Highly Stable Duplex Formation by Artificial Nucleic Acids Acyclic Threoninol Nucleic Acid (aTNA) and Serinol Nucleic Acid (SNA) with Acyclic Scaffolds

The stabilities of duplexes formed by strands of novel artificial nucleic acids composed of acyclic threoninol nucleic acid (aTNA) and serinol nucleic acid (SNA) building blocks were compared with duplexes formed by the acyclic glycol nucleic acid (GNA), peptide nucleic acid (PNA), and native DNA and RNA. All acyclic nucleic acid homoduplexes examined in this study had significantly higher thermal stability than DNA and RNA duplexes. Melting temperatures of homoduplexes were in the order of aTNA>PNA≈GNA≥SNA?RNA>DNA. Thermodynamic analyses revealed that high stabilities of duplexes formed by aTNA and SNA were due to large enthalpy changes upon formation of duplexes compared with DNA and RNA duplexes. The higher stability of the aTNA homoduplex than the SNA duplex was attributed to the less flexible backbone due to the methyl group of D ‐threoninol on aTNA, which induced clockwise winding. Unlike aTNA, the more flexible SNA was able to cross‐hybridize with RNA and DNA. Similarly, the SNA/PNA heteroduplex was more stable than the aTNA/PNA duplex. A 15‐mer SNA/RNA was more stable than an RNA/DNA duplex of the same sequence.     

Stimulated emission cross sections and temperature-dependent spectral shifts of neutral nitrogen-vacancy centers in diamonds

The neutral nitrogen-vacancy (NV⁰) defects in diamond are photostable color centers, suitable for a wide range of applications in science and engineering. However, the photophysical properties of the centers have not yet been fully characterized. This work measured the stimulated emission cross sections of NV⁰ in a single-crystal diamond by two-photon excitation of its matrix at 344 nm. From the measured photoluminescence spectrum and the fluorescence lifetime of 20 ± 1 ns, we determined a peak stimulated emission cross section of 1.43 ± 0.07 × 10⁻¹⁷ cm² at 650 nm for the NV⁰ centers. In addition, we have also examined the thermal shifts of the zero-phonon line of NV⁰ centers in nanoscale diamonds (~100 nm in diameter) over the temperature range of 30–120°C. A temperature measurement sensitivity of 0.2 K·Hz^−1/2 was achieved, which is about two-fold better than that of NV⁻, despite that the fluorescence intensity of NV⁰ is about six-fold lower than that of NV⁻ in the same nanoparticles. The result is attributed to the smaller electron–phonon coupling strength of the neutral center, compared with its negatively charged counterpart.     

Molecular Design for Reversing the Photoswitching Mode of Turning ON and OFF DNA Hybridization

A new photoswitch for DNA hybridization involving para‐substituted azobenzenes (such as isopropyl‐ or tert‐butyl‐substituted derivatives) with L ‐threoninol as a linker was synthesized. Irradiation of the modified DNA with visible light led to dissociation of the duplex owing to the destabilization effect of the bulky substituent on the trans‐azobenzene. In contrast, trans‐to‐cis isomerization (UV light irradiation) facilitated duplex formation. The direction of this photoswitching mode was entirely reversed relative to the previous system with an unmodified azobenzene on D ‐threoninol whose trans form turned on the hybridization, and cis form turned it off. Such reversed and reversible photoswitching of DNA hybridization was directly demonstrated by using fluorophore‐ and quencher‐attached oligonucleotides. Furthermore, it was revealed that the cis‐to‐trans thermal isomerization was greatly suppressed in the presence of the complementary strand owing to the formation of the more‐stable duplex in the cis form.     

Ultraviolet action spectrum (238-405 nm) for inhibition of glycine uptake in E. coli.

Abstract— Initial rate of uptake of ³H-glycine by Escherichia coli B/r was measured immediately after irradiation with monochromatic light. Uptake was proportional to time for at least 2 min in both control and irradiated samples. Inhibition of uptake is an exponential function of fluence to about 20% remaining activity, beyond which it is much more resistant to irradiation, suggesting two different uptake systems. The principal (sensitive) system shows an F₃₇ of 2.2 kJ/m² at 280 nm and 110 kJ/m² at 334 nm. The response is independent of cell killing and of presence of the rel gene. The chromophore remains unidentified, although an action spectrum suggests a protein chromophore in the far-UV (below 300 nm) region and a menaquinone chromophore in the near-ultraviolet (above 300 nm). A 10–20%, stimulation of uptake rate, which we cannot account for, is observed at low fluences (generally below 100 kJ/m²) at 313, 366 and 405 nm, but not at 334 nm.     

Photoinactivation of the Coronavirus Surrogate phi6 by Visible Light

To stop the coronavirus spread, new inactivation approaches are being sought that can also be applied in the presence of humans or even on humans. Here, we investigate the effect of visible violet light with a wavelength of 405 nm on the coronavirus surrogate phi6 in two aqueous solutions that are free of photosensitizers. A dose of 1300 J cm^?2 of 405 nm irradiation reduces the phi6 plaque‐forming unit concentration by three log‐levels. The next step should be similar visible light photoinactivation investigations on coronaviruses, which cannot be performed in our lab.     

Photoregulation of DNA triplex formation by azobenzene

Formation and dissociation of DNA triplex are reversibly photoregulated by cis <--> trans isomerization of the azobenzene tethered to the third strand. When the azobenzene takes the trans from, a stable triplex is formed. Upon the isomerization of trans-azobenzene to its cis form by UV light irradiation (300 < lambda < 400 nm), however, the modified oligonucleotide is removed from the target duplex. The triplex is re-formed on photoinduced cis --> trans isomerization (lambda > 400 nm). The photoregulating activity significantly depends on the position of azobenzene in the third strand, as well as on the geometric position (meta or para) of its amido substituent. For m-amidoazobenzene, the photoregulation is the most effective when it is tethered to the 5'-end of the third strand. However, p-amidoazobenzene should be introduced into the middle of the strand for effective regulation. In the optimal cases, the change of T(m) of the triplex, caused by the cis <--> trans isomerization of azobenzene, is greater than 30 degrees C. UV-visible and CD spectroscopy, as well as computer modeling studies, clearly demonstrate that the trans-azobenzene intercalates between the base pairs in the target duplex and thus stabilizes the triplex by stacking interactions. On the other hand, nonplanar cis-azobenzene destabilizes the triplex due to its steric hindrance against the adjacent base pairs.     

Psoralen-Derivatized Oligothymidine Methylphosphonates form Triple Helices with DNA and Crosslink to a Specific Strand

Oligothymidine methylphosphonates derivatized at the 5′-end with 4′-aminoalkyl-4,5′,8-trimethylpsoralen (AMT) were prepared. The interaction of these oligonucleoside methylphosphonates with double-stranded DNA was studied. Oligothymidine tnethylphosphonates, T₇ and T₁₄, were found to form triple helix with an oligodeoxyribonucleotide 45-mer DNA duplex which contains an A₁₅-T₁₅ sequence. Upon irradiation with 365 nm (UV light, AMT crosslinked to accessible thymidine residues in the target DNA. Both AMT-derivatized T₇ and T₁₄ crosslink to the T₁₅ containing strand of the double-stranded DNA target, but they do not crosslink to the A₁₅ containing strand which also contains a potential thymidine crosslinking site. Methylphosphonate oligomer, T₇, was derivatized with AMT using either an ethyl-, butyl- or hexyl-linker. The efficiency of crosslinking is affected by the length of the aminoalkyl linker arm connecting the AMT to the methylphosphonate oligomer. The relative crosslinking efficiencies of the oligomers with these three types of linkers were different. Greatest crosslinking, 45%, was obtained using an oligomer having a butyl-or a hexyl-linker. The interaction of oligothymidine methylphosphonates with DNA can be enhanced by using two shorter AMT-oligomers instead of using one full-length AMT-derivatized oligomer. This strategy was demonstrated by the interaction of AMT-derivatized T₇ with duplex DNA 35-mer and 45-mer target. The extent of crosslinking to the 45-mer target, whose binding site can accommodate two molecules of AMT-derivatized T₇, is 45% whereas that with the 35-mer target, which can accommodate only one T₇ molecule, is only 3%. The results of our experiments suggest that AMT-derivatized oligothymidine methylphosphonates can form triple-stranded complex and psoralen photoadduct with DNA. The formation of such complexes may be useful in probing and controlling gene expression at the DNA level.     

8-METHOXYPSORALEN-PHOTOINDUCED DNA CROSSLINKS AS DETERMINED IN YEAST BY ALKALINE STEP ELUTION UNDER DIFFERENT REIRRADIATION CONDITIONS. RELATION WITH GENETIC EFFECTS

Abstract— DNA damage induced by 8-methoxypsoralen (8-MOP) plus near UV light (UVA) was analyzed in diploid yeast using the alkaline step elution technique. The presence of 8-MOP and UVA induced DNA interstrand cross-links was revealed by the increase of DNA retained on elution filters as compared to untreated controls. The fraction of DNA retained on filters increased linearly with UVA dose. The amount of cross-links was estimated from the fraction of DNA retained on filters using a dose of -radiation leading to a number of DNA strand breaks at least equivalent to the number of 8-MOP induced photoadducts.
When 8-MOP treated cells were exposed to monochromatic light, 365 nm light induced monoadducts and cross-links whereas 405 nm light induced only monoadducts. When submitting 8-MOP plus 405 nm light treated cells to 365 nm irradiation, after removal of unbound 8-MOP by washing, a portion of 8-MOP plus 405 nm light induced monoadducts was converted into cross-links. The amount of monoadducts transformed into cross-links was dependent on the dose of 365 nm irradiation up to a maximum likely to correspond to the number of suitably positioned furan-side monoadducts that could be converted into biadducts. When 8-MOP plus 365 nm light treated cells were reirradiated with 365 nm light, following the same protocol, the maximum level of cross-linking obtainable in yeast was lower than that obtained with 8-MOP in a 405 nm plus 365 nm reirradiation protocol.
In the presence of 8-MOP single exposures to 405 nm light were found to be only slightly genotoxic. However, when followed by second exposures to 365 nm light, a dose-dependent increase in genetic effects, i.e. mutation and gene conversion, was observed in parallel to the induction of DNA crosslinks. These results stress again the prominent role of DNA cross-links in the genotoxicity of 8-MOP.     

High-Intensity 405 nm Light Inactivation of Listeria monocytogenes

The antimicrobial properties of light is an area of increasing interest. This study investigates the sensitivity of the significant foodborne pathogen Listeria monocytogenes to selected wavelengths of visible light. Results demonstrate that exposure to wavelength region 400–450 nm, at sufficiently high dose levels (750 J cm^?2), induced complete inactivation of a 5 log₁₀ population. Exposure to wavelengths longer than 450 nm did not cause significant inactivation. Analysis of 10 nm bandwidths between 400 and 450 nm confirmed 405(±5) nm light to be most effective for the inactivation of L. monocytogenes, with a lesser bactericidal effect also evident at other wavelengths between 400 and 440 nm. Identification of the optimum bactericidal wavelength enabled the comparison of inactivation using 405(±5) nm filtered light and a 405 nm light‐emitting diode (LED) array (14 nm FWHM). Results demonstrate similar inactivation kinetics, indicating that the applied dose of 405 nm light is the important factor. Use of the 405 nm LED array for the inactivation of L. monocytogenes and other Listeria species resulted in similar kinetics, with up to 5 log₁₀ reductions with a dose of 185 J cm^?2. Comparative data for the 405 nm light inactivation of L. monocytogenes and other important foodborne pathogens, Escherichia coli, Salmonella enteritidis and Shigella sonnei, are also presented, with L. monocytogenes showing higher susceptibility to inactivation through 405 nm light exposure.     

INDUCTION OF DNA-PROTEIN CROSSLINKS IN HUMAN CELLS BY ULTRAVIOLET and VISIBLE RADIATIONS: ACTION SPECTRUM

Abstract— DNA-protein crosslinking was induced in cultured human P3 teratocarcinoma cells by irradiation with monochromatic radiation with wavelengths in the range254–434 nm (far-UV, near-UV, and blue light). Wavelength 545 nm green light did not induce these crosslinks, using the method of alkaline elution of the DNA from membrane filters. The action spectrum for the formation of DNA-protein crosslinks revealed two maxima, one in the far-UV spectrum that closely coincided with the relative spectrum of DNA at 254 and 290 nm, and one in the visible light spectrum at 405 nm, which has no counterpart in the DNA spectrum. The primary events for the formation of DNA-protein crosslinks by such long-wavelength radiation probably involve photosensitizers. This dual mechanism for DNA-protein crosslink formation is in strong contrast to the single mechanism for pyrimidine dimer formation in DNA, which apparently has no component in the visible light spectrum.     

IN VIVO INDUCTION OF 4-THIOURIDINE-CYTIDINE ADDUCTS IN tRNA OF E. COLI B/r BY NEAR-ULTRAVIOLET RADIATION*

Abstract— Near-ultraviolet (near-UV; 320–405 nm) irradiation of Escherichia coli B/r induces the formation in vivo of ⁴Srd-Cyd adducts in transfer RNA, as evidenced by (1) fluorescence spectrum changes of tRNA extracted from irradiated cells and reduced with NaBH₄, (2) thin-layer chromatography on cellulose of hydrolysates of trichloroacetic acid-precipitable extracts of irradiated cells, and (3) comparison of these findings with adduct formation induced by near-UV irradiation of purified mixed tRNA from E. coli. The kinetics of induction of the ⁴Srd-Cyd adduct in vivo, and the near-UV fluences required, provide strong support for our earlier hypothesis that formation of these adducts is responsible for near-UV-induced growth delay in E. coli.     

Wavelength sensitivity of the photoinduced reaction in polycarbonate

Bisphenol A polycarbonate (PC) was irradiated with monochromatic light of wavelengths 260, 280, 300, 320, 340, 400, and 500 nm by use of the Okazaki large spectrograph (OLS). The quantum yield of main-chain scission (?_cs), efficiency of photo-Fries rearrangement (E_r), and effects of wavelength on ?_cs and E_r were investigated. It was found that photodegradation and photo-Fries rearrangement of PC took place by the irradiation of 260–300 nm light, but did not by the irradiation at λ ≧ 320 nm. The ?_cs has a maximum value in the case of the irradiation with 260 nm light, while E_r was found to have a maximum value by the irradiation of 280 nm light. © 1993 John Wiley & Sons, Inc.     

Light-Induced Self-Escape of Spherical Nucleic Acid from Endo/Lysosome for Efficient Non-Cationic Gene Delivery

Developing non-cationic gene carriers and achieving efficient endo/lysosome escape of functional nucleic acids in cytosol are two major challenges faced by the field of gene delivery. Herein, we demonstrate the concept of self-escape spherical nucleic acid (SNA) to achieve light controlled non-cationic gene delivery with sufficient endo/lysosome escape capacity. In this system, Bcl-2 antisense oligonucleotides (OSAs) were conjugated onto the surface of aggregation-induced emission (AIE) photosensitizer (PS) nanoparticles to form core–shell SNA. Once the SNAs were taken up by tumor cells, and upon light irradiation, the accumulative ¹O₂ produced by the AIE PSs ruptured the lysosome structure to promote OSA escape. Prominent in vitro and in vivo results revealed that the AIE-based core–shell SNA could downregulate the anti-apoptosis protein (Bcl-2) and induce tumor cell apoptosis without any transfection reagent.     

Visible‐Light‐Triggered Cross‐Linking of DNA Duplexes by Reversible [2+2] Photocycloaddition of Styrylpyrene

Reversible photo‐cross‐linking of a DNA duplex through the [2+2] photocycloaddition of styrylpyrene is reported. Styrylpyrene moieties on d ‐threoninol linkers were introduced into complementary positions on DNA strands. Irradiation of the styrylpyrene pair in the duplex with visible light at λ=455 nm induced a [2+2] photocycloaddition between styrylpyrenes that cross‐linked the two strands of the duplex. Two diastereomers were formed after [2+2] photocycloaddition as a result of rotation of the styrylpyrene residues. Also, the cycloreversion reaction was induced by UV light at λ=340 nm, which reversibly yielded the uncross‐linked strands.     

DNA Functionality with Photoswitchable Hydrazone Cytidine**

A new family of hydrazone modified cytidine phosphoramidite building block was synthesized and incorporated into oligodeoxynucleotides to construct photoswitchable DNA strands. The E-Z isomerization triggered by the irradiation of blue light with a wavelength of 450 nm was investigated and confirmed by ¹H NMR spectroscopy and HPLC in the contexts of both nucleoside and oligodeoxynucleotide. The light activated Z form isomer of this hydrazone-cytidine with a six-member intramolecular hydrogen bond was found to inhibit DNA synthesis in the primer extension model by using Bst DNA polymerase. In addition, the hydrazone modification caused the misincorporation of dATP together with dGTP into the growing DNA strand with similar selectivity, highlighting a potential G to A mutation. This work provides a novel functional DNA building block and an additional molecular tool that has potential chemical biology and biomedicinal applications to control DNA synthesis and DNA-enzyme interactions using the cell friendly blue light irradiation.     

THE FORMATION OF PHOTOREVERSIBLE CYCLOBUTANE-TYPE PYRIMIDINE DIMERS IN ULTRAVIOLET-IRRADIATED POTATO VIRUS X*

Abstract— Photoreversible cyclobutane-type pyrimidine dimers were found in ³²P-labeled RN A isolated from intact potato virus X irradiated with 254 nm light. The number of dimers was correlated with the biological infectivity of the ultraviolet-treated virus. Assuming that incorporated ³²P is homogeneously distributed in the viral RNA chain, it can be calculated that about 5·7±1·7 dimers are present in each strand of virus per lethal biological hit.     

Photoreactivation of RNA in UV-irradiated insect eggs (Smittia sp., Chironomidae, Diptera) II. Evidence for heterogeneous light-dependent repair activities

Abstract. Two biological effects of UV radiation upon Smittia eggs are observed, both of which seem to be associated with the formation of pyrimidine dimers in the RNA (largely ribosomal) of the eggs. While irradiation of the anterior pole region causes the formation of an aberrant segment pattern (double abdomen induction), irradiation of entire eggs leads to an arrest of their development (inactiva-tion). Both UV effects are photoreversible with different action spectra of the photoreactivating light. A dose rate dependence of the photoreactivation can be observed after both UV effects. The saturating dose rate is about 6 W/m² (at 440 nm) after UV induction of double abdomens. Upon UV inactivation, the saturating dose rate level for the photoreactivating light is much higher, and a single light flash causes both a considerable biological reactivation and the disappearance of about 7 × 10⁹ pyrimidine dimers from the total RNA per egg. The results indicate the presence of heterogeneous light-dependent repair activities acting upon UV induced pyrimidine dimers in the RNA of the eggs.     

Infrared multiphoton dissociation of small-interfering RNA anions and cations

Infrared multiphoton dissociation (IRMPD) on a linear ion trap mass spectrometer is applied for the sequencing of small interfering RNA (siRNA). Both single-strand siRNAs and duplex siRNA were characterized by IRMPD, and the results were compared with that obtained by traditional ion trap-based collision induced dissociation (CID). The single-strand siRNA anions were observed to dissociate via cleavage of the 5′ P—O bonds yielding c- and y-type product ions as well as undergo neutral base loss. Full sequence coverage of the siRNA anions was obtained by both IRMPD and CID. While the CID mass spectra were dominated by base loss ions, accounting for ∼25% to 40% of the product ion current, these ions were eliminated through secondary dissociation by increasing the irradiation time in the IRMPD mass spectra to produce higher abundances of informative sequence ions. With longer irradiation times, however, internal ions corresponding to cleavage of two 5′ P—O bonds began to populate the product ion mass spectra as well as higher abundances of [a − Base] and w-type ions. IRMPD of siRNA cations predominantly produced c- and y-type ions with minimal contributions of [a − Base] and w-type ions to the product ion current; the presence of only two complementary series of product ions in the IRMPD mass spectra simplified spectral interpretation. In addition, IRMPD produced high abundances of protonated nucleobases, [G + H]⁺, [A + H]⁺, and [C + H]⁺, which were not detected in the CID mass spectra due to the low-mass cut-off associated with conventional CID in ion traps. CID and IRMPD using short irradiation times of duplex siRNA resulted in strand separation, similar to the dissociation trends observed for duplex DNA. With longer irradiation times, however, the individual single-strands underwent secondary dissociation to yield informative sequence ions not obtained by CID.     

Flow-injection fluorimetric determination of menadione using on-line photo-reduction in micellar media

A very sensitive fluorimetric method for the determination of menadione using a flow injection system is proposed. The method is based on the on-line reduction of menadione in dodecylsulphate micelles upon irradiation with UV light. The strong fluorescence of the reduced menadione in micellar medium is measured at 410 nm with excitation at 340 nm. The method shows a linear range between 2.42 and 245 ng ml⁻¹ and a limit of detection of 0.18 ng ml⁻¹. The sample throughput was 90 injections per hour. The applicability of the assay was demonstrated by analysing this vitamin in commercial pharmaceutical preparations.     

Molecular structure and photoreaction of poly(methylpropylsilane)

The molecular structure and photoreaction of poly(methylpropylsilane) (PMPrS) are investigated. The ²⁹Si-NMR spectra reveal that PMPrS is a linear polymer with no blanches. Fine multiple splitting of ²⁹Si-NMR is observed at room temperature. This multiple splitting is thought to be due to molecular conformation. The photo-oxidation reaction of the PMPrS film is found to be caused by light irradiation at the UV absorption band, 330 nm. Quantum efficiencies of scission and crosslink related to photodegradation are evaluated. There is little difference in either the molecular structure or photoreactivities between the high and the low molecular weight portions of the bimodal molecular weight distributions of PMPrS.