G-rich telomeric DNA sequences can form G-quadruplex structures. The heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and a shortened derivative (UP1) are active in telomere length regulation, and it has been reported that UP1 can unwind G-quadruplex structures. Here, we investigate the interaction of hnRNP A1 with G-quadruplex DNA structures containing the human telomere repeat (TTAGGG) by gel retardation assays, ensemble fluorescence energy transfer (FRET) spectroscopy, and single molecule FRET microscopy. Our biochemical experiments show that hnRNP A1 binds well to the G-quadruplex telomeric DNA. Ensemble and single molecule FRET measurements provide further insight into molecular conformation: the telomeric DNA overhang is found to be in a folded state in the absence of hnRNP A1 and to remain predominantly in a compact state when complexed with hnRNP A1. This finding is in contrast to the previously reported crystal structures of UP1-telomere DNA complexes where the DNA oligo within the protein-DNA complex is in a fully open conformation.

HIV-1 reverse transcription is primed by a cellular tRNAlys3 molecule that binds to the primer binding site (PBS) in the genomic RNA. An additional interaction between the tRNA molecule and the primer activation signal (PAS) is thought to regulate the initiation of reverse transcription. The mechanism of tRNA annealing onto the HIV-1 genome was examined using ensemble and single-molecule Förster Resonance Energy Transfer (FRET) assays, in which fluorescent donor and acceptor molecules were covalently attached to an RNA template mimicking the PBS region. The role of the viral nucleocapsid (NC) protein in tRNA annealing was studied. Both heat annealing and NC-mediated annealing of tRNAlys3 were found to change the FRET efficiency, and thus the conformation of the HIV-1 RNA template. The results are consistent with a model for tRNA annealing that involves an interaction between the tRNAlys3 molecule and the PAS sequence in the HIV-1 genome. The NC protein may stimulate the interaction of the tRNA molecule with the PAS, thereby regulating the initiation of reverse transcription.

Based on inspiration from multi-mode interference self-imaging and theoretical FDTD simulations, a 1x3 beam splitter was designed, fabricated and characterized. Measurements show that for TE-polarized incident light the power is distributed equally between the output ports within 1dB in the range from 1541nm to 1552nm, and the total transmission of the 1x3 splitter is equal to the corresponding length of a single-linedefect PhCW within the measurement uncertainty. (14), 1623-1625 (2004). 12. L. B. Soldano, and E. C. M. Pennings, "Optical multimode interference devices based on self-imagingprinciples and applications," J. Lightwave Technol. 13(4), 615-627 (1995). 13. H. J. Kim, I. Park, B. H. O, S. G. Park, H. Lee, and S. G. Lee, "Self-imaging phenomena in multi-mode photonic crystal line-defect waveguides: application to wavelength de-multiplexing," Opt. Express 12(23), 5625-5633 (2004), http://www.opticsinfobase.org/oe/abstract.cfm?URI=OPEX-12-23-5625. 14. Z. J. Li, Y. Zhang, and B. J. Li, "Terahertz photonic crystal switch in silicon based on self-imaging principle," ©2010 Optical Society of AmericaOpt. Express 14(9), 3887-3892 (2006), http://www.opticsinfobase.org/abstract.cfm?URI=oe-14-9-3887. 416-419 (1973). 18. R. Ulrich, "Image-formation by phase coincidences in optical-waveguides," Opt. Commun. 13(3), 259-264 (1975). 19. J. M. Heaton, R. M. Jenkins, D. R. Wight, J. T. Parker, J. C. H. Birbeck, and K. P. Hilton, "Novel 1-to-N way integrated optical beam-splitters using symmetrical mode mixing in GaAs/AlGaAs multimode wave-guides,"

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The power imbalance between different waveguide outputs is compensated by manipulating the dispersion of the guided propagation in the multimode interference (MMI) region. This is attainable using a tapered region at the beginning of the MMI region that has been verified through simulation and experiment. From this, the fabrication tolerance for the diameters of holes in a tapered 1×3 photonic crystal waveguide (PhCW) splitter is relaxed up to a range of at least 27 nm. The output power is well-balanced to within 1 dB. The effective bandwidth of the splitters shifts only around 13 nm, for a reduction of 10 nm in the diameter of the PhCW holes. The optimized component is an outstanding ultracompact 1×3 splitter for the photonic integrated circuit (PIC).

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