Skip to Content

DNA Ladder Related Questions 

 

Yes, all the DNA markers of SMOBIO have been passed in the QC processes including repeated optical density measurements to ensure the quantity of total DNA. 

We do not recommend to do the labeling reaction directly.

The reasons are as follows:

  1. Our DNA marker is pre-mixed with loading buffer that contains Tris-HCl, EDTA, and glycerol, may affect radio-labeling. 

  2. Our DNA marker is a mixture of PCR products and restriction enzyme digested DNA fragments. Digested dsDNA may still have phospho-group on their 5' end.

To enhance the efficiency of the labeling reaction, here are two steps suggested being done prior to the labeling reaction:

  1. Purify DNA marker by EtOH precipitation or DNA purification kits to remove loading buffer.

  2. Remove phospho-group by using phosphatase, ex CIAP (Calf intestinal alkaline phosphatase)

SMOBIO's AccuBand™ series DNA markers (DM1200, DM2000, DM2200 and DM2400) are suitable for DNA PAGE.

DNA fragments with identical in size are indistinguishable on agarose gels, but, on acrylamide gels, even slight differences in DNA sequence can lead to noticeably different migration rates. To provide increased intensity of DNA marker/ladder bands, multiple DNA fragments with identical in size but different in DNA sequences are used.

SMOBIO's AccuBand™ series DNA markers (DM1200, DM2000, DM2200 and DM2400) are more suitable for DNA PAGE.

SMOBIO's AccuBand™ series DNA markers (DM1200, DM2000, DM2200 and DM2400) are suitable for DNA PAGE.

SMOBIO's AccuBand™ DNA markers are not at denatured form, therefore,  you need to denature DNA ladder by yourself.

Here is the protocol to denature DNA ladder:

  1. Mix 5 μL of DNA Ladder with an equal volume of denaturing solution [95% (v/v) formamide, 10 mM EDTA (pH 8.0), 0.1% (w/v) bromophenol blue, 0.1% (w/v) xylene cyanol]. 

  2. Incubate at 70°C for 5 minutes. 

  3. Electrophorese the sample in a denaturing polyacrylamide/urea gel

Yes, it is possible to view the fluorescent signals under blue light and UV light. 

The fluorescent signals of a fluorescent DNA ladder might be reduced if frequently exposed to light for a long term. Therefore, we suggest keeping fluorescent DNA ladders from exposure the light. 

SMOBIO’s fluorescent DNA ladders is better in intensity and accuracy than a fluorescent marker produced by mixing non-fluorescent one with reagents containing fluorescent DNA dyes such as DL5000. In another aspect, DL5000 is designed for quick screening, not intended for preparation of DNA ladders which needs careful calibration. Therefore we suggest using our fluorescent DNA ladders directly.