Saturday, August 27, 2016

What is the Importance of 260/230 ratio in a Nanodrop reading?

Well, most of us are familiar about the 260/280 ratio.The ratio of absorbance at 260 nm and 280 nm is used to assess the purity of DNA and RNA. A ratio of ~1.8 is generally accepted as “pure” for DNA; a ratio of ~2.0 is generally accepted as “pure” for RNA. If the ratio is appreciably lower in either case, it may indicate the presence of protein, phenol or other contaminants that absorb strongly at or near 280 nm. 

But you might have also observed the machine also takes a 260/230 ratio reading but might not have bothered about it because most us only depend on the 260/280 ratio for quality check of nucleic acids(DNA or RNA). This ratio is used as a secondary measure of nucleic acid purity. The 260/230 values for “pure” nucleic acid are often higher than the respective 260/280 values. Expected 260/230 values are commonly in the range of 2.0-2.2. If the ratio is appreciably lower than expected, it may indicate the presence of contaminants which absorb at 230 nm. 

Contaminants like EDTA, carbohydrates and phenol all have absorbance near 230 nm. 

The TRIzol reagent is a phenolic solution which absorbs in the UV both at 230 nm and ~270 nm. 

Guanidine HCL used for DNA isolations will absorb at ~230 nm while guanidine isothiocyanate, used for RNA isolations will absorb at ~260 nm.



Wednesday, August 24, 2016

Why shouldn't we turn on white light in the laminar airflow chamber immediately after UV treatment?

By fact UV sterillzation is based on the principle of mutation caused by UV C occurring in the DNA of several micro-organisms like bacteria,fungi and protozoa due to thymidine dimer formation(covalent bond formation in between two adjacent thymines in the same strand of the dsDNA which hinders biological processes like cellular DNA replication and transcription)between 245 to 300nm wavelength of UV. This mutation is reverted back by an enzyme called photolyase in the cell which starts working at 480nm(visible region of the spectrum). The phenomenon is called photo-reactivation. If the mutation is fixed then the cells may again start to replicate normally and cause contamination. Thus, it is a general procedure to switch off UV and leave the LFC in dark for at least 15 minutes before turning the white lights on.

Thursday, February 25, 2016

Why 70% ethanol is normally used as a sterillant instead of absolute ethanol?

First of all 100% ethanol is highly volatile and tends to evaporate before entering into the tissue significantly. Secondly when absolute ethanol enters the cell first it encounters the cell wall and immediately starts coagulating proteins present in the cell wall before actually considerably entering into the cell and therefore the protective coagulated layer stops further inflow of more ethanol into the cell. In this case the cell is protected and stays dormant and again functions normally when favourable conditions reappear. But if we use 70% ethanol it evaporates much slower than absolute ethanol undoubtedly and it also coagulates proteins and dissolves lipid but at a very slower rate; enough for it to completely get into the cell and then starts coagulating proteins and dissolving lipids and thus the cell dies.why 70% ethanol is standardized for surface sterilization? It may be because perhaps the dilution is enough for entering into the surface layers of the plant tissue where the pathogens may get into and does not go too deep into the plant tissue so that the plant cells beneath the surface tissues are not considerably harmed.

Friday, February 19, 2016

Can the same PCR program have different completion time in different thermo-cyclers?

Yes !!! the same PCR program may have slightly different completion time for the same reaction (having the same number of cycles) in two different thermo-cyclers due to difference in the ramp rate of the machines. For example if I keep two sets of PCR with the same program; one in a Bio-Rad machine and the other one in an Eppendorf machine then one may have a completion time of 1hr 48mins and the other may have completion time of 2hrs 5mins.