Since the last report, we have continued to define the structural features of conformationally biased and/or locked nucleosides. We have expanded our work on monofluorinated nucleosides to difluorinated analogues with fluorine atoms in both the 2'- and 3'-positions. We are using NMR spectroscopy in an attempt to estimate the magnitude of the F-F gauche effect that may be operable in these molecules and how other stereoelectronic effects may counterbalance this tendency. To do this, we have installed a state-of-the-art HF NMR probe to perform proton/fluorine correlated NMR experiments to examine the environment around the fluorine atoms in full detail. In addition, we now have several DNA oligomers that have been constructed with one or more of the conformationally """"""""locked"""""""" [3.1.0] bicyclic systems outlined in project Z01 BC 06174-15 LMC by Dr. Marquez. We have determined that all oligomers containing the modified base pairs form stable duplexes in solution at 25 deg C and are in the process of measuring the melt temperatures for these duplexes. We have been able to ascertain by NMR that in the new constructs, the cyclopropyl protons from the modified base pairs resonate at distinct frequencies to allow for reporting on nearby proton neighbors by different forms of correlated spectroscopies. The three dimensional folds of these oligos are being explored by a battery of NMR methods. Our collaborator, Dr. Alex Mackerrel of the University of Maryland, Baltimore, has developed force field parameters to allow accurate calculations of these structures with the NMR-derived restraints. For this project we will 1) Complete the work on the description of the fluorinated nucleosides; 2) More accurately define the structural parameters of the [3.1.0] nucleoside monomers and 3) Solve the structures of all the novel DNA oligomers we have on hand. Our goal is to accurately describe any bending that may be imparted to the DNA global conformations by the introduction of the modified nucleic acid monomers.
| Wu, Zhengrong; Maderia, Melissa; Barchi Jr, Joseph J et al. (2005) Changes in DNA bending induced by restricting nucleotide ring pucker studied by weak alignment NMR spectroscopy. Proc Natl Acad Sci U S A 102:24-8 |
| Maier, Martin A; Choi, Yongseok; Gaus, Hans et al. (2004) Synthesis and characterization of oligonucleotides containing conformationally constrained bicyclo[3.1.0]hexane pseudosugar analogs. Nucleic Acids Res 32:3642-50 |
