You may run your 100 bp DNA on 15% NATIVE PAGE using 2X TBE running buffer. Further, you may detect your band of interest under UV followed by EtBr staning. Further, you may elute your DNA by Crush and Soak method rather going for conventional Gel elution Kit (as recovery is less with small size DNA) . I followed this appoach and obtained 60 bp ss DNA Crush and Soak is a very simple and good approach for small size DNA recovery. Briefly, excised the gel (contaning DNA band of interest) to a microfuge tube and crush it to homogenized state by sterile tip. Add two volumes of Na-acetate solution and incubate till the gel dissolves completely at 65oC. Centrifuge and obtain the fine supernatant (contains DNA). Recover your DNA of interest by ethanol precipitation. (add chilled ethanol to the supernatant and keep for 2 hrs at -20 to -80 oC), centrifuge to 14000 g and discard the supernatant. You may dry the obtained DNA precipitate (very minute amount white color) and dissolve in TE/H20 for quantification (UV 260 nm).

Hope you may find my answer useful!

Good Luck!

run a 12% (7M Urea) denaturing PAGE will work for you. You can elute the DNA using using 0.3M NaCl and ethanol.

I was told that you can detect DNA in polyacrilamide gel by silver staining. I don't know whether ethidium bromide or GelRed work for polyacrilamide gel, but you might give it a shot... it won't hurt...

You may run your 100 bp DNA on 15% NATIVE PAGE using 2X TBE running buffer. Further, you may detect your band of interest under UV followed by EtBr staning. Further, you may elute your DNA by Crush and Soak method rather going for conventional Gel elution Kit (as recovery is less with small size DNA) . I followed this appoach and obtained 60 bp ss DNA Crush and Soak is a very simple and good approach for small size DNA recovery. Briefly, excised the gel (contaning DNA band of interest) to a microfuge tube and crush it to homogenized state by sterile tip. Add two volumes of Na-acetate solution and incubate till the gel dissolves completely at 65oC. Centrifuge and obtain the fine supernatant (contains DNA). Recover your DNA of interest by ethanol precipitation. (add chilled ethanol to the supernatant and keep for 2 hrs at -20 to -80 oC), centrifuge to 14000 g and discard the supernatant. You may dry the obtained DNA precipitate (very minute amount white color) and dissolve in TE/H20 for quantification (UV 260 nm).

Hope you may find my answer useful!

Good Luck!

Dear Murali,

choosing the best gel to run, it is important to know what kind of information you want to get. For example, are you interested to obtain information about the fragment lengths or basepairs differences between fragments of the same length?

With regard to the staining protocol I recommend you the modified silver staining method of Bendouza et al., 2006 Biotechnol. Agron. Soc Environ., 10 (2), 77-81.

Andrea

For running 91 bps DNA you can use wide range of acrylamide gel concentration. For staining I think Silver staining is better than EtBr

I use 12% (7M Urea) denaturing PAGE gel (although a range between 8-14% would be fine), run in 1 X TBE (for around 1 hr at 220V), and then stain with SYBR Gold Nucleic Acid Gel Stain.

Are you running ssDNA or dsDNA? Why do you need to run a PAGE? My new favorite way to cut a DNA band from a gel, because of the time saved by using this method, is to use eGels. You can use a 2% eGel, add up to 25uL of sample, run for 15-30min, break the casing apart (which is tricky even with the tool sold specifically for the purpose, but I have also successfully used a spatula...much trickier), visualize with UV, and cut the band out with a razor or special pipet tip, then use any gel purification column (Zymo, Qiagen, etc). I used to pour agarose gels, and run for hours. And PAGE gel purification isn't as simple. But, if you need to run a PAGE, and you are running ssDNA, then I agree that a 10% to 15% TBE-U gel would work great...or for best results, you can pour your own...assuming that you might have similar sized products you do not want to co-elute. This is the messier and more time consuming approach.

Run a 12% PAGE with 1X TBE and stain with EtBr.

You can elute the DNA fragments following @Irshad Baig's recommendation.

It is one of the most efficient methods to resolve and purify short DNA fragments from PAGE gels.

Hi Murali,

One option to staining the gel is to use UV without stain with a reflective TLC plate. We would lay the gel on celephane then on top of the TLC plate. The banding pattern could easily been seen with UV light. The procedure worked very well for gel purification of longer oligonucleotides.

Are you running polyacrylamide gel because of the low product size? Why not try regular agarose gel at 2.5-3% and run it with a borate buffer such as SB or LB? You can run the gel much faster, and easily resolve a 91 bp product. Afterwards you purify the band with your method of choice. If you clone your product, it's always a good idea to use crystal violet instead of ethydium bromide so you can visualize the band while the gel is running, and also avoid UV exposure when cutting the band out of the gel.