Factors influencing resistance of UV-irradiated DNA to the restriction endonuclease cleavage

Perfluorooctanoic acid (PFOA)-induced alterations of biomolecules in the wetland plant Alismaorientale

Perfluoroalkyl substances (PFASs) have been widely studied by researchers due to their environmental persistence, chemical stability and potential toxicity. Some researchers have reported the physiological and biochemical toxicity of PFASs on plants through traditional and innovative methods; however, the changes in biological macromolecules caused by PFASs are rarely studied. Here, Fourier transform infrared spectroscopy (FTIR) was used to study how exposure to perfluorooctanoic acid (PFOA) alters the structure and function of biomolecules of the wetland plant Alisma orientale. Biomass results showed that PFOA had negative effects on plant growth. FTIR results showed that PFOA could result in changes in the structures, compositions, and functions of lipids, proteins and DNA in plant cells. In the treatment groups, the ratios of CH₃ to lipids and carbonyl esters to lipids increased compared with the control, while the ratios of CH₂ to lipids and olefinicCH to lipids decreased, which indicated lipid peroxidation caused by PFOA exposure. Changes in the compositions and secondary structures of proteins were also found, which were indicated by the decreased ratio of amide I to amide II and the increased ratio of β-sheet to α-helix in the treatment groups compared to the control. Moreover, PFOA affected the composition of DNA by promoting the B- to A-DNA transition. These results showed that the mechanism of PFOA toxicity toward plants at the biochemical level could be illustrated by FTIR.

Label-free and real-time imaging of dehydration-induced DNA conformational changes in cellular nucleus using second harmonic microscopy

Dehydration-induced DNA conformational changes have been probed for the first time with the use of second harmonic microscopy. Unlike conventional approaches, second harmonic microscopy provides a label-free and real-time approach to detect DNA conformational changes. Upon dehydration, cellular DNA undergoes a transition from B- to A-form, whereas cellular nuclei change from invisible to visible under second harmonic microscopy. These results showed that DNA is a second order nonlinear optical material. We further confirmed this by characterizing the nonlinear optical properties of extracted DNA from human cells. Our findings open a new path for SHG imaging. DNA can change its conformations under many circumstances. For example: normal cells turning into cancerous cells and drug molecules binding with DNA. Therefore, the detection of DNA conformational changes with second harmonic microscopy will be a useful tool in cancer therapy and new drug discovery.

Detection of an en masse and reversible B- to A-DNA conformational transition in prokaryotes in response to desiccation

The role that DNA conformation plays in the biochemistry of cells has been the subject of intensive research since DNA polymorphism was discovered. B-DNA has long been considered the native form of DNA in cells although alternative conformations of DNA are thought to occur transiently and along short tracts. Here, we report the first direct observation of a fully reversible en masse conformational transition between B- and A-DNA within live bacterial cells using Fourier transform infrared (FTIR) spectroscopy. This biospectroscopic technique allows for non-invasive and reagent-free examination of the holistic biochemistry of samples. For this reason, we have been able to observe the previously unknown conformational transition in all four species of bacteria investigated. Detection of this transition is evidence of a previously unexplored biological significance for A-DNA and highlights the need for new research into the role that A-DNA plays as a cellular defence mechanism and in stabilizing the DNA conformation. Such studies are pivotal in understanding the role of A-DNA in the evolutionary pathway of nucleic acids. Furthermore, this discovery demonstrates the exquisite capabilities of FTIR spectroscopy and opens the door for further investigations of cell biochemistry with this under-used technique.

Differential effects of dopaminergic neurotoxins on DNA cleavage

AIMS

Environmental and endogenous toxins are considered to increase the risk of dopaminergic neurodegeneration. Parkinson's disease is a neurological disorder occurring due to the death of dopaminergic neurons in substantia nigra. The present study investigated the effect of parkinsonian neurotoxins salsolinol and rotenone on plasmid and genomic DNA.

MAIN METHODS

Salsolinol or rotenone (0-1000 μM) alone or in presence of divalent metals (copper or iron) was incubated with plasmid DNA pBR322 (1 μg) or calf thymus DNA (1 μg). In order to study their effects on restriction endonuclease sites, the plasmid DNA was incubated with the neurotoxins (salsolinol or rotenone), extracted and subjected to restriction enzyme digestion (BamHI, EcoRV, HindIII, SalI).

KEY FINDINGS

Exposure of rotenone or salsolinol alone to the plasmid or calf thymus DNA did not induce any strand scission or damage. However, salsolinol in the presence of divalent copper induced strand scission and damage in both plasmid and genomic DNA. All of the tested restriction endonucleases linearized the plasmid DNA pre-treated with salsolinol or rotenone suggesting that these neurotoxins did not selectively damage the restriction enzyme sites in the DNA.

SIGNIFICANCE

The above observations suggest that salsolinol and rotenone differentially interact with DNA in inducing damage in the presence of copper, and behave similarly in their binding to DNA by not damaging the selected restriction endonuclease cleavage sites.

CONCLUSION

Risk for neuronal degeneration can be significantly augmented by the environmental and endogenous toxins in the presence of various metals due to their deleterious effects on DNA.

Photochemical probing of the B--a conformational transition in a linearized pUC19 DNA and its polylinker region

We induced the B-to-A conformational transition by ethanol in a linearized pUC19 DNA. A primer extension method was used in combination with UV light irradiation to follow the transition, based on pausing of DNA synthesis due to the presence of damaged bases in the template. Primer extension data highly correlated with the results of another method monitoring the B-A transition, i.e. inhibition of restriction endonuclease cleavage of UV light-irradiated DNA. Primer extension enabled us to locate damaged nucleotides within the region of interest. Most damaged nucleotides were located in B-form trimers, exclusively containing both pyrimidine bases (TTC, TCT, CTC, and CTT), and in a cytosine tetramer. The amount of damaged bases decreased in the course of B-A transition. Some of the damage even disappeared in the A-form, which mainly concerns the C(4) and C(3) blocks. The cleavage was nearly restored in the A-form within this region (Eco88I). On the contrary the decrease of damage was less significant with thymine dimers, only dropping to 50-60% of the B-form level. Consequently, the cleavage with EcoRI and HindIII remained mostly as before the transition (75% and 60% of uncleaved DNA preserved). We found significant differences in the B- and A-form pattern of UV light-damaged bases within the same region (polylinker) of DNA embedded within long (plasmid) or short (127 bp fragment) DNA molecules. The B-A transition of the fragment was found less cooperative than with linearized plasmid, which was confirmed by both CD spectroscopy and restriction cleavage inhibition.

Mapping the B-A conformational transition along plasmid DNA

A simple method is presented to monitor conformational isomerizations along genomic DNA. We illustrate properties of the method with the B-A conformational transition induced by ethanol in linearized pUC19 plasmid DNA. At various ethanol concentrations, the DNA was irradiated with ultraviolet light, transferred to a restriction endonuclease buffer and the irradiated DNA was cleaved by 17 restriction endonucleases. The irradiation damaged DNA and the damage blocked the restrictase cleavage. The amount of uncleaved, i.e. damaged, DNA depended on the concentration of ethanol in a characteristic S-shape way typical of the cooperative B-A transition. The transition beginning and midpoint were determined for each restriction endonuclease. These data map the B-A transition along the whole polylinker of pUC19 DNA and six evenly distributed recognition sequences within the rest of the plasmid. The transition midpoints fell within the B-A transition region of the plasmid simultaneously determined by CD spectroscopy. The present method complements the previous methods used to study the B-A transition. It can be employed to analyze multikilobase regions of genomic DNA whose restriction endonuclease cleavage fragments can be separated and quantified on agarose gels.