TMPyP binding evokes a complex, tunable nanomechanical response in DNA.

TMPyP is a porphyrin capable of DNA binding and used in photodynamic therapy and G-quadruplex stabilization. Despite its broad applications, TMPyP's effect on DNA nanomechanics is unknown. Here we investigated, by manipulating λ-phage DNA with optical tweezers combined with microfluidics in equilibrium and perturbation kinetic experiments, how TMPyP influences DNA nanomechanics across wide ranges of TMPyP concentration (5-5120 nM), mechanical force (0-100 pN), NaCl concentration (0.01-1 M) and pulling rate (0.2-20 µm/s). Complex responses were recorded, for the analysis of which we introduced a simple mathematical model. TMPyP binding, which is a highly dynamic process, leads to dsDNA lengthening and softening. dsDNA stability increased at low (<10 nM) TMPyP concentrations, then decreased progressively upon increasing TMPyP concentration. Overstretch cooperativity decreased, due most likely to mechanical roadblocks of ssDNA-bound TMPyP. TMPyP binding increased ssDNA's contour length. The addition of NaCl at high (1 M) concentration competed with the TMPyP-evoked nanomechanical changes. Because the largest amplitude of the changes is induced by the pharmacologically relevant TMPyP concentration range, this porphyrin derivative may be used to tune DNA's structure and properties, hence control the wide array of biomolecular DNA-dependent processes including replication, transcription, condensation and repair.

Single-Molecule Mechanics in Ligand Concentration Gradient.

Single-molecule experiments provide unique insights into the mechanisms of biomolecular phenomena. However, because varying the concentration of a solute usually requires the exchange of the entire solution around the molecule, ligand-concentration-dependent measurements on the same molecule pose a challenge. In the present work we exploited the fact that a diffusion-dependent concentration gradient arises in a laminar-flow microfluidic device, which may be utilized for controlling the concentration of the ligand that the mechanically manipulated single molecule is exposed to. We tested this experimental approach by exposing a λ-phage dsDNA molecule, held with a double-trap optical tweezers instrument, to diffusionally-controlled concentrations of SYTOX Orange (SxO) and tetrakis(4-N-methyl)pyridyl-porphyrin (TMPYP). We demonstrate that the experimental design allows access to transient-kinetic, equilibrium and ligand-concentration-dependent mechanical experiments on the very same single molecule.

How realistic are painted lightnings? Quantitative comparison of the morphology of painted and real lightnings: a psychophysical approach.

Inspired by the pioneer work of the nineteenth century photographer, William Nicholson Jennings, we studied quantitatively how realistic painted lightnings are. In order to answer this question, we examined 100 paintings and 400 photographs of lightnings. We used our software package to process and evaluate the morphology of lightnings. Three morphological parameters of the main lightning branch were analysed: (i) number of branches Nb, (ii) relative length r, and (iii) number of local maxima (peaks) Np of the turning angle distribution. We concluded: (i) Painted lightnings differ from real ones in Nb and Np. (ii) The r-values of painted and real lightnings vary in the same range. (iii) 67 and 22% of the studied painted and real lightnings were non-bifurcating (Nb = 1, meaning only the main branch), the maximum of Nb of painted and real lightnings is 11 and 51, respectively, and painted bifurcating lightnings possess mostly 2-4 branches, while real lightnings have mostly 2-10 branches. To understand these findings, we performed two psychophysical experiments with 10 test persons, whose task was to guess Nb on photographs of real lightnings which were flashed for short time periods Δt = 0.5, 0.75 and 1 s (characteristic to lightnings) on a monitor. We obtained that (i) test persons can estimate the number of lightning branches quite correctly if Nb ≤ 11. (ii) If Nb > 11, its value is strongly underestimated with exponentially increasing difference between the real and estimated numbers. (iii) The estimation is independent of the flashing period Δt of lightning photos/pictures. (iv) The estimation is more accurate, if skeletonized lightning pictures are flashed, rather than real lightning photos. These findings explain why artists usually illustrate lightnings with branches not larger than 11.

Accuracy of the hypothetical sky-polarimetric Viking navigation versus sky conditions: revealing solar elevations and cloudinesses favourable for this navigation method.

According to Thorkild Ramskou's theory proposed in 1967, under overcast and foggy skies, Viking seafarers might have used skylight polarization analysed with special crystals called sunstones to determine the position of the invisible Sun. After finding the occluded Sun with sunstones, its elevation angle had to be measured and its shadow had to be projected onto the horizontal surface of a sun compass. According to Ramskou's theory, these sunstones might have been birefringent calcite or dichroic cordierite or tourmaline crystals working as polarizers. It has frequently been claimed that this method might have been suitable for navigation even in cloudy weather. This hypothesis has been accepted and frequently cited for decades without any experimental support. In this work, we determined the accuracy of this hypothetical sky-polarimetric Viking navigation for 1080 different sky situations characterized by solar elevation θ and cloudiness ρ, the sky polarization patterns of which were measured by full-sky imaging polarimetry. We used the earlier measured uncertainty functions of the navigation steps 1, 2 and 3 for calcite, cordierite and tourmaline sunstone crystals, respectively, and the newly measured uncertainty function of step 4 presented here. As a result, we revealed the meteorological conditions under which Vikings could have used this hypothetical navigation method. We determined the solar elevations at which the navigation uncertainties are minimal at summer solstice and spring equinox for all three sunstone types. On average, calcite sunstone ensures a more accurate sky-polarimetric navigation than tourmaline and cordierite. However, in some special cases (generally at 35° ≤ θ ≤ 40°, 1 okta ≤ ρ ≤ 6 oktas for summer solstice, and at 20° ≤ θ ≤ 25°, 0 okta ≤ ρ ≤ 4 oktas for spring equinox), the use of tourmaline and cordierite results in smaller navigation uncertainties than that of calcite. Generally, under clear or less cloudy skies, the sky-polarimetric navigation is more accurate, but at low solar elevations its accuracy remains relatively large even at high cloudiness. For a given ρ, the absolute value of averaged peak North uncertainties dramatically decreases with increasing θ until the sign (±) change of these uncertainties. For a given θ, this absolute value can either decrease or increase with increasing ρ. The most advantageous sky situations for this navigation method are at summer solstice when the solar elevation and cloudiness are 35° ≤ θ ≤ 40° and 2 oktas ≤ ρ ≤ 3 oktas.

Celestial polarization patterns sufficient for Viking navigation with the naked eye: detectability of Haidinger's brushes on the sky versus meteorological conditions.

If a human looks at the clear blue sky from which light with high enough degree of polarization d originates, an 8-shaped bowtie-like figure, the yellow Haidinger's brush can be perceived, the long axis of which points towards the sun. A band of high d arcs across the sky at 90° from the sun. A person can pick two points on that band, observe the yellow brushes and triangulate the position of the sun based on the orientation of the two observed brushes. This method has been suggested to have been used on the open sea by Viking navigators to determine the position of the invisible sun occluded by cloud or fog. Furthermore, Haidinger's brushes can also be used to locate the sun when it is below the horizon or occluded by objects on the horizon. To determine the position of the sun using the celestial polarization pattern, the d of the portion of the sky used must be greater than the viewer's degree of polarization threshold d* for perception of Haidinger's brushes. We studied under which sky conditions the prerequisite d > d* is satisfied. Using full-sky imaging polarimetry, we measured the d-pattern of skylight in the blue (450 nm) spectral range for 1296 different meteorological conditions with different solar elevation angles θ and per cent cloud cover ρ. From the measured d-patterns of a given sky we determined the proportion P of the sky for which d > d*. We obtained that P is the largest at low solar elevations θ ≈ 0° and under totally or nearly clear skies with cloud coverage ρ = 0%, when the sun's position is already easily determined. If the sun is below the horizon (-5° ≤ θ < 0°) during twilight, P = 76.17 ± 4.18% for [Formula: see text] under clear sky conditions. Consequently, the sky-polarimetric Viking navigation based on Haidinger's brushes is most useful after sunset and prior to sunrise, when the sun is not visible and large sky regions are bright, clear and polarized enough for perception of Haidinger's brushes.

North error estimation based on solar elevation errors in the third step of sky-polarimetric Viking navigation.

The theory of sky-polarimetric Viking navigation has been widely accepted for decades without any information about the accuracy of this method. Previously, we have measured the accuracy of the first and second steps of this navigation method in psychophysical laboratory and planetarium experiments. Now, we have tested the accuracy of the third step in a planetarium experiment, assuming that the first and second steps are errorless. Using the fists of their outstretched arms, 10 test persons had to estimate the elevation angles (measured in numbers of fists and fingers) of black dots (representing the position of the occluded Sun) projected onto the planetarium dome. The test persons performed 2400 elevation estimations, 48% of which were more accurate than ±1°. We selected three test persons with the (i) largest and (ii) smallest elevation errors and (iii) highest standard deviation of the elevation error. From the errors of these three persons, we calculated their error function, from which the North errors (the angles with which they deviated from the geographical North) were determined for summer solstice and spring equinox, two specific dates of the Viking sailing period. The range of possible North errors ΔωN was the lowest and highest at low and high solar elevations, respectively. At high elevations, the maximal ΔωN was 35.6° and 73.7° at summer solstice and 23.8° and 43.9° at spring equinox for the best and worst test person (navigator), respectively. Thus, the best navigator was twice as good as the worst one. At solstice and equinox, high elevations occur the most frequently during the day, thus high North errors could occur more frequently than expected before. According to our findings, the ideal periods for sky-polarimetric Viking navigation are immediately after sunrise and before sunset, because the North errors are the lowest at low solar elevations.

Adjustment errors of sunstones in the first step of sky-polarimetric Viking navigation: studies with dichroic cordierite/ tourmaline and birefringent calcite crystals.

According to an old but still unproven theory, Viking navigators analysed the skylight polarization with dichroic cordierite or tourmaline, or birefringent calcite sunstones in cloudy/foggy weather. Combining these sunstones with their sun-dial, they could determine the position of the occluded sun, from which the geographical northern direction could be guessed. In psychophysical laboratory experiments, we studied the accuracy of the first step of this sky-polarimetric Viking navigation. We measured the adjustment error e of rotatable cordierite, tourmaline and calcite crystals when the task was to determine the direction of polarization of white light as a function of the degree of linear polarization p. From the obtained error functions e(p), the thresholds p* above which the first step can still function (i.e. when the intensity change seen through the rotating analyser can be sensed) were derived. Cordierite is about twice as reliable as tourmaline. Calcite sunstones have smaller adjustment errors if the navigator looks for that orientation of the crystal where the intensity difference between the two spots seen in the crystal is maximal, rather than minimal. For higher p (greater than p crit) of incident light, the adjustment errors of calcite are larger than those of the dichroic cordierite (p crit=20%) and tourmaline (p crit=45%), while for lower p (less than p crit) calcite usually has lower adjustment errors than dichroic sunstones. We showed that real calcite crystals are not as ideal sunstones as it was believed earlier, because they usually contain scratches, impurities and crystal defects which increase considerably their adjustment errors. Thus, cordierite and tourmaline can also be at least as good sunstones as calcite. Using the psychophysical e(p) functions and the patterns of the degree of skylight polarization measured by full-sky imaging polarimetry, we computed how accurately the northern direction can be determined with the use of the Viking sun-dial under 10 different sky conditions at 61° latitude, which was one of the main Viking sailing routes. According to our expermiments, under clear skies, using calcite or cordierite or tourmaline sunstones, Viking sailors could navigate with net orientation errors [Formula: see text]. Under overcast conditions, their net navigation error depends on the sunstone type: [Formula: see text], [Formula: see text] and [Formula: see text].