A method of analyzing a polynucleotide comprising: A) directing to a nanopore an excitation beam having a predetermined polarization state, translocating a polynucleotide through the nanopore, wherein nucleotides of the polynucleotide are labeled with fluorescent labels having absorption dipoles and wherein the nanopore spatially orients the fluorescent labels so that during translocation the absorption dipoles are substantially unresponsive to the excitation beam, detecting changes in fluorescent signals generated by the fluorescent labels as nucleotides with fluorescent labels exit the nanopore and absorption dipoles thereof become responsive to excitation by the excitation beam with the predetermined polarization state, and identifying nucleotides exiting the nanopore from the changes in fluorescent signals; or B) directing to a nanopore an excitation beam comprising a predetermined polarization state, translocating a polynucleotide through the nanopore, wherein nucleotides of the polynucleotide are labeled with fluorescent labels having absorption dipoles and wherein the nanopore spatially orients the fluorescent labels so that during translocation absorption dipoles are maximally responsive to excitation by the excitation beam in the predetermined polarization state, detecting optical signals generated by the fluorescent labels on nucleotides within the nanopore, and identifying nucleotides of the polynucleotide from the optical signals. A) directing to a nanopore an excitation beam having a predetermined polarization state, translocating a polynucleotide through the nanopore, wherein nucleotides of the polynucleotide are labeled with fluorescent labels having absorption dipoles and wherein the nanopore spatially orients the fluorescent labels so that during translocation the absorption dipoles are substantially unresponsive to the excitation beam, detecting changes in fluorescent signals generated by the fluorescent labels as nucleotides with fluorescent labels exit the nanopore and absorption dipoles thereof become responsive to excitation by the excitation beam with the predetermined polarization state, and identifying nucleotides exiting the nanopore from the changes in fluorescent signals; or translocating a polynucleotide through the nanopore, wherein nucleotides of the polynucleotide are labeled with fluorescent labels having absorption dipoles and wherein the nanopore spatially orients the fluorescent labels so that during translocation the absorption dipoles are substantially unresponsive to the excitation beam, detecting changes in fluorescent signals generated by the fluorescent labels as nucleotides with fluorescent labels exit the nanopore and absorption dipoles thereof become responsive to excitation by the excitation beam with the predetermined polarization state, and identifying nucleotides exiting the nanopore from the changes in fluorescent signals; or B) directing to a nanopore an excitation beam comprising a predetermined polarization state, translocating a polynucleotide through the nanopore, wherein nucleotides of the polynucleotide are labeled with fluorescent labels having absorption dipoles and wherein the nanopore spatially orients the fluorescent labels so that during translocation absorption dipoles are maximally responsive to excitation by the excitation beam in the predetermined polarization state, detecting optical signals generated by the fluorescent labels on nucleotides within the nanopore, and identifying nucleotides of the polynucleotide from the optical signals. translocating a polynucleotide through the nanopore, wherein nucleotides of the polynucleotide are labeled with fluorescent labels having absorption dipoles and wherein the nanopore spatially orients the fluorescent labels so that during translocation absorption dipoles are maximally responsive to excitation by the excitation beam in the predetermined polarization state, detecting optical signals generated by the fluorescent labels on nucleotides within the nanopore, and identifying nucleotides of the polynucleotide from the optical signals.