A computational approach to predict suitable target sites for trans-acting minimal hammerhead ribozymes.
Trans-acting hammerhead ribozymes are challenging tools for diagnostic, therapeutic, and biosensoristic purposes, owing to their specificity, efficiency, and great flexibility of use. One of the main problems in their application is related to the difficulties in the design of active molecules and identification of suitable target sites.The aim of this chapter is to describe ALADDIN, "SeArch computing tooL for hAmmerheaD ribozyme DesIgN," an open-access tool able to automatically identify suitable cleavage sites and provide a set of hammerhead ribozymes putatively active against the selected target.ALADDIN is a fast, cheap, helpful, and accurate tool designed to overcome the problems in the design of trans-acting minimal hammerhead ribozymes.
National Research Council, Institute of Clinical Physiology, Pisa, Italy.
Alberto
A
Mercatanti
Caterina
C
Lande
Lorenzo
L
Citti
D001483:Base Sequence; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D009690:Nucleic Acid Conformation; D016337:RNA, Catalytic / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D013816:Thermodynamics
D016337:RNA, Catalytic; C427204:hammerhead ribozyme