Albany 2013: Book of Abstracts

category image Albany 2013
Conversation 18
June 11-15 2013
©Adenine Press (2012)

Accelerating Nucleic Acid Design Using Pre-Selected Sequences

Nanoscale nucleic acids could potentially be designed to be catalysts, pharmaceuticals, or probes for detecting pathogens.

We hypothesize that designing nucleic acid molecules from pre-selected sequences, rather than from random sequences, would increase the speed of designing large molecules and also increase the accuracy of design. Helices should be formed in the optimal folding free energy change range, have maximal structure probability and minimal ensemble defect. Loops should be composed of sequences with the lowest ensemble free energy change. All sequences should have low tendency to cross- and self-hybridize. These features are observed in RNA sequences with known structure.

We demonstrate that pre-selected sequences accelerate the design of structures that are mimics of biologically relevant structures. This is implemented as a new structure design component of RNA structure (http://rna.urmc.rochester.edu/RNAstructure.html). This work is a collaboration with Celadon Laboratories, Inc. (http://www.celadonlabs.com/).

Stanislav Bellaousov
David H. Mathews

Department of Biochemistry
University of Rochester
601 Elmwood Avenue, Box 712
Rochester, New York 14642

Tel: (585) 275-1734