I would like to know is there any techniques using which i can judge the size of amplified PCR product without using ladder or gene ruler in electrophoresis gel.
I think Loganathan is right.Look up the apparent sizes of your loading dye(s) for the concentration of gel used. Plot 1/distance moved for the dye size and read off the distance therefore the size of your product. you could run other pcr products of known size to get an estimate or restriction digest lambda or plasmid dna but buying a size ladder is best if possible
Using ladder is most inexpensive and easiest way to compare your PCR product size. you can extract the DNA from gel and send it sequencing, it will describe the product size perfectly
@Masuma. Thanks but i am interested to know can we judge the product size by loading dye itself or can we judge the product size by knowing the rate of migration of product with different gels atleast a fair idea..
Without gene ruler we can use two method for PCR product size identification,
1. if it is universal primer. We can get the information by using online database .
2.In 1% agarose gel bromophenol blue migrates fragment of about 300 base pairs, in 2% agarose as 150 bp
I think Loganathan is right.Look up the apparent sizes of your loading dye(s) for the concentration of gel used. Plot 1/distance moved for the dye size and read off the distance therefore the size of your product. you could run other pcr products of known size to get an estimate or restriction digest lambda or plasmid dna but buying a size ladder is best if possible
you can use some other previous PCR products as size marker. in routine diagnostic assays may you have some products which are not useful. you can save them for future size estimations.
going back to your explanation of 2 days ago. It should be possible to get a reasonable estimate of size by using exactly the same apparatus and extreme care in buffer and gel preparation and addition of exactly the same amount of ETBR and always running the same voltage and time, Running dyes or dna samples of known size in a couple of early runs will give you a plot of distance against size ( log it or plot reciprocal of distance to linearise the plot) and if all other factors are constant ( room temperature, sample salt concentration and as mentioned above) you will get some idea of size of fragment if your fragments are small, Run 3 different dyes in your sample for increased accuracy but the results will only be approximate but if you are always running the same amplimer this may be ok for checking that amplification has occurred
Assuming you didn't load ALL of your PCR products into the gel, just buy the ladder and re-run your gel. Or ask a company for a trial size sample. Ladder is cheap, your time is valuable, don't bother with estimating.
As others said using ladder is an easy, simple and quick procedure to estimate the size of target.
If its out of curiosity i will recommend you to use a combination of know sized PCR product and some one restriction enzyme in the case your PCR product is large.
Regards
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