Novel Protecting Group Chemistry for Nucleic Acids

DESCRIPTION (provided by applicant): Thermolabile protecting groups of nucleic acids which can be removed during genomic methods will be developed. Protecting groups for nucleobase substituents involved in Watson-Crick hydrogen bonding will be identified and used to block hybridization. Subsequent removal of the thermolabile group at elevated temperature for 10-30 minutes, and as part of the genomic method, will release the desired nucleic acid and allow the genomic method to be initiated under controlled conditions of time and temperature. The technology is expected to eliminate non-specific reactions and false readings caused by mis-matched hybrids, primers annealed to non-target template, mis-priming, and partially complementary primers at ambient temperature. The primary objective is to prevent premature or erroneous formation of hybridized nucleic acids during sample preparation procedures that lead to undesirable events of sequence recognition. The specific aims are (1) development of chemistry for reversible, thermolabile, covalent modification of nucleic acids and (2) preparation and characterization of modified nucleic acids suitable for specific genomic methods. Nucleosides and small nucleotides will be used as model compounds to investigate candidate chemistries and the kinetics of deprotection. These chemistries will be applied to and evaluated with oligonucleotide primers, genomic DNA, and nucleoside triphosphates. This project will result in a new class of compounds and technology for health related applications in genomic methods such as SNP (single nucleotide polymorphism) analysis and allele-specific oligonucleotide (ASO) hybridization which are the basis of DNA microarrays, PCR amplification, and DNA sequencing applied to medical diagnostics and health related research. Commercial applications include modified nucleic acids, specialty chemicals, and new instrumentation for utilizing the technology in probe based diagnostics, health related research, and pathogen detection. Other applications include drug discovery and the study of drug response genes (pharmacogenomics), biodefense and bioterrorism where 'ruggedized' reagents may be needed, drug delivery, and therapeutics.