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Exciton-coupled chromophore dimers are an emerging class of optical probes for studies of site-specific biomolecular interactions. Applying accurate theoretical models for the electrostatic coupling of a molecular dimer probe is a key step for simulating its optical properties and analyzing spectroscopic data. In this work, we compare experimental absorbance and circular dichroism (CD) spectra of ‘internally-labeled’ (iCy3)2 dimer probes inserted site-specifically into DNA fork constructs to theoretical calculations of the structure and geometry of these exciton-coupled dimers. We compare transition density models of varying levels of approximation to determine conformational parameters of the (iCy3)2 dimer-labeled DNA fork constructs. By applying an atomistically detailed transition charge (TQ) model, we can distinguish between dimer conformations in which the stacking and tilt angles between planar iCy3 monomers are varied. A major strength of this approach is that the local conformations of the (iCy3)2 dimer probes that we determined can be used to infer information about the structures of the DNA framework immediately surrounding the probes at various positions within the constructs, both deep in the duplex DNA sequences and at sites at or near the DNA fork junctions where protein complexes bind to discharge their biological functions.

 

We present a theoretical proof that the “quantum enhancement” of two-photon absorption, thought to be a means to improve molecular spectroscopy and imaging, is tightly bounded by the physics of photonic entanglement and nonlinear response.

 

Abstract Regulatory protein access to the DNA duplex ‘interior’ depends on local DNA ‘breathing’ fluctuations, and the most fundamental of these are thermally-driven base stacking-unstacking interactions. The smallest DNA unit that can undergo such transitions is the dinucleotide, whose structural and dynamic properties are dominated by stacking, while the ion condensation, cooperative stacking and inter-base hydrogen-bonding present in duplex DNA are not involved. We use dApdA to study stacking-unstacking at the dinucleotide level because the fluctuations observed are likely to resemble those of larger DNA molecules, but in the absence of constraints introduced by cooperativity are likely to be more pronounced, and thus more accessible to measurement. We study these fluctuations with a combination of Molecular Dynamics simulations on the microsecond timescale and Markov State Model analyses, and validate our results by calculations of circular dichroism (CD) spectra, with results that agree well with the experimental spectra. Our analyses show that the CD spectrum of dApdA is defined by two distinct chiral conformations that correspond, respectively, to a Watson–Crick form and a hybrid form with one base in a Hoogsteen configuration. We find also that ionic structure and water orientation around dApdA play important roles in controlling its breathing fluctuations. 

Fluorescence-detected Fourier transform (FT) spectroscopy is a technique in which the relative paths of an optical interferometer are controlled to excite a material sample, and the ensuing fluorescence is detected as a function of the interferometer path delay and relative phase. A common approach to enhance the signal-to-noise ratio in these experiments is to apply a continuous phase sweep to the relative optical path, and to detect the resulting modulated fluorescence using a phase-sensitive lock-in amplifier. In many important situations, the fluorescence signal is too weak to be measured using a lock-in amplifier, so that photon counting techniques are preferred. Here we introduce an approach to low-signal fluorescence-detected FT spectroscopy, in which individual photon counts are assigned to a modulated interferometer phase (‘phase-tagged photon counting,’ or PTPC), and the resulting data are processed to construct optical spectra. We studied the fluorescence signals of a molecular sample excited resonantly by a pulsed coherent laser over a range of photon flux and visibility levels. We compare the performance of PTPC to standard lock-in detection methods and establish the range of signal parameters over which meaningful measurements can be carried out. We find that PTPC generally outperforms the lock-in detection method, with the dominant source of measurement uncertainty being associated with the statistics of the finite number of samples of the photon detection rate.

 

The authors demonstrate a form of two‐photon‐counting interferometry by measuring the coincidence counts between single‐photon‐counting detectors at an output port of a Mach–Zehnder Interferometer (MZI) following injection of broad‐band time‐frequency‐entangled photon pairs (EPP) generated from collinear spontaneous parametric down conversion into a single input port. Spectroscopy and refractometry are performed on a sample inserted in one internal path of the MZI by scanning the other path in length, which acquires phase and amplitude information about the sample's linear response. Phase modulation and lock‐in detection are introduced to increase detection signal‐to‐noise ratio and implement a “down‐sampling” technique for scanning the interferometer delay, which reduces the sampling requirements needed to reproduce fully the temporal interference pattern. The phase‐modulation technique also allows the contributions of various quantum‐state pathways leading to the final detection outcomes to be extracted individually. Feynman diagrams frequently used in the context of molecular spectroscopy are used to describe the interferences resulting from the coherence properties of time‐frequency EPPs passing through the MZI. These results are an important step toward the implementation of a proposed method for molecular spectroscopy—quantum‐light‐enhanced 2D spectroscopy.