Nucleosomes are stable DNA-histone protein complexes that must be unwrapped and disassembled for genome expression, replication, and repair. Histone posttranslational modifications (PTMs) are major regulatory factors of these nucleosome structural changes, but the molecular mechanisms associated with PTM function remains poorly understood. Here we demonstrate that histone PTMs within distinct structured regions of the nucleosome directly regulate the inherent dynamic properties of the nucleosome. Precise PTMs were introduced into nucleosomes by chemical ligation. Single molecule magnetic tweezers measurements determined that only PTMs near the nucleosome dyad increase the rate of histone release in unwrapped nucleosomes. In contrast, FRET and restriction enzyme analysis reveal that only PTMs throughout the DNA entry-exit region increase unwrapping and enhance transcription factor binding to nucleosomal DNA. These results demonstrate that PTMs in separate structural regions of the nucleosome control distinct dynamic events, where the dyad regulates disassembly while the DNA entry-exit region regulates unwrapping. These studies are consistent with the conclusion that histone PTMs may independently influence nucleosome dynamics and associated chromatin functions.histone acetylation | chromatin dynamics | native chemical ligation

Optical trapping is a powerful manipulation and measurement technique widely employed in the biological and materials sciences1–8. Miniaturizing optical trap instruments onto optofluidic platforms holds promise for high throughput lab-on-chip applications9–16. However, a persistent challenge with existing optofluidic devices has been controlled and precise manipulation of trapped particles. Here we report a new class of on-chip optical trapping devices. Using photonic interference functionalities, an array of stable, three-dimensional on-chip optical traps is formed at the antinodes of a standing-wave evanescent field on a nanophotonic waveguide. By employing the thermo-optic effect via integrated electric microheaters, the traps can be repositioned at high speed (~ 30 kHz) with nanometer precision. We demonstrate sorting and manipulation of individual DNA molecules. In conjunction with laminar flows and fluorescence, we also show precise control of the chemical environment of a sample with simultaneous monitoring. Such a controllable trapping device has the potential for high-throughput precision measurements on chip.

A series of multiporphyrin arrays has been studied to probe the contribution of energy transfer between secondneighbor ("nonadjacent") porphyrins and to determine the rate of energy transfer between identical porphyrins at adjacent sites. The arrays, organized in linear or branched architectures, contain up to 21 constituents, domains of 2-5 zinc porphyrins, and a single energy trap. The study has involved iterative cycles of molecular design, synthesis, determination of rates via transient absorption spectroscopy, and kinetic analysis. A rate constant of (30 ( 10 ps) -1 is deduced for bidirectional energy transfer between adjacent zinc porphyrins joined by a diphenylethyne linker. The value is (50 ( 10 ps) -1 when the porphyrin-linker internal rotation is hindered by o,o′-methyl groups on one aryl ring of the linker. Rates of nonadjacent energy transfers are typically only 5-10-fold less than the rates of adjacent transfers. Thus, the nonadjacent pathway has a significant impact on the overall rate of energy flow to the trap, even in architectures as small as triads. These findings provide information that will be essential for the rational design of multichromophore arrays whose function is to transfer excitation energy efficiently over large distances to a trap site.