For the past several years, the Laboratory of Medicinal Chemistry has been involved in the synthesis of nucleoside analogues containing various modifications on the sugar ring. In addition, carbocyclic nucleosides based on a rigid bicyclo[3.1.0] template have also been prepared. These analogues have been designed based on the assumption that the particular structural modification may bias the conformation of the sugar ring to favor a specific ring pucker. In order to define their precise conformations, we have studied these analogues under varying conditions using NMR spectroscopy. We found that deoxy- and/or dideoxy analogues containing a fluorine atom on the 2' or 3'carbon prefer very distinct sugar puckers depending on the position and the stereochemistry of this highly electronegative atom. In addition, coupling constant and NOE studies have allowed us to define the preferred ring conformations and rotamer distributions of several [3.1.0]bicyclo nucleoside analogues. We discovered that certain enzymes, such as adenosine deaminase, prefer analogues with only 3'-endo (Northern) sugar puckers. In extending the conformational analysis to mono- and triphosphate nucleotides of the fluorinated analogues, it was shown that phosphorylation does not affect the pseudorotational equilibrium in solution, and that the ring pucker is still driven by the position of the fluorine atom. We have included 19F and 31P NMR in our analysis and refined our pseudorotational calculations using 1H-19F coupling constants. Using 2-dimensional spectrocopy, we are characterizing the structural features of nucleic acid oligomers containing some of the afoermentioned modified nucleotides. The short term goals of the project are 1) to continue to study the solution structures of each individual analogue to examine specific conformational trends that emerge from distinct chemical modifications; 2) Create a database of these trends (coupling constants, reactivity, pseudorotational parameters)to compare with future synthetic analogues, and 3) to precisely define the structures of DNA oligomers containing these analogue monomers by multidimensional and multinuclear NMR spectroscopy ad molecular dynamics simulations using the most updated force fields for nucleic acid structure calculations.
| 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 |
