AMBER Archive (2007)

Subject: AMBER: Question about NAB (Nucleic Acid Builder)

From: Cenk Andac (cenk_andac_at_yahoo.com)
Date: Wed Jul 11 2007 - 03:30:18 CDT

Dear all,

I have an RNA hairpin system whose crystal structure is available. I would like to throw in a single-stranded anti-sense d(CCG) DNA into the system and base-pair it with a complemetary sequence (with three nicely stacking bases) in the loop region of the RNA hairpin without disturbing much of the crystal structure coordinates in the system. Is this doable by the NAB (Nucleic Acid Builder ) program?
If so, is there any tutorials/program scripts on the web or in the manual on how to implement this?
Any program script that you may send may be helpful.

best regards,

jenk

 

   Cenk Andac, M.S., Ph.D. Student
 
 School of Pharmacy at
 Gazi University-Ankara Turkiye
 
  
  Address: Bandirma Sok. No:6
 
 Etiler, Ankara, 06330 Turkey
 
 Cell: +90-(536)-4813012
 
 E-Mail:cenk_andac_at_yahoo.com

       
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