This proposal describes a major new initiative to develop tethered DNA bases. These new bases consist of the four standard DNA bases A, T, G, and C, modified to hold an appendage capable of additional hydrogen bonding (beyond Watson-Crick) and base-stacking interactions with the complementary DNA strand. As such, these """"""""super bases"""""""" should be capable of hybridizing complementary sequences with higher affinity and selectivity. They may also selectively bind DNA base mismatches providing a mechanism for detecting single nucleotide polymorphisms (SNPs). The development of each new DNA super-base will follow four distinct steps: (1) Synthesis. The syntheses are generally short and start with simple, available materials. More sophisticated bases have been designed as back-ups and their synthesis, if needed, will require somewhat more effort. (2) Characterization. Beyond establishing the molecular structure, it is important to examine the possibility of undesirable tautomeric equilibria. (3) Model Studies. Prior to inserting super-bases into oligonucleotides or testing their ability to recognize mismatches, we will perform model studies in an organic solvent to determine the quality of the hydrogen bonding interactions. Favorable binding qualifies a base for further study and development. (4) Recognition of oligonucleotides. Super-bases will be incorporated into oligonucleotides and their ability to bind target bases examined. Dimeric super-bases will be synthesized and their ability to recognize mismatches will be examined. Beyond the fundamental interest in this type of recognition various applications can be envisioned. These include the use of super-bases in therapeutic oligonucleotides (e.g., antisense), detection of SNPs, as nonprocessable duplex anchors for chemical and molecular biology studies, etc.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM065249-02
Application #
6623068
Study Section
Medicinal Chemistry Study Section (MCHA)
Program Officer
Lograsso, Philip
Project Start
2002-08-01
Project End
2006-07-31
Budget Start
2003-08-01
Budget End
2004-07-31
Support Year
2
Fiscal Year
2003
Total Cost
$298,001
Indirect Cost
Name
University of Illinois Urbana-Champaign
Department
Chemistry
Type
Schools of Arts and Sciences
DUNS #
041544081
City
Champaign
State
IL
Country
United States
Zip Code
61820