Superoxides

Superoxides

  • Norbert Bittner asked a question:
    Can an increased level of hydrogen peroxide reverse the reaction of superoxide dismutase in an assay ?

    I'm having the problem that in my SOD assay (NBT assay, Pyrogallol assay) the sample reaction is showing a faster O2- production than the blank of the SOD standards. Means that the samples are way darker in color after 5min of reaction than the SOD blank. I'm working with Sephadex desalted pine crude extracts.

  • P. Pardha-Saradhi added an answer:
    What is the mechanism of superoxide anion free radical scavenging assay?

    what is the mechanism of superoxide anion free radical scavenging assay of plant extract?

    P. Pardha-Saradhi · University of Delhi

    Protocols that are widely being used (that we also use) involve (i) generation of superoxide anion radicals (either by exposing riboflavin to light in presence of electron donors, or throught PMS-NADH system or  xanthine-xanthine oxidase system); and (ii) reaction of superoxide anion radicals with certaing molecules/biomolecules to yield a product that can be determined spectrophotometrically (production of nitrite in first case, formation of formazan in the second case and reduction of cytochrome c in third case); Higher the concentration of superoxide anion radicals more would the generation of nitrite, formazon or reduction od cytochrome C. Therefore, in presence of superoxide desmutase that uses superoxide anion radicals as substrate, one would expect decrease in the formation of nitrite, formazan or reduction of cytochrome C. Accordingly, higher the SOD activity lesser would be the formation of nitrite, formazan or reduction of cytochrome C.

  • Samuel Chuah added an answer:
    Can all members of Reactive Oxygen species induce breakage in Graphene Oxide sheets? (GQD production)

    Photo- Fenton reaction mediated fabrication of Graphene Quatum Dots is well recorded. Keeping in view of the oxidative action of the hydroxyl ions hence produced, I am curious about the ability of other reactive species (like that of superoxide ion, singlet oxygen) in breaking the GO sheets.

    Thanks.

    Samuel Chuah · Monash University (Australia)

    From my limited knowledge on oxidation of GO, the attachment of oxygen functional groups to the basal plane of GO (epoxide, carboxyl, hydroxyl and carbonyl) does break the grapheme sheets

  • Nai-Kei Wong added an answer:
    Does anyone know the rate constant for the generation of superoxide by NOX enzymes please and if so the reference?

    Kinetics of redox enzymes

    Nai-Kei Wong · The University of Hong Kong

    Thank you for sharing. It's an interesting question with few references, in part because NOX is a complex requiring multiple subunits to function. The in vitro reconstitution work was an admirable effort. 

  • Micheal S Ward added an answer:
    Normalisation of OXPHOS by CS (ie complex respiration rates) is standard protocol. So should OXPHOS by-products (ie SO) also be treated as such?

    I am a diabetic complications researcher and I'm carrying out a number of measurements on freshly isolated mitochondria, such as respiration by Seahorse technology. I normalise this data by citrate synthase activity as I realise the enzyme is rate limiting in the TCA cycle for citrate production. Therefore I have been attempting to reconcile if normalisation of by-products of OXPHOS are also needed in the likes of superoxide, hydrogen peroxide which I have measured by MitoSOX and Amplex red assays respectively. I am also carrying out MnSOD activity assays for identification of possible changes in dissipating enzyme activities.

    Micheal S Ward · Mater Research

    Hi Alexander,

    Thank you for the response, I have downloaded your excerpt and will read through it as I have some of your work on other mitochondrial topics. I find your pieces of work to be quite frank and offering a facts based opinion that differs with deemed 'conventional' methods being highly published and fascinating which allows for my greater critical analysis.

    Thank you.

  • Emilia Wojtera added an answer:
    Does anybody know another form of generate superoxide radicals for superoxide dismutase determination diferent of xanthine and xanthine oxidase?

    High I need proof another form of generate superoxide radicals for superoxide dismutase determination with the reduction of citocrome C, that be different of radicals generate by xanthine/xanthine oxidase.

    Thanks

    Emilia Wojtera · Nencki Institute of Experimental Biology

    You can use hypoxanthine or xanthine, try with diazoxide, ET-1, AngII... 

  • Alexander V Panov added an answer:
    Does ambient proton concentration (pH) alter the behavior of ROS/RNS?

    Let me preface this by saying I am not a biochemist.   My logic may be very incorrect, but I'm looking for some guidance from someone who has a much stronger grasp on this field.    Or if anyone can point me toward an appropriate reference.   It's not an easy topic to google search; too many unrelated results.

    My question is more of a curiosity.  I am wondering whether the behavior/concentration ROS like super-oxide and others (the more reactive species) would interact with the ambient proton concentration in a cellular compartment.  To put this question another way, I'm wondering if decreasing the pH would tend to "quench"/reduce the generation of highly reactive and potentially damaging species.  

    Isn't this essentially what antioxidant  compounds do?   They function as proton donors?   I suspect there is a deeper level of information related to the energetic exchange that I'm not aware of.     

    To also ask the reverse question:  Would the biological generation of ROS/RNS (say, via mitochondrial dysfunction) alter the availability of protons/influence the local pH? 

    Alexander V Panov · Institute of Molecular Biology and Biophysics

    I would like to add another 5 cents to the current discussion.
    When discussing pH, we should remember several important issues: 1) pH is in most bulk environments, we usually consider cytosol and mitochondrial matrix, is highly buffered. In the matrix pH may remain constant even though the ΔΨ may drop significantly; 2) the mitochondrial matrix is a hard gel, therefore, if there are changes in pH they occur locally in a narrow space either near an enzyme, which produces or consumes a proton, or near the membrane; 3) The metabolic events, including production of superoxide radicals or their removal, which are coupled to other metabolic events, occur in the multienzyme complexes and proceed usually irreversibly.
    One of the most important species of ROS is the hydroperoxyl radical, also known as the perhydroxyl radical, which is the protonated form of superoxide with the chemical formula HO2. Hydroperoxyl is formed through the transfer of a proton to an oxygen atom. The concentration of O2 in the lipid phase of the membrane is 4-5 times higher than in the extra-membrane environment, and the superoxide anion is rapidly extruded from the membranes. The superoxide anion, O2•−, and the hydroperoxyl radical are in equilibrium in aqueous solution: O2•− + H2O is in equilibrium with HO2 + OH−. The protonation/deprotonation equilibrium exhibits a pKa of 4.88; consequently, about 0.3% of any superoxide present in the cytosol of a typical cell is in the protonated form. Although HO2 is also less hydrophobic and thus excluded from the lipid phase of membranes, nevertheless, it is more soluble in lipids than superoxide anion. I think that major formation of HO2 occurs not in the cytosol, but in the water-containing space near the superoxide-producing center inside the membrane. Unlike O2−, which predominantly acts as a reductant, HO2 can act as an oxidant in a number of biologically important reactions, such as the abstraction of hydrogen atoms from tocopherol and polyunsaturated fatty acids in the lipid bilayer. As such, it may be an important initiator of lipid peroxidation. The concentration of HO2 in the membrane may depend on local pH. I think that changes of pH in the bulk environments (cytosol or incubation medium) have little influence on reactions, which occur locally in the membranes and the membrane’s micro-environment near the enzyme’s center where superoxide is formed.

  • David Tapley added an answer:
    What is the best activity assay for Catalase & SOD activity in Cnidarian?

    I need a kit that is sensitive and not time consuming. Thank you.

    David Tapley · Salem State University

    I used several methods on cnidarian tissues in the past -- I ended up settling on the nitro blue tetrazolium method for SOD (Spitz and Oberly) and the modified (as in the Sigma catalog) method of Beers and Sizer for CAT. Message me with your email and I can probably dig up my old protocols and send them to you. 

  • Daniel Medeiros Lima added an answer:
    What is the best method for quantify ROS in heart sections?

    What of method is more specific to measure ROS in cardiac sections of rats? DHE is not very specific, however I see many publications using the method.

    Thank you for your help.

    Daniel Medeiros Lima · Rio de Janeiro State University

    Thanks Adam and Karel, their information were of great help.

  • Ryan D. Taylor added an answer:
    Any suggestions on BMPO Spin Trap Hydroxyl/Superoxide Adduct formation rates?

    I am looking for information on the formation rates of two radical adducts BMPO/OH and BMPO/OOH. There are many studies on the formation of these radical adducts using xanthine oxidase or Fenton reactons but there does not appear to be anything on competitive reaction rates (cases where the OH radical and OO- radical are competitively reacting with BMPO). 

    Any insight would be greatly appreciated. 

    Ryan D. Taylor · University of California, Davis

    Thank you for that great information Deborah! I really appreciate the insight.

  • Tarana Arman added an answer:
    What is the minimum amount of DHE (Dihydroethidium) that could be used to detect the superoxide ions in saccharomyces cerevisiae?

    I have induced a chromium stressed condition for the yeast culture and want to assess the ROS increase in them. However, I am unable to decide upon the upper and lower limits for the amount of DHE to be used.

    Tarana Arman · BITS Pilani, Hyderabad

    Thanks Philippe, your answer was indeed helpful.

  • Mustafa Yavuz Köker added an answer:
    Does CD40 expression on B cells require reactive oxygen species?

    CD40 expression on B cell has superoxide dependent pathway? So since CGD patients lacks superoxide production do they express CD40 on B cells?

    Mustafa Yavuz Köker · Erciyes Üniversitesi

    NADPH oxidase activity order Neutrophil>monocytes>eosinophil>dendiritic cell>B cell,

    For CD40, I think yes. But it is very complex, need pathway analysis. CD40 deficiency is another immunodeficiency. NADPH oxidase modulate it, but does not dependent. I think.

  • Karel Chalupsky added an answer:
    Does anyone know of a protocol for qualitative assessment of the presence of superoxide dismutase in bacteria?

    I would like to screen my bacterial isolates for their ability to detoxify superoxide through superoxide dismutase. I would like to know of any rapid qualitative test to assess if my isolates have this enzyme. Most of the searches I have initially done involve spectophotometric analysis.

    Karel Chalupsky · Institute of Molecular Genetics AS CR

    Cytochrome

    25 µM cytochrome in PBS was incubated for 5min at 37 C with addition of KO2. The absorbance was read spectrophotometrically at 550 nm against distilled water blank. Reduction of cytochrome c in the presence of SOD (100U/ml) was subtracted from the values without SOD. The absorbance differences between comparable wells with or without SOD were converted to equivalent O2•− release by using the molecular extinction coefficient for cytochrome c of 21 mM−1 cm−1

    Superoxide dismutase
    30000Units (sigma # S-8160)
    Stock 30000U/ml (30U/ul) then freeze aliquots of 50ul
    30 U/ul so 50ul =1500U then add 250 ul water ->1500 U /300 ul = 5 U/ul
    dilute above 1 : 4 with PBS so have 1 U/ul -> then 60ul = 60 U

    Add 60ul of SOD to a well of 6-well plate containing the 480 ul PBS (sample)
    the total volume will be 600ul so the conc. of SOD is 100 U/ml

    Cytochrome c partially acetylated (Sigma # C-4186)
    Cytochrome c from hourse heart ( # C-2506)
    6.19 mg cytochrome / 2 ml = 3.1mg / ml = 250uM
    Solution is only good for a few hours!
    Light and oxygen sensitive keep solution in the dark and covered!

    Add 60 ul of cytochrome c to sample solution – final volume 600ul (final c of cytochrome c is 25uM)

    Read absorbance at 540, 540 and 560nm

    To calculate the cytochrome c absorbance use the pathlenght corrected values only:
    Take average of the readings at 540nm and 560 nm (540nm + 560nm)/2
    From the readings at 550nm subtract this average 550nm –[( 540nm+560nm)/2]
    This subtracts the baseline from absorbance 550nm peak for reduced cytochrome c


    Potassium superoxide solution (3mg in 1ml) in absolute DMSO was used as superoxide donor. Due to low solubility and possibly water content in DMSO, the real concentration of superoxide anion was detected by cytochrome c reduction and calculated using molecular extinction coefficient for cytochrome c of 21 mM−1 cm−1 .
    USE xanthin oxidase system as superoxide generation system. It is more reliable and physiologic.

  • Tatiana Y. Karogodina added an answer:
    Anyone has experience on EPR on total tissue to measure superoxides and hydroxyl free radicals ?

    Hi, I am trying to measure superoxide levels using EPR with DMPO as a spin trap. I had tried in isolated mitochondria and I got nice spectra (only in presence of inhibitors). Now I like to use total tissue, kidney and heart. If any of you have tried this can you provide conditions such as buffers and  how you homogenize the tissue.

    Also, anyone has experience in injecting spin trap into animals  and measuring EPR later ? Ideally I want to perform in vivo measurements, or something close to that.

    Thank you 

    Tatiana Y. Karogodina · Russian Academy of Sciences

    Dear Manjula

    I suggest to see papers of Komarov DA. For example this one: http://www.ncbi.nlm.nih.gov/pubmed/22162021

    Tatyana

  • P. Pardha-Saradhi added an answer:
    What si the best protocol for NBT staining in tomato leaves for detection of superoxide radicals?
    Can anyone please suggest the best protocol for NBT staining (for suproxide radicals) in tomato leaves. Could you also suggest how, after staining, I can efficiently remove chlorophyll without damaging leaves and heat burning.
    P. Pardha-Saradhi · University of Delhi

    Dear Praveen,

    Following NBT staining for 12 to 24 h), you can remove all pigments (including chlorophylls) with the exception of formazon by dipping leaves in clearing reagent (3:1 ratio of TCA and phenol). Kindly handle clearing agent carefull taking all necessary precautions. You can leave leaves for 6 to 24 h depending on intensity of various pigments (if you want to hasten the process you may keep it in oven for 30 to 60 min at 60oC). Subsequently, decant clearing reagent carefully without damaging leaves (or you can lift the leaves carefully with a good blunt forceps and transfer to a fresh petriplate or a plastic box and add lactophenol. If you wish you can replace lactophenol after few hours. You can infact store your cleared leaves with nice colour of formazon in lactophenol as long as you want. Be careful in using clearing reagent. If you take proper precautions you will find this method to be most simple.

    Good Luck

  • Francisco J Sánchez-Gómez added an answer:
    Can anyone suggest specific scavenger(s) for superoxide but not for ROS?

    I am looking for the reagent which can scavenge superoxide in living cells. Most of ROS scavenger, like tempol, inhibit not only superoxide accumulation but also reactive nitrogen spices (RNS). But I am actually looking at the effect of RNS in oxidative stress but not superoxide. Dose anyone know the cell permeable superoxide scavenger?

    Francisco J Sánchez-Gómez · Spanish National Research Council

    We have used PEG-SOD, a cell permeable analogue to dismutate superoxide, but, you have to take in account the kinetics of the enzymes, doses and toxicity. Other compound you can use is TIRON. It is very effective and specific for superoxide.

    Free Radic Biol Med. 2014 Jun;71:146-56. doi: 10.1016/j.freeradbiomed.2014.03.011. Epub 2014 Mar 15.
    Acute hypoxia produces a superoxide burst in cells.

    Supplementary material.

  • Benson Solomon added an answer:
    Is there any other superoxide radical scavengers except TBA? Can you also give the referance?

    I want to identity that if the superoxide radicals were involved in Fenton reaction. I need to use superoxide radical scavengers except TBA. Thank you.

    Benson Solomon · University of South Carolina

    MCLA and lucigenin are two superoxide probes our group has used for superoxide measurements

  • Mathieu Pierre added an answer:
    What is best chemical to induce oxidative stress selectively by superoxide anions?
    But not by other ions such as hydroxyl etc. I wants to elevate superoxide level selectively in the cells.
    Mathieu Pierre · Université de Poitiers

    you can use DCMU

  • Praveen Roylawar asked a question:
    How to: superoxide radical detection by spectrofluorometer?

    I did Nbt staining in tomato leaves to detect superoxide radicals (Blue formazol formation). Now I want to detect the same radicals using a spectrofluorometer. Can anyone please explain to me how to do it ? Can I use the same sample (formazol precipitated sample) for spectrofluorometric analysis or do I have to use an unstained sample?

    Thank you.

  • Katarina Venglovska added an answer:
    Does anyone have any suggestions on doing an SOD assay using the Marklund and Marklund protocol?
    I am performing the SOD assay using the pyrogallol protocol by Marklund and Marklund for estimating SOD from serum. I am not getting the desired results. I'm using a 30 mM concentration of pyrogallol, but my reading of serum is more than the pyrogallol reading.
    Can anyone suggest any solutions.
  • Shane Vontelin van Breda added an answer:
    Can anyone give advice on Fenton reaction inhibition in M. tuberculosis?
    I am investigating the mechanism of action of a cationic peptide against MTB. I suspect one of the mechanisms is by the Fenton reaction. One way I would like to prove this is by use of thiourea and dipyridyl, as they have been used before in inhibiting the Fenton reaction.

    Does anybody have an idea of what concentrations I should begin looking at against MTB?

    Has anybody got any experience investigating and inhibiting Fenton reaction again against MTB?

    I would also like to ask about the preparation of thiourea and dipyridyl. Should it be added to bacterial media, then autoclaved? Or should the compounds be added to the autoclaved media using filter sterilization?

    Thanks
    Shane Vontelin van Breda · University of Pretoria

    Thank you Boris.

  • Rajesh Kumar Tewari added an answer:
    Why should blank samples not have PMS in scavenging activity of anion superoxide?
    I´m following this protocol:

    Superoxide radicals are generated in PMS-NADH systems by oxidation of NADH and assayed by the reduction of NBT. In these experiments, the superoxide radicals were generated in 3 ml of Tris-HCl buffer (16 mM, pH 8.0) containing 1 ml of NBT (50 mM) solution, 1 ml NADH (78 mM) solution and sample solution of fraction (25 – 500 mg/ml) in ethanol. The reaction started by adding 1 ml of PMS solution (10 mM) to the mixture. The reaction mixture was incubated at 25 °C for 5 min, the absorbance was read at 560 nm by spectrophotometer (Schimadzu UV-Vis 1700) against blank samples using ascorbic acid as a control. Decreased absorbance of the reaction mixture indicated the increasing of superoxide anion scavenging activity. The percentage inhibition of superoxide anion generation was calculated using the following formula:
    % inhibition = [(A0-A1)/A0] x 100
    where A0 was the absorbance of the control , and A1 was the absorbance in the presence of fraction or standards.
    Rajesh Kumar Tewari · University of Vienna

    Ascorbic acid can directly reduce NBT to formazan. I really do not see the relevance of using Ascorbic acid in your experimental system. 

  • Just Genius added an answer:
    Has anyone detected superoxide anions with luminescence method?
    For measurement of superoxide anions induced by Angiotensin II in VSMC cell lines, I used luminol and enhancer incubated with pretreated cells but the value of light intensity was only about 200 per 105 cells after 30 mins incubation. Could that be right? Why is the light intensity so low?
    Just Genius · AbbVie
    Hi again! As far as I know, luminol will primarily detect hydrogen peroxide, not superoxide. Lucigenin may be the better probe, but you may also consider fluorescent dyes (e.g. available from Molecular Probes). In the experimental setup you describe, light emission will be dependent on the presence of (intrinsic) SOD which converts superoxide into H2O2. The readings of your instrument are arbitrary and depend on the detector setup and the instrument settings (integration time, blank value substraction detector gain etc), so 200 counts may be entirely OK. You may use xanthine+xanthineoxidase as a positive control (it will generate superoxide anions). Or you treat some leucocytes with LPS and measure the oxidative burst (works even with full blood). This would be a nice "biological" positive control.
    Good luck!
  • Olivier Coste asked a question:
    Can antioxidant molecules interfere with an NBT assay for oxidative burst and give a "false negative"?
    If my molecule activates macrohpages oxidative burst but at the same time scavenges the superoxide radicals, is it going to give a false negative?
  • Reena Arora asked a question:
    Does anyone have experience with MitoSOX assay?
    I was wondering if anyone has done a MitoSOX assay in 96 well plate?
  • Devendra Kumar added an answer:
    When is the exact time that superoxide radicals are produce in plants?
    In a walnut.
    Devendra Kumar · Indian Agricultural Research Institute
    its also depend on type of pathogen, resistance gene...but most case within 30 minute........reference-NO way back: nitric oxide and programmed cell death in
    Arabidopsis thalianasuspension cultures
    Andrew Clarke, Radhika Desikan, Roger D. Hurst, John T. Hancock and Steven J. Neill*
  • Rajbardhan Mishra added an answer:
    What is the protocol for Reactive oxygen species(ROS) assay especially superoxide when we co-culture, neutrophils with cancer cells.
    ..
    Rajbardhan Mishra · Institute Animal Physiology and Genetics AS CR, v.v.i.
    Thank you so much. I hope it will help me.
  • Marcin Nowicki added an answer:
    Does anyone know simple protocols for analysase, superoxide, dismutase and ascorbate peroxidase enzyme activity in plants?
    The papers do not mention standard concentrations to be used for measuring enzyme activity, could someone help me with that?
    Marcin Nowicki · Research Institute of Horticulture in Skierniewice
    Nature Protocls has it all. I highly recommend it (successfully used an Ascorbate microtiterplate assay few years back).
    http://tiny.cc/59jfmw

    http://www.nature.com/nprot/journal/v2/n4/full/nprot.2007.101.html

About Superoxides

Highly reactive compounds produced when oxygen is reduced by a single electron. In biological systems, they may be generated during the normal catalytic function of a number of enzymes and during the oxidation of hemoglobin to METHEMOGLOBIN. In living organisms, SUPEROXIDE DISMUTASE protects the cell from the deleterious effects of superoxides.

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