, play a key role in allosteric regulation. There is an urgent need for experimental methods to probe the fastest of these motions.

Temporal behavior of the singlet molecular oxygen emission in imidazolium and morpholinium ionic liquids and its implications.

The solvent effect of ionic liquids on the lifetime of singlet molecular oxygen, O2((1)Δg), was investigated by means of time-resolved near-IR emission spectroscopy. O2((1)Δg) was generated by photosensitization of methylene blue in morpholinium and imidazolium ionic liquids, both comprising various alkyl chains of different lengths. The measured time profiles of O2((1)Δg) luminescence for the (1)Δg → (3)Σg(-) transition were represented by a single-exponential decay function.

Does excited-state proton-transfer reaction contribute to the emission behaviour of 4-aminophthalimide in aqueous media?

4-Aminophthalimide (AP) is an extensively used molecule both for fundamental studies and applications primarily due to its highly solvent-sensitive fluorescence properties. The fluorescence spectrum of AP in aqueous media was recently shown to be dependent on the excitation wavelength. A time-dependent blue shift of its emission spectrum is also reported.

Effect of the alkyl chain length on the rotational dynamics of nonpolar and dipolar solutes in a series of N-alkyl-N-methylmorpholinium ionic liquids.

Rotational dynamics of two dipolar solutes, 4-aminophthalimide (AP) and 6-propionyl-2-dimethylaminonaphthalene (PRODAN), and a nonpolar solute, anthracene, have been studied in N-alkyl-N-methylmorpholinium (alkyl = ethyl, butyl, hexyl, and octyl) bis(trifluoromethansulfonyl)imide (Tf2N) ionic liquids as a function of temperature and excitation wavelength to probe the microheterogeneous nature of these ionic liquids, which are recently reported to be more structured than the imidazolium ionic liquids (Khara and Samanta, J. Phys. Chem.

Fluorescence response of coumarin-153 in N-alkyl-N-methylmorpholinium ionic liquids: are these media more structured than the imidazolium ionic liquids?

The fluorescence behavior of coumarin-153 (C153) has been studied in four N-alkyl-N-methylmorpholinium ionic liquids differing in the alkyl chain length attached to the N-methylmorpholinium cation as a function of the excitation wavelength and temperature to understand some of the physicochemical characteristics of these largely unexplored ionic liquids. While the polarity of the ionic liquid with the smallest alkyl chain length is found comparable to that of the commonly used imidazolium ionic liquids, the probe molecule experiences a less polar environment with increasing chain length of the alkyl group attached to the morpholinium cation. The room temperature steady-state fluorescence spectrum of C153 in these solvents is found to be dependent on the excitation wavelength, and this effect is most pronounced in long chain containing ionic liquids.

Fluorescence quenching of CdS quantum dots by 4-azetidinyl-7-nitrobenz-2-oxa-1,3-diazole: a mechanistic study.

Fluorescence quenching of CdS quantum dots (QDs) by 4-azetidinyl-7-nitrobenz-2-oxa-1,3-diazole (NBD), where the two quenching partners satisfy the spectral overlap criterion necessary for Förster resonance energy transfer (FRET), is studied by steady-state and time-resolved fluorescence techniques. The fluorescence quenching of the QDs is accompanied by an enhancement of the acceptor fluorescence and a reduction of the average fluorescence lifetime of the donor. Even though these observations are suggestive of a dynamic energy transfer process, it is shown that the quenching actually proceeds through a static interaction between the quenching partners and is probably mediated by charge-transfer interactions.

Rotational dynamics of positively and negatively charged solutes in ionic liquid and viscous molecular solvent studied by time-resolved fluorescence anisotropy measurements.

Rotational dynamics of two negatively and positively charged solutes, 1-anilinonaphthalene-8-sulfonate (ANS) and ethidium bromide (EB), respectively, have been studied in an ionic liquid, 1-butyl-3-methylimidazolium tetrafluoroborate ([bmim][BF(4)]) and a conventional viscous solvent, glycerol, at different temperatures to obtain insight into the nature of various forces that operate in the ionic liquid. The fluorescence anisotropy of the systems decays exponentially with time in both the solvents. Under isoviscous conditions, the reorientation time of each probe molecule is found to be very similar in ionic liquid and glycerol indicating that the electrostatic forces exert negligible influence on the charged solute molecules.