High-throughput platform for real-time monitoring of biological processes by multicolor single-molecule fluorescence.

Zero-mode waveguides provide a powerful technology for studying single-molecule real-time dynamics of biological systems at physiological ligand concentrations. We customized a commercial zero-mode waveguide-based DNA sequencer for use as a versatile instrument for single-molecule fluorescence detection and showed that the system provides long fluorophore lifetimes with good signal to noise and low spectral cross-talk. We then used a ribosomal translation assay to show real-time fluidic delivery during data acquisition, showing it is possible to follow the conformation and composition of thousands of single biomolecules simultaneously through four spectral channels. This instrument allows high-throughput multiplexed dynamics of single-molecule biological processes over long timescales. The instrumentation presented here has broad applications to single-molecule studies of biological systems and is easily accessible to the biophysical community.

Picosecond pulses from a cryogenically cooled, composite amplifier using Yb:YAG and Yb:GSAG.

A cryogenic Yb amplifier using two laser materials, Gd3Sc2Al3O12 and Y3Al5O12 (YAG), has been used to obtain 70 W average power at 5 kHz pulse repetition frequency; the output was compressed to 1.6 ps, compared with an input compressible to 1.4 ps. The gain broadening obtained by combining two media enables shorter pulses than using Yb:YAG alone but retains the power-scaling advantages of cryogenic Yb:YAG.

Real-time DNA sequencing from single polymerase molecules.

We present single-molecule, real-time sequencing data obtained from a DNA polymerase performing uninterrupted template-directed synthesis using four distinguishable fluorescently labeled deoxyribonucleoside triphosphates (dNTPs). We detected the temporal order of their enzymatic incorporation into a growing DNA strand with zero-mode waveguide nanostructure arrays, which provide optical observation volume confinement and enable parallel, simultaneous detection of thousands of single-molecule sequencing reactions. Conjugation of fluorophores to the terminal phosphate moiety of the dNTPs allows continuous observation of DNA synthesis over thousands of bases without steric hindrance. The data report directly on polymerase dynamics, revealing distinct polymerization states and pause sites corresponding to DNA secondary structure. Sequence data were aligned with the known reference sequence to assay biophysical parameters of polymerization for each template position. Consensus sequences were generated from the single-molecule reads at 15-fold coverage, showing a median accuracy of 99.3%, with no systematic error beyond fluorophore-dependent error rates.

Parallel confocal detection of single molecules in real time.

The confocal detection principle is extended to a highly parallel optical system that continuously analyzes thousands of concurrent sample locations. This is achieved through the use of a holographic laser illumination multiplexer combined with a confocal pinhole array before a prism dispersive element used to provide spectroscopic information from each confocal volume. The system is demonstrated to detect and identify single fluorescent molecules from each of several thousand independent confocal volumes in real time.

Composition Space of the (CuO, (1)/(2)Nb(2)O(5))/(HF)(x)().pyridine/H(2)O System. Structure and Synthesis of [pyH(+)](2)[CuNb(2)(py)(4)O(2)F(10)](2-) and CuNb(py)(4)OF(5).

Single crystals of [pyH(+)](2)[CuNb(2)(py)(4)O(2)F(10)](2)(-) and CuNb(py)(4)OF(5) were synthesized in a (HF)(x)().pyridine/pyridine/water solution (150 degrees C, 24 h, autogeneous pressure) using CuO and Nb(2)O(5) as reagents. The compound [pyH(+)](2)[CuNb(2)(py)(4)O(2)F(10)](2)(-) contains clusters of [CuNb(2)(py)(4)O(2)F(10)](2)(-) anions linked through N-H(+).F hydrogen bonds to the [pyH(+)] cations. In contrast CuNb(py)(4)OF(5) is a unidimensional compound consisting only of chains, perpendicular to the c axis, of alternating [Cu(py)(4)(O/F)(2/2)](0.5+) and [NbF(4)(O/F)(2/)(2)](0.5)(-) octahedra. The chains change direction between the [110] and [1&onemacr;0] every c/2. Crystal data for [pyH(+)](2)[CuNb(2)(py)(4)O(2)F(10)](2)(-): tetragonal, space group I4(1)22 (No. 98),with a = 11.408(3) Å, c = 30.36(1) Å, and Z = 4. Crystal data for CuNb(py)(4)OF(5): monoclinic, space group C2/c (No. 15), with a = 10.561(3) Å, b = 13.546(6) Å, c = 16.103(4) Å, beta = 97.77(2) degrees, and Z = 4.