Thursday, October 8, 2009

Estimation of Disulfide Bonds Using Ellman’s Reagent

Ellman’s reagent has been widely used for the quantitation of thiols in peptides and proteins. It has also been used to assay disulfides present after blocking any free thiols (e.g., by carboxymethylation) and reducing the disulfides prior to reaction with the reagent. It is also commonly used to check the efficiency of conjugation of sulfhydryl- containing peptides to carrier proteins in the production of antibodies.

Thursday, September 24, 2009

Separation of DNA Fragments Using PAGE Method

This method is able to separate DNA fragments with the size of as small as 10 bp and up to 1 kb with the resolution of as little as 1 bp. While agarose gel electrophoresis is only able to separate DNA fragments with the bigger size that PAGE does or in the size range of 100 nucleotides to around 10 – 15 kb.

Sunday, September 20, 2009

Polyacrylamide Gel Electrophoresis: Advantages and Disadvantages

You must have known that agarose gel electrophoresis is generally adequate for resolving nucleic acid fragments in the size range of 100 nucleotides to around 10-15 kb. But, for nucleic acid which its fragments below those range, it will be difficult to separate and hard to visualize because of diffusion within the gel matrix. These problems are solved by native polyacrylamide gel electrophoresis (PAGE). Using native PAGE, fragments as small as 10 bp and up to 1 kb can be separated with a resolution of as little as 1 bp.

Saturday, August 29, 2009

Rapid Boiling Method for Plasmid DNA Isolation

In the previous post, it had already explained about how to extract plasmid DNA by using alkaline lysis method. In this particular post, it will be explained the other method to extract plasmid DNA instead of using alkaline lysis method. It is Rapid Boiling method, an alternative to alkaline lysis method that was developed by Holmes and Quigley. Here, the cells are lysed partially allowing plasmids to escape, whereas the bacterial chromosomal DNA remains trapped in the cell debris. High temperature is then used to denature the chromosomal DNA, after which reannealing allows the plasmids to reassociate. Centrifugation removes the chromosomal DNA along with the cell debris, leaving the plasmid in suspension, from where it is recovered by isopropanol precipitation.

Tuesday, August 25, 2009

Plasmid DNA Extraction Using Alkaline Lysis Method

Plasmids can be isolated by a variety of methods many of which rely on the differential denaturation and reannealing of plasmid DNA compared to chromosomal DNA. One commonly used technique developed by Birnboim and Doly involves alkaline lysis. This method essentially relies on bacterial lysis by sodium hydroxide and sodium dodecyl sulfate (SDS), followed by neutralization with a high concentration of low-pH potassium acetate. This gives selective precipitation of the bacterial chromosomal DNA and other highmolecular-weight cellular components. The plasmid DNA remains in suspension and is precipitated with isopropanol.

Monday, June 29, 2009

96-Well DNA Isolation Method From Leaf

The following protocol provides a high throughput, low cost method of producing a superior DNA yield of high quality which is suitable for TILLING, map based cloning or any application which requires long term DNA storage. The protocol has been designed for DNA extraction from leaf material, preferably young leaf tissue should be used as this minimizes samples being contaminated with polysaccharides and phenolics.


Extraction Buffer

  1. 200 mM Tris-HCL pH 7.5
  2. 250 mM NaCl
  3. 25 mM EDTA
  4. 0.5% SDS


  1. 10 mM Tris-HCl pH 8.0
  2. 0.1 mM EDTA pH 8.0

TE and RNAse A

  • For 2 plates: 20 ml TE and 20μl DNAse-free RNase A (10 mg/ml)

The Methods are:
  1. Pre-heat extraction buffer to 65°C.
  2. Label collection tubes (Qiagen Cat. No. 19560) and add a single tungsten carbide bead (Qiagen Cat no. 69997) to each tube.
  3. Prepare ice bucket and tube of ethanol to wash forceps after each harvest.
  4. Harvest material (3 growing tips) into a single collection tube.
  5. Add 400 microliters of extraction buffer to each tube (use a multi-pipettor). Put on lids (Qiagen Cat. No. 19566).
  6. Homogenise material on the mixer mill (Retsch MM300) for 2 min/30s.
  7. Incubate at 65oC for 30 min to 1 hour.
  8. Centrifuge for 10 minutes at full speed.
  9. Label a new rack of collection tubes.
  10. Remove 300 microliters of supernatant into a new collection tube (use a multi-pipettor set speed to slow) with extended length tips.
  11. Carefully add 200 microliters of phenol:chloroform to each tube (THIS PROCEEDURE SHOULD BE CARRIED OUT IN THE FUME HOOD), use 200 microliters manual multi-pipettor with filter tips
  12. Put lids onto the tubes and invert several times, so the samples are well mixed. Centrifuge for 10-15 minutes.
  13. Label a set of storage plates.
  14. Using a manual multi-pipettor with filter tips very carefully remove 200 microliters of the upper layer to a new storage plate (AB Gene Cat. No. AB 0765) (THIS PROCEEDURE SHOULD BE CARRIED OUT IN THE FUME HOOD).
  15. Using a multi-pipettor add 1/10th vol. of 3 M sodium acetate ( approximately 20 microliters) and an equal volume of isopropanol (approximately 220 microliters). Put on lids, mix well, and leave at -20oC for a maximum of 1 hour.
  16. Leave plates on desk until the have reached room temperature, as spinning when still frozen at high speeds can cause the plate to crack. Centrifuge at 5600 rpm for 45 minutes.
  17. Remove supernatant and add 100 microliters of TE containing RNAse A at a final concentration of 10 microliters/ml and incubate 30 min at 37oC.
  18. Repeat the precipitation step (step 15). After centrifugation at 5600 rpm for 45 minutes remove the supernatant and add 200 microliters 70% ethanol. Put on lids and leave for 15 minutes or overnight.
  19. Remove ethanol and leave to air dry. Add 100 microliters of TE and store in fridge/freezer.

Kindly Regards.

Reference: Number 17 in References

Monday, June 8, 2009

RNA Extraction From Fresh Blood

RNA can be extracted from blood since whole blood contains nucleated white cells that constitute an easily accessible source. RNA extraction from blood will be more successful if the nucleated white cells are first isolated from the red cells since the red cells are a rich source of ribonucleases that are able to degrade RNA. It is important to minimize degradation by following the appropriate recommendations for handling RNA. The methods of RNA extraction usually comprises of three steps which are cell lysis, partitioning of RNA into a solvent fraction, and recovery of RNA from the solvent by precipitation.

Monday, June 1, 2009

DNA Extraction From Fresh Bone

You can extract nucleic acids, such as DNA, from bone samples in order to analyze gene expressions, to look for somatic mutations of tumors or other pathological tissue, or for genotyping archive material when other sources of DNA are not available. You can use several kits that have already provided by biotech companies. But, if you are extracting DNA from large number samples, you can use a homemade method as described here to be effective in cost.

Friday, May 22, 2009

Cleave DNA Using Restriction Endonulease, A Bacterial Enzyme

In order to manipulate DNA you have to posses the ability to cleave DNA at specific sites by using bacterial enzyme, which is restriction endonulease. Restriction endonucleases are bacterial enzymes that cleave duplex DNA at specific target sequences with the production of defined fragments. The name of the enzyme (such as BamHl, EcoRl, AluI, and so on) tells us about the origin of the enzyme but does not give us any information about the specificity of cleavage. The recognition site for most of the commonly used enzymes is a short palindromic sequence, usually either 4, 5, or 6 bp in length, such as AGCT (for AZul),GAATTC (for EcoRl), and so on. Each enzyme cuts the palindrome at a particular site, and two different enzymes may have the same recognition sequence but cleave the DNA at different points within that sequence.

Monday, May 11, 2009

Agarose Gel Electrophoresis of Nucleic Acids

After amplify DNA template using PCR method, now you can continue your work by using gel electrophoresis in a gel composed of agarose in order to separate DNA fragments based on its molecular weight. The percentage of agarose used depends on the size of fragments to be resolved. In general a 0.8-1% gel may be used for effective separation of DNA fragments of 100-1500 base pairs.

Wednesday, May 6, 2009

Bacterial DNA Extraction for Pulsed-field Gel Electrophoresis

Pulsed-field gel electrophoresis (PFGE) is a method used to separate large DNA fragments such as those obtained after digestion with restriction endonucleases that cut infrequently. To avoid possible risks of shearing bacterial DNA during the extraction and digestion steps, bacterial cells are immobilized prior to processing by incorporation in agarose gel. DNA extraction for PFGE is characterized by the need to prolong contact between agarose plugs and the lysis solution that must be distributed throughout the gel. However, the duration of DNA preparation has been shortened since the initial description of the method. The method described in this posting works well with Gram-positive and Gram-negative rods of clinical interest.

Thursday, April 23, 2009

Polymerase Chain Reaction (PCR): Basic Principle

Polymerase chain reaction (PCR) is a primer mediated enzymatic amplification of specifically cloned or genomic DNA sequences. PCR process was invented by Kary Mullis and it has been automated for routine use in laboratories worldwide. The main purpose of the PCR process is to amplify template DNA using thermostable DNA polymerase enzyme which catalyzes the buffered reaction in which an excess of an oligonucleotide primer pair and four deoxynucleoside triphosphates (dNTPs) are used to make millions of copies of the target sequence.

Monday, April 13, 2009

The Measurement of Tryptophan Content by Using UV-Spectrometer

The absorption of protein solutions in the UV is the result of tryptophan and tyrosine (and to a very minor, and negligible, extent phenylalanine and cysteine). The absorption maximum will depend on the pH of the solution, and spectrophotometric measurements are usually made in alkaline solutions. Absorption curves for tryptophan and tyrosine show that at the points of intersection, 257 and 294 nm, the extinction values are proportional to the total tryptophan + tyrosine content. Measurements are normally made at 294.4 nm, since this is close to the maximum in the tyrosine curve, and in conjunction with the extinction at 280 nm, the concentrations of each of the two amino acids may be calculated. This is the method of Goodwin and Morton.

Saturday, April 11, 2009

Bicinchoninic Acid (BCA) Method: A Protein Assay

The Bicinchoninic acid (BCA) assay first was described by Smith, et al. BCA assay is similar to Lowry assay since it also depends on the conversion of Cu(2+) to Cu(+) under alkaline conditions. The Cu(+) is then detected by reaction with BCA. The reaction results in the development of an intense purple color with an absorbance maximum at 562 nm. BCA method and Lowry are of similar sensitivity, but BCA method is more advantageous compared to Lowry in a few things, here are the advantages:

Tuesday, March 31, 2009

Protein Assay using UV-Spectrophotometer at 280 nm

It is possible to estimate protein concentration in a solution by using simple spectrometer. Absorption of radiation in the near UV (280 nm) by proteins depends on the Tyrosine and Tryptophan content (also to a very small extent on the amount of Phenylalanine and disulfide bond).

Sunday, March 29, 2009

Surfactant Properties: How to Quantitatively Measure

In order to measure the properties of surfactant, we can use the surface tension, emulsification activity, and hemolytic activity as the parameters. Here are the methods:

Tuesday, March 24, 2009

DNA Extraction Using Prepman Ultra

In my previous posting I’ve slightly given the bacterial DNA extraction method using Instagene matrix. In this particular posting, I want to give you the more simple method to extract DNA, which is using Prepman Ultra. According to the producer, Applied Biosystem, Prepman ultra is applicable to successfully preparing DNA template from bacteria, yeast, filamentous fungi, both from a plate or from tissue smears.

PCR Components

The Polymerase Chain Reaction (PCR) created a revolution in molecular biology research and its applications. PCR is an in vitro method that enzymatically amplifies specific DNA sequences using oligonucleotide primers that flank the region of interest in the target DNA. The principle involves a repetitive series of cycles each of which consist of template denaturation, primer annealing, and extension of the annealed primers by a DNA polymerase to create the exponential accumulation of a specific fragment whose ends are determined by the 5’ ends of the primers. The PCR is so named because it involves a polymerase and the products synthesized in each cycle can serve as templates in the next so the number of DNA copies approximately doubles at every cycle to create a chain reaction similar to the principles in a nuclear reactor.

Sunday, March 22, 2009

Bradford Method: Colorimetric Protein Assay

Bradford method is a common colorimetric method to determine protein concentration in a sample solution. The Bradford method of protein determination is based on the binding of a dye, Coomasie Blue G, to the protein. This binding shifts the absorbtion maximum of the dye from red to blue. The absorbance of the solution is measured at 595 nm and is proportional to protein concentration when compared to a standard curve. Two types of assay are described here: the standard assay, which is suitable for measuring between 10 and 100 microgram of protein, and the microassay, which detects between 1 and 10 microgram of protein.

Friday, March 20, 2009

Quantitative Estimation of DNA Concentrations

DNA, RNA, and protein strongly absorb ultraviolet light in the 260 to 280 nm range. UV spectroscopy can be used as a quantitative technique to measure nucleic acid concentration and protein contamination. Nucleic acids strongly absorb at 260 nm and less strongly at 280 nm while proteins do the opposite. The general rules for determining the concentrations of nucleic acids at 260 nm are:

Thursday, March 19, 2009

Estimation of DNA Concentrations

The determination of the concentration of DNA or RNA in solution is a fundamental task in molecular biology. DNA is usually the limiting reagent in most experiments; therefore, the knowledge of its concentration is critical. Determination of the DNA concentration can be estimated either by qualitatively comparing the fluorescence of DNA bands in an agarose gel to a standard or by spectrophotometric means.

Tuesday, March 17, 2009

Measurement of Biosurfactant Activity

Biosurfactant activity was measured by an oil displacement test. This method is so sensitive that only a small amount of sample is required to measure the surfactant activity. Here is the method:

Wednesday, March 11, 2009

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Wednesday, February 25, 2009

Isolation of Yeast Genomic DNA

Isolating genomic DNA from yeast involves culturing the microbe, harvesting the cell, enzymatically removing the cell wall, lysing the protoplast, and finally separating the DNA from the other cell debris.
Materials that you need are:

Yeast culture-prepared previously

Spectrophotometer with cuvettes

50 mM EDTA, pH 8-ice cold

50 mM Tris, pH 9.5, 2% 2-mercaptoethanol

1.2 M sorbitol, 50 mM Tris, pH 7.5

Lyticase solution-500 U/ml in 50 mM Tris, pH 7.5

10% Sodium Dodecyl Sulfate (SDS)-used for checking protoplast formation

Lysis buffer-100 mM Tris, pH 7.5, 100 mM EDTA, 150 mMNaCl, 50 micrograms/ml RNase A

Lysis buffer with 2% SDS

95% Ethanol-stored at minus 20 degree Celcius

TE buffer-10 M Tris, pH 8, 1 mM EDTA

3 M potassium acetate, pH 5.5

Here are the step by step methods:

Bacterial DNA Extraction using InstaGene® Matrix

In spite of using Phenol and Chloroform to extract bacterial DNA template, you can use the InstaGene matrix to be more efficient. This DNA extraction method is very easy, fast, and practical. Here is the procedure:

Tuesday, February 24, 2009


Here are the references of the blog:
  1. Prieto, L.M. et al., “The production of rhamnolipid by a Pseudomonas aeruginosa strain isolated from a southern coastal zone in Brazil”, Chemosphere (2008), doi:10.1016/j.chemosphere.2008.01.003.
  2. Burden, D.W.; Whitney, D.B., "Biotechnology, Proteins to PCR, A Course in Strategies and Lab techniques", Birkhauser Boston, 1995.
  3. Thaniyavarn, J. et al., "Production and Characterization of Biosurfactants from Bacillus licheniformis F2.2" , Biosci. Biotechnol. Biochem., 67 (6), 1239-1244, 2003
  4. Eeles, R.A.; Stamps, A.C., "Polymerase Chain Reaction (PCR) The Technique And Its Applications", The Institute of Cancer Research, The Royal Marsden Hospital, Sutton, Surrey, United Kingdom, 1993.
  5. Aitken, A.; Learmonth, M., "The Protein Protocols Handbook, Second Edition: Protein Determination by UV Absorption", Humana Press, 2002.
  6. Aitken, A.; Learmonth, M., "The Protein Protocols Handbook, Second Edition: Quantitation of Tryptophan in Proteins ", Humana Press, 2002.
  7. Heptinstall. J and Rapley. R, “The Nucleic Acid Protocols Handbook: Spectrophotometric Analysis of Nucleic Acids”, Humana Press, 2000.
  8. Walker, J.M., "The Protein Protocols Handbook, Second Edition: The Bicinchoninic Acid (BCA) Assay for Protein Quantitation", Humana Press, 2002.
  9. Waterborg, J.H., "The Protein Protocols Handbook, Second Edition: The Lowry Method for Protein Quantitation", Humana Press, 2002.
  10. Kruger, N.J., "The Protein Protocols Handbook, Second Edition: The Bradford Method for Protein Quantitation", Humana Press, 2002.
  11. Kolmodin, L. A, Williams, J.F, “The Nucleic Acid Protocols Handbook: Polymerase Chain Reaction, Basic Principles and Routine Practice”, Humana Press Inc., Totowa, NJ, 2000.
  12. Chachaty. E, Saulnier. P, “The Nucleic Acid Protocol Handbook: Bacterial DNA Extraction for Polymerase Chain Reaction and Pulsed-Field Gel Electrophoresis”, Humana Press Inc., Totowa, NJ, 2000.
  13. Williams. D. R, Rapley. R, “The Nucleic Acid Protocol Handbook: Agarose Gel Electrophoresis of Nucleic Acids”, Humana Press Inc., Totowa, NJ, 2000.
  14. Smith. D. R, “The Nucleic Acid Protocol Handbook: Restriction Endonuclease Digestion of DNA”, Humana Press Inc., Totowa, NJ, 2000.
  15. Stewart, T.L., Mann, V., “Methods in Molecular Medicine, Vol. 80: Bone Research Protocols”, Humana Press Inc., Totowa, NJ, 2003.
  16. Theophilus, B. D. M., “Methods in Molecular Biology, Vol. 86: RNA Isolation and Characterization Protocols”, Humana Press Inc., Totowa, NJ, 1998.
  17. Perry, J., Parniske, M., "Lotus japonicus Handbook: 96-WELL DNA ISOLATION METHOD", 2005 Springer.
  18. Winstanley, C., Rapley, R., “The Nucleic Acid Protocols Handbook: Extraction and Purification of Plasmid DNA”, Humana Press Inc., Totowa, NJ, 2000.
  19. Bogner, P., Killeen, A. A., “Molecular Diagnostics: For the Clinical Laboratorian, Second Edition: Extraction of Nucleic Acids”, Humana Press Inc., Totowa, NJ, 2005.
  20. Harwood. A. J, “The Nucleic Acid Protocol Handbook: Native Polyacrylamide Gel Electrophoresis”, Humana Press Inc., Totowa, NJ, 2000.
  21. Aitken. A, Learmonth. M, “The Protein Protocols Handbook, Second Edition: Estimation of Disulfide Bonds Using EIIman's Reagent”, Humana Press Inc., Totowa, NJ, 2002.
  22. Miller. R. M, Zhang. Y, “Methods in Biotechnology, Vol 2 Bioremediation Protocols: Measurement of Biosurfactant-Enhanced Solubilization and Biodegradation of Hydrocarbons”, Humana Press Inc., Totowa, NJ, 1997.
  23. Boerner. S. A, Lee. Y. K, Kaufmann. S. H, Bible. K. C., “The Protein Protocols Handbook, Second Edition: The Nitric Acid Method for Protein Estimation in Biological Samples", Humana Press, 2002.

Monday, February 23, 2009

How to measure emulsification index (E24)

In biotechnology field, this method is used to measure the emulsification ability of biosurfactant. Emulsification index (E24) is used to characterize the biosurfactant in emulsifying, generally, the hydrophobic phase in hydrophilic phase.

Following s are the emulsification index procedure based on the published journal titled “The production of rhamnolipid by a Pseudomonas aeruginosa strain isolated from a southern coastal zone in Brazil” by L.M. Prieto, et al.:

Sunday, February 22, 2009


Saturday, February 21, 2009

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