Category: Electrophoresis

Percent Agarose Gel

Agarose concentration in a gel is expressed in percentage of agarose to the volume of the buffer (w/v). For example,…

How to Study Changes in Buffer pH During Agarose Gel Electrophoresis?

Changes in electrophoresis buffer pH is an important parameter to consider when optimizing already existing reagents or conditions or testing…

TBE (Tris-Borate-EDTA) Electrophoresis Buffer Calculator

The TBE (Tris-Borate-EDTA) electrophoresis buffer contains Tris base, Boric acid, EDTA and has pH 8.3. Usually the stock TBE electrophoresis…

Tips to Reduce Run-time of Agarose Gel Electrophoresis

Usually agarose gel electrophoresis is performed at constant low voltage (5 – 10 V/cm). High voltage results in excessive heat…

Tracking dyes for Agarose Gel Electrophoresis

There are several dyes (Bromophenol blue, Bromocresol green, Orange G, Xylene cyanol FF) that can be used for the preparation…

Protocol: Visualizing DNA Bands in Agarose Gel Using GelRed – Precast Method

GelRed is a DNA staining dye and can be used to visualize DNA embedded in agarose gel. Both precast (GelRed…

Preparation of 6X DNA Loading Dye (Bromophenol Blue and Glycerol)

Overview DNA loading dye containing only one tracking dye Bromophenol blue (BPB) can be used to analyze larger DNA fragments…

Electroendosmosis in Agarose Gel Electrophoresis

In agarose gel electrophoresis, electroendosmosis (EEO) can be defined as ‘the active water transport towards cathode (negative electrode) from anode…

Protocol: Size Determination of Plasmid DNA Using Agarose Gel Electrophoresis

OVERVIEW Plasmids are circular DNA. Their size can not be determined in their native state as the migration of circular…

Protocol: Size Determination of DNA fragment Using Agarose Gel Electrophoresis

OVERVIEW Approximate size of DNA fragments can easily be determined by agarose gel electrophoresis. This analysis is quite useful to…

Recommended Agarose Gel Percentage for Efficient Separation of DNA Fragments

Agarose Gel is a porous matrix that acts as a sieve through which negatively charged linear DNA fragments migrate under an…

Preparation of 6X DNA Loading Dye (Xylene Cyanol FF and Sucrose)

Overview DNA sample is mixed with DNA loading dye prior to loading into the wells of agarose gel.  DNA loading…

Preparation of 6X DNA Loading Buffer (Orange G, Xylene Cyanol FF and Ficoll 400)

A 10 ml of 6X DNA loading dye can be prepared by dissolving and mixing 40 mg orange G, 25 mg xylene cyanol FF, 1.5 g Ficoll 400 and 0.1 ml of 1M Tris.Cl, pH 7.6 in sterile deionized or distilled water to a final volume of 10 ml.

Mobility of Xylene Cyanol in Agarose Gel

% agarose gel Mobility of xylene cyanol corresponding to DNA fragment (bp) in 1X TBE buffer Mobility of xylene cyanol…