COMPUTER FOLDING OF RNA MOLECULES USING MONTE CARLO METHODS

Award Information
Agency:
Department of Health and Human Services
Branch
n/a
Amount:
$261,000.00
Award Year:
1988
Program:
SBIR
Phase:
Phase II
Contract:
n/a
Award Id:
7265
Agency Tracking Number:
7265
Solicitation Year:
n/a
Solicitation Topic Code:
n/a
Solicitation Number:
n/a
Small Business Information
1977 Concourse Drive, San Jose, CA, 95131
Hubzone Owned:
N
Minority Owned:
N
Woman Owned:
N
Duns:
n/a
Principal Investigator:
Ahmad Waleh Phd
(408) 434-6780
Business Contact:
() -
Research Institute:
n/a
Abstract
THE DEVELOPMENT OF EFFICIENT METHODS FOR PREDICTING SECONDARY STRUCTURES OF SINGLE STRANDED NUCLEIC ACIDS IS OF GREAT IMPORTANCE IN UNDERSTANDING MANY FUNDAMENTAL PROCESSESIN GENETICS AND MOLECULAR BIOLOGY. PRESENTLY AVAILABLE ENERGY MINIMIZATION TECHNIQUES YIELD ONLY ONE STRUCTURE WHICH IS OFTEN DIFFERENT FROM BIOLOGICALLY SIGNIFICANT RNA SECONDARY STRUCTURES. APPLICATION OF THESE COMPUTATIONALLY COMPLEX ALGORITHMS IS LIMITED TO RELATIVELY SHORT RNA STRANDS. APPLIED SCIENCES CONSULTANTS, INC. PROPOSES THAT FOLDING PATTERNS OF RNAS BE PREDICTED BY EMPLOYING AN ALGORITHM BASED ON MONTE CARLO METHODS OF STATISTICAL MECHANICS, WHICH INCLUDES AN ANNEALING PROCEDURE. MONTE CARLO METHODS, IN CONTRAST TO MINIMIZATION ROUTINES, SCAN MANY LOCAL MINIMA, CALCULATE STATISTICALLY AVERAGED PROPERTIES, AND PREDICT MELTING PATTERNS. THESE METHODS ARENOT LIMITED BY COMPUTER STORAGE REQUIREMENTS AND THEREFORE CAN HANDLE RNAS OF THE ORDER OF A FEW THOUSAND NUCLEOTIDES. PRELIMINARY RESULTS FOR SMALL RNAS ARE PRESENTED AND A FEASIBILITY STUDY IS PROPOSED TO EVALUATE THE EFFICIENCY OF THE NEW ALGORITHM, DETERMINE MELTING AND REFOLDING OF SHORT RNA MOLECULES, AND PREDICT SECONDARY STRUCTURES OF SELECTED LONG RNAS. LONG-TERM GOALS INCLUDE GENERALIZATION AND FURTHER IMPROVEMENT OF THE ALGORITHM AND THE DEVELOPMENT OF A RAPID AND RELIABLE SOFTWARE FOR ANALYSIS OF LARGE RNA SEGMENTS. BOTH THE METHOD AND THE RESULTS OF THE PROPOSED STUDIES ARE EXPECTED TO BE OF INTEREST TO THE SCIENTIFIC AND BUSINESS COMMUNITIES IN THE HEALTH-RELATED AREAS OF PHARMACOLOGY, GENETIC ENGINEERING, AND MOLECULAR BIOLOGY.

* information listed above is at the time of submission.

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