The phenomenon of Förster Resonance Energy Transfer, commonly used to measure the distances between fluorophore molecules and to study interactions between fluorescent-tagged proteins in life sciences, can also be applied in nanocommunication networks to transfer information bits. The mechanism offers a relatively large throughput and very small delays, but at the same time the channel bit error rate is too high and the transmission ranges are too limited for communication purposes. In this paper, multiple donors at the transmitter side and multiple acceptors at the receiver side are considered to decrease the bit error rate. As nanoantennas, the DyLight fluorescent dyes, which are very well suited to long range nanocommunication due to their large Förster distances and high degrees of labeling, are proposed. The reported results of the recent laboratory experiments confirm efficient communication on distances over 10 nm.

Nanocommunication has gained significant attention in the last few years, as a means to establish information transfer between future nanomachines. Comparing with other communication techniques for nanoscale (calcium ions signaling, molecular or catalytic nanomotors, pheromones propagation, bacteria-based communication), the phenomenon called Förster Resonance Energy Transfer (FRET) offers significantly smaller propagation delays and high channel throughput. In this paper, we report our recent experiments on FRET-based nanonetworks performed in the Laboratory of Cell Biophysics of the Jagiellonian University, Kraków. We propose to use Alexa Fluor dyes as nano transmitters and receivers, as they enable to create multiple-input multioutput (MIMO) FRET communication channels and thus enhance FRET efficiency. We measure FRET efficiency values, calculate bit error rates for the measured scenarios, and extend the calculations to consider a general case of MIMO (n, m) FRET channels.

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We here describe a technique termed STRIDE (SensiTive Recognition of Individual DNA Ends), which enables highly sensitive, specific, direct in situ detection of single- or double-strand DNA breaks (sSTRIDE or dSTRIDE), in nuclei of single cells, using fluorescence microscopy. The sensitivity of STRIDE was tested using a specially developed CRISPR/Cas9 DNA damage induction system, capable of inducing small clusters or individual single- or double-strand breaks. STRIDE exhibits significantly higher sensitivity and specificity of detection of DNA breaks than the commonly used terminal deoxynucleotidyl transferase dUTP nick-end labeling assay or methods based on monitoring of recruitment of repair proteins or histone modifications at the damage site (e.g. γH2AX). Even individual genome site-specific DNA double-strand cuts induced by CRISPR/Cas9, as well as individual single-strand DNA scissions induced by the nickase version of Cas9, can be detected by STRIDE and precisely localized within the cell nucleus. We further show that STRIDE can detect low-level spontaneous DNA damage, including age-related DNA lesions, DNA breaks induced by several agents (bleomycin, doxorubicin, topotecan, hydrogen peroxide, UV, photosensitized reactions) and fragmentation of DNA in human spermatozoa. The STRIDE methods are potentially useful in studies of mechanisms of DNA damage induction and repair in cell lines and primary cultures, including cells with impaired repair mechanisms.

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