Re: Oligos

Anthony Yeung (AT_Yeung@FCCC.edu)
Fri, 24 Apr 1998 16:50:10 -0400

Steven Seeholzer of my group, SH_Seeholzer@fccc.edu, has writen a Windows
program for your questions 2 and 3, for DNA oligo. It gives correct values
for MALDI-TOF, it is cut and paste and easy to use. We believe some
programs available on the WEB may be off by one proton. The ABI 394
synthesizer also gives molecular weights that are incorrect for MALDI-TOF,
one proton off for each guanine. The next update of Steve's program will
have DNA modifications that are common, RNA, and user programable X, Y and
Z residues to enable antisense work and DNA repair studies. If a few people
wants this, we can email or send the program on disk. Otherwise, sometime
in the future, we can put the program on our WWW site for download.
Extinction coefficients are pH dependent and possibily modification
dependent. The pH dependent UV scan curves of the four common nucleotides
are given in a bochure, circular OR-10, 1976, by PL Biochem of the Pabst
Brewing company, the former associate of Pharmacia that grey beards will
remember as the authority on nucleotides. They will have a copy of this
bochure. I can also send you photocopies if you ask for it. Perhaps there
are other publications with these curves.
Hope this helps.

Tony

At 02:30 PM 4/24/98 -0400, Kenneth Williams wrote:
>Does someone know of a nice resource (book/reviews or preferably Web site)
>that has some/all of the following very basic information for common and
>modified nucleotides found in RNA/DNA:
>
>1. Extinction coefficients - at both 280 and 260 nm - in RNA/DNA
>2. Mono and avg MWs
>3. Simple programs for calculating above for oligos
>
>Thanks very much
>
>
>
>Ken Williams, Ph.D.
>Director, HHMI Biopolymer/Keck Laboratory
>Professor (Adjunct) Research
>Molecular Biophysics and Biochemistry
>
>
>Visit the HHMI Biopolymer/Keck Laboratory Web Page at:
>
> http://info.med.yale.edu/wmkeck/
>
>
>

************************************
Dr. Anthony T. Yeung, Ph.D.
Director, Fannie E. Rippel Biotechnology Facility
Member, Institute for Cancer Research
Fox Chase Cancer Center
7701 Burholme Ave. Philadelphia, PA 19111
Voice: 215-728-2488
FAX: 215-728-3647
email: AT_Yeung@FCCC.edu
http://www.fccc.edu/research/labs/yeung/
************************************