That depends. Has to do with plates in separation (physical biochemistry concept). One could separate small amounts effectively (just as in traditional PAGE-based sequencing). Large amounts will exceed the separation capacity and cause break-through between the two. There is a mass-effect that causes some of the larger fragments to migrate with the smaller, and vice versa. When you run them again (now a smaller mass) the larger band will show some fraction of smaller and vice versa. So, the key is to use a system that has adequate separation. Liquid chomatography might allow better separation.

Dear Zhiwei Chen,

capillary electrophoresis allows to resolve 1nt difference in this length range.

I propose to use Snapshots (micro sequencing) method. 

HPLC (even anion-exchange) will not really help you with so long oligonucleotides. PAGE is good enough, but I agree with Vladimir that capillary electrophoresis is able to provide better resolution.

As stated in my answer, it depends on the amount to be separated (mass; load capacity). For analytical purposes PAGE will be fine, capillary electrophoresis will be better, but if the intent is purification, almost any of the methods (PAGE, CE, LC) will have problems.  So, the real question is what is the intent: analytic separation or purification for subsequent use?

That's true!

Thank you all!

I am looking for analytical instead of preparative methods. For PAGE, do you think regular large PAGE gels (e.g., 6% or 10%, 19:1, 20 cm long, 1 or 0.75 mm thickness, TBE, 7 M Urea) could have single-base resolution? For CE, do you have any suggestion for the instrument?

Dear Zhiwei Chen,

ABI Sequencers from 310 to 3500

What purpose of such research (QC)?

To Vladimir: Thanks! Are these sequencers quantitative or qualitative? I use it for QC. THX!

Dear Zhiwei , both qualitative and quantitative simultaneously. Good luck

I would try Denaturing Gradient Gel Electrophoresis (DGGE). It is a qualitative technique.