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.
| Quinn, Jordan R; Zimmerman, Steven C; Del Bene, Janet E et al. (2007) Does the A.T or G.C base-pair possess enhanced stability? Quantifying the effects of CH...O interactions and secondary interactions on base-pair stability using a phenomenological analysis and ab initio calculations. J Am Chem Soc 129:934-41 |
| Quinn, Jordan R; Zimmerman, Steven C (2005) Structure-function studies on a synthetic guanosine receptor that simultaneously binds Watson-Crick and Hoogsteen sites. J Org Chem 70:7459-67 |
