The structure of a modified protein fragment (I-I-C-N-N-P-H-I-I) associated with a dodecylphosphocholine (DPC) micelle has been shown to contain a type I or type III hairpin turn between residues N5 and I8 using a combination of NMR and computer simulation methods. The fragment in solution without the micelle, in contrast, has no discernable secondary structure. Molecular dynamics simulations of DPC micelles and peptide/micelle complexes suggest that the peptide lies flat on the micelle surface, and showed rapid rearrangement of the lipids to accommodate the bound peptide. According to a search performed using the basic local alignment search tool (BLAST), the sequences N-P-H-I and N-P-H-V are present as hairpin turns in eight of nine proteins whose crystal structures were available. The addition of isoleucine residues and the use of lipid micelles to stabilize hairpin conformations equivalent to those found in proteins generates new possibilities for reproducing biologically important hairpin-turns from short, linear peptides. A report of this research has been accepted for publication in Biopolymers. SP-Chiral oligodeoxyribonucleoside phosphorothioates (PS-ODNs) have demonstrated superior stability to nucleases found in human serum as well as to either RP-PS-ODNs or P-diastereomeric PS-ODNs. They are thus thought to be superior therapeutic agents against cancer and infectious disease as well as for antisense therapeutic applications. The use of deoxyribonucleoside cyclic N-acylphosphoramidites for P-stereocontrolled synthesis of selected PS-ODNs has been reported, and since the P-stereochemistry of any given dinucleoside phosphorothioate can be unambiguously determined, it is therefore possible to deduce the absolute configuration at P(III) of the diastereomerically pure deoxyribonucleoside cyclic N-acylphosphoramidite that was used to prepare the dinucleotide. However, the validity of such a determination depends on whether the base-assisted condensation of the cyclic phosphoramidite proceeds through a single nucleophilic substitution event. In this regard, a direct method for assigning the absolute configuration of deoxyribonucleoside cyclic N-acylphosphoramidites at P(III) would confirm or reject the possibility of additional nucleophilic substitution events taking place during the phosphitylation reaction. A successful assignment of the absolute configuration of a deoxyribonucleoside cyclic N-acylphosphoramidite at phosphorus has been accomplished for the first time using an M-GOESY NMR technique developed in this lab. The method is convenient, rapid, and unequivocally confirms that the condensation of deoxyribonucleoside cyclic N-acylphosphoramidites with base-activated nucleosidic 5'-hydroxyls proceeded via a single SN2 nucleophilic substitution event, which is consistent with the P-stereochemistry determined for the parent dinucleoside phosphorothioates. M-GOESY NMR techniques may therefore find application in the analysis of recognition processes involving specific chiral centers of biologically active molecules.
