Secondary structure of poliovirus RNA: correlation of computer-predicted with electron microscopically observed structure

A secondary structure map of poliovirus 1, strain Mahoney, RNA was determined by psoralen crosslinking the (+) strand and visualizing the structures in the electron microscope. Hairpins and looped hairpins were observed, and the size and distribution were measured. To orient map features the 3' end of the RNA was linked to polybromodeoxyuridine [poly(BUdR)]SV40 and histograms were constructed from these measurements. Secondary structure maps of the RNA were likewise constructed from the results of computer prediction programs for secondary structure. The programs used were those of M. Zuker (RNA2 and FOLD) which calculate a minimal global energy for a given sequence. Many single hairpins predicted by both RNA2 and FOLD showed a correlation with the histograms of hairpin structures of RNA crosslinked with psoralen. A secondary structure map was also constructed for the entire 7433 bases using the option in FOLD which allows multi-branch loops by folding uniformly stepped overlapping segments. Any structure that occurred at or greater than a given frequency was selected and mapped with respect to genome position. A correlation in structured regions was seen between psoralen-derived and computer-predicted maps of secondary structure. Furthermore, a region of large loops from base position 681 to 3899 was noted that corresponded to frequently observed large loop(s) in electron micrographs of psoralen preparations of RNA. Agreement between the two methods of determining secondary structure strengthens the credibility of the computer-aided methods used for predicting secondary structure and allows us to suggest an overall secondary structure map for poliovirus RNA.

Fluorescence studies on the interaction of furocoumarins with DNA in the dark

The dark interaction of furocoumarins with DNA has been studied by a fluorescence quenching technique. The intrinsic fluorescence of psoralen, 4,5', 8-trimethylpsoralen (TMP) and 8-methoxypsoralen (8-MOP) was quenched to an appreciable extent upon their noncovalent binding to DNA molecule. The analysis of the binding data revealed that TMP binds to DNA with higher efficiency than 8-MOP and psoralen, their apparent Scatchard binding constants being 13.2 X 10(5) M-1, 7.1 X 10(5) M-1, and 12.2 X 10(5) M-1, respectively. The interaction of furocoumarins with DNA was strongly dependent on the conformational stability of DNA in the particular interaction media. The perturbation of DNA structure by changing the ionic environment decreased its interaction with furocoumarins. However, the interaction was facilitated by the presence of an electron-donating moiety in the parent compound, psoralen.

[Photogeneration of singlet oxygen by psoralens]

Photosensitized luminescence of singlet (1 delta g) molecular oxygen with the maximum at 1272 nm has been found in solutions of psoralen, angelicin and 8-methoxypsoralen in CCl4. The luminescence excitation spectra, quantum yields of generation (gamma g) and rate constants of quenching (Kq) of 1 delta g by psoralens have been measured. The gamma g values 0,0055, 0,0026, 0,002 and Kq values 9 X 10(3), 11 X 10(3) and 12 X X 10(3) have been obtained for psoralen, angelicin and 8-methoxypsoralen, respectively. The role of 1 delta g in a photobiological action of psoralens is discussed.

[Dark oxidation of unsaturated lipids and dihydroxy phenylalanine by photooxidized furocoumarins]

Well-known skin photosensitizers furocoumarins--psoralen, angelio in and 8-methoxypsoralen were shown to photosensitize oxidation of unsaturated lipids and dihydroxyphenylalanine via a two-step mechanism. At the first step (UV-irradiation at 366 nm) photooxidation of furocoumarins occurred, at the second step--the photooxidized furocoumarins oxidized unsaturated lipids or dihydroxyphenylalanine in darkness. The photochemical activity of furocoumarins in the two-step reaction decreased as follows: psoralen greater than angelicin greater than 8-methoxypsoralen. Similar photoreactions appear to participate in induction of phototoxic effects of furocoumarins.

The reactivities of furocoumarin excited states with DNA in solution. A laser flash photolysis and fluorescence study

The effect of DNA on both the fluorescence emission spectra and yields and lifetimes of the triplet stae of psoralen and 8-methoxypsoralen in aqueous solution has been determined. The changes in the fluorescence spectra are similar in nature for both of these furocoumarins and are attributed to binding of the drug to DNA. The yield of the 8-methoxypsoralen triplet state when bound to DNA was found to be similar, if not identical, to that measured in the absence of DNA. This contrasts sharply with data obtained for psoralen from which it is concluded that either the yield of bound psoralen triplet states is very low, if not zero, or that the lifetime of such species is less than 50 ns. The relevance of this data to the molecular basis of skin photosensitisation by furocoumarins is discussed.

Tryptophan metabolism in animals with dermatitis. II) In guinea pigs

Tryptophan load in guinea pigs after induction of a photodermatitis from psoralen caused marked increase of urinary excretion of total metabolites "via kynurenine" in comparison with that obtained before dermatitis. Xanthurenic acid is the metabolite which showed the most increased levels in urine during dermatitis. This dermatitis from furocoumarin caused an alteration of tryptophan metabolism in guinea pigs as well as rats, but species differences in the excretion of metabolites after amino acid load are observed.

Tryptophan metabolism in animals with dermatitis. I) In Rats

Tryptophan metabolism "via kynurenine" after load of amino-acid has been studied in urine of rats before and after induction of experimental light-conditioned dermatitis with psoralen. Tryptophan load in animals during the acute phase of dermatitis (one day after induction) causes a markedly increased urinary excretion of total metabolites in comparison with that obtained before dermatitis. After six days of dermatitis, when the skin damage was in repair, the excretory values after tryptophan load in rats are only slightly increased indicating that the metabolic disturbance is correlated with the skin damage.

Homology-dependent cutting in trans of DNA in extracts of Escherichia coli: an approach to the enzymology of genetic recombination

An in vitro system is described in which the cutting of crosslinked phiX replicative form (RF) I DNA molecules by the uvr system of Escherichia coli induces the cutting of homologous undamaged DNA during incubation with crude extracts of thermally induced E. coli (lambda precA+) lysogens. This reaction, which has also been observed in intact E. coli lysogens infected with lambda phages, is dependent on the presence of functional recA+ and uvrB+ gene products. Extracts from thermally induced lambda precA+ lysogens of E. coli proved to be substantially more active than extracts from nonlysogenic cells of the same strain. The results provide preliminary evidence for an endonuclease activity that cuts intact superhelical DNA in response to interaction with homologus damaged DNA. In the present paper, we describe an in vitro system in which both the endonucleolytic cutting of DNA containing crosslinks and the induced cutting of undamaged DNA can be studied without purification of the participating enzymes. Although the information obtained is fragmentary and often puzzling, we feel that this system can contribute to an understanding of the complex mechanisms involved in repair and recombination.

Action of T4 endonuclease V on DNA containing various photoproducts

The action of T4 endonuclease V on DNA containing various photoproducts was investigated. (1) The enzyme introduced strand breaks in DNA from ultraviolet-irradiated vegetative cells of Bacillus subtilis but not in DNA from irradiated spores of the same organism. DNA irradiated with long wavelength (360 nm peak) ultraviolet light in the presence of 4,5',8-trimethylpsoralen was not attacked by the enzyme. These results indicate that 5-thyminyl 5,6-dihydrothymine (spore photoproduct) and psoralen mediated cross-links in DNA are not recognized by T4 endonuclease V. (2) DNA of phage PBS1, containing uracil in place of thymine, and DNA of phage SPO1, containing hydroxymethyluracil in place of thymine, were fragmented by the enzyme when the DNA's had been irradiated with ultraviolet light. T4 endonuclease V seems to act on DNA with pyrimidine dimers whether the dimers contain thymine residues or not.

Psoralen-DNA photoreaction: controlled production of mono- and diadducts with nanosecond ultraviolet laser pulses

Samples of DNA which contain adducts of a new psoralen derivative, but no cross-links, have been prepared by irradiating mixtures of DNA and the derivative with single, 15-nanosecond pulses of laser light. Succeeding pulses introduce cross-links. The ability to rapidly and selectively create monoadducts and corss-links may allow the use of psoralens as probes of dynamic processes in living cells.

The effects of indomethacin on long-wave ultraviolet-induced delayed erythema

Indomethacin, a known inhibitor of prostaglandin synthesis, administered topically as a 2.5% solution, intradermally in 10 mug doses, and orally in a dose of 150 mg/day for 2 days did not diminish the delayed erythema produced a long-wave ultraviolet light (320-400 nm). The delayed phototoxic erythema produced by 8-methoxypsoralen and subsequent exposure the long-wave ultraviolet light was similarly unaffected. By comparison, topical and intradermal indomethacin treatment produced sustained decrease in the erythemal response to ultraviolet radiation in the UVB ranges (290-320 nm).

Cutaneous effects of pulsed nitrogen gas laser irradiation

The effects of pulsed nitrogen gas laser emission (337.1 nm wavelength) were studied on human skin. The laser provides high-intensity monochromatic UVA radiation and can elicit delayed erythema in an actual exposure time of about 1 msec (105,000 pulses, each lasting 10 nsec, delivered over 210 sec). The effects of nitrogen laser irradiation were compared clinically and histologically with conventional erythemogenic UVA and UVB exposures from xenon arc or mercury arc lamps and were found to be similar in many respects. The minimal erythema dose is comparable to that obtained using more conventional continuous light sources which have more than 100 times lower intensity. A phototoxicity comparison of oral and topically applied psoralens is presented, indicating that the laser may prove useful in comparing photosenitizing capacity of certain compounds.

Electron microscopy of DNA crosslinked with trimethylpsoralen: test of the secondary structure of eukaryotic inverted repeat sequences

It has been suggested that inverted repeat (palindrome) sequences, which are widespread in eukaryotic genomes, exist in two alternate configurations, a linear form and a cruciform. To investigate the relative frequency of these forms, the DNA of intact mouse tissue culture cells was covalently crosslinked with 4,5',8-trimethylpsoralen (me3-psoralen) in order to prevent rearrangement of the DNA secondary structure during DNA isolation. The distribution of me3-psoralen crosslinks was determined by electron microscopy after denaturation of the DNA in the presence of glyoxal. Because of the high frequency and the relatively uniform distribution of the me3-psoralen crosslinks, it could be concluded that almost all of the inverted repeat sequences had been crosslinked. In spite of this, no significant number of cruciforms was detected by electron microscopy. To determine whether the me3-psoralen might itself be disrupting cruciform structures, cruciforms were first produced in isolated Tetrahymena rDNA by heat treatment and then crosslinked in vitro. The crosslinking was found to stabilize rather than disrupt these cruciforms. We conclude that the inverted repeat sequences of the mouse tissue culture cells we tested are predominantly in linear forms rather than in cruciform structures inside the cell.

Psoralen-crosslinked secondary structure map of single-stranded virus DNA

The photochemical crosslinking of DNA by 4,5',8-trimethylpsoralen (trioxsalen) has been used to freeze the secondary structures of single-stranded DNA molecules of bacteriophage fd at different ionic strengths. These secondary structures (hairpins or looped hairpins) have been visualized in the electron microscope. Most of the single-stranded circular fd DNA molecules show only one hairpin after irradiation at 15 degrees in 20 mM NaCl in the presence of trioxsalen. As the ionic strength is increased, more hairpins appear on the DNA molecules. To map these secondary structures, double-stranded supercoiled fd DNA (RFI) was cleaved with the restriction enzyme HindII, which makes only one cut on each RFI molecule. After denaturation and crosslinking of the linear single-stranded fd DNA (a mixture of viral and complementary strands), all the hairpins have been mapped on the DNA molecule with respect to this HindII site. The results show that these hairpins occur at specific sites. The most stable hairpin has been assigned to the position where the initiation site for the conversion of single-stranded fd DNA to the double-stranded covalently closed form has been mapped. The remaining hairpins map in or near regions corresponding to in vitro promoter sites on the fd DNA.

Cross-linking of DNA in situ as a probe for chromatin structure

The photochemical cross-linking of DNA in situ in chromatin is blocked over short intervals. Electron microscopy of DNA cross-linked in chromatin reveals the lengths of protected regions and provides a map of their sites along the DNA. Protected regions occur most frequently in tandem and have a basic length of 160 to 200 base pairs.

Conformational changes of nucleic acids and poly (d(A-T)-d(A-T)) caused by photoaddition of furocoumarins

DNA's of various AT content, poly[d(A-T)-d(A-T)], and double-stranded RNA were irradiated with UV light at 365 nm in the presence of linear (xanthotoxin) or angular (angelicin) furocoumarins. The covalent photobinding is strongly dependent on the spatial arrangement of furocoumarin molecules at the polymer conformation. CD measurements demonstrate that the bifunctional photochemical binding of xanthotoxin with double-stranded DNA's and poly[d(A-T)-d(A-T)] is accompanied by conformational changes which involve probably decreasing helical twisting of the double helix. This effect is greatly enhanced with increasing AT content. The formation of A-like structures is very unlikely since the B leads to A transition induced by ethanol addition was found to be strongly suppressed in xanthotoxin photoreacted DNA. The B-type helix appears to be the most sensitive conformation with minor restriction to produce photochemically induced cross-links.