NMR Studies of Backbone-Alkylated DNA: Duplex Stability, Absolute Stereochemistry, and Chemical Shift Anomalies of Prototypal Isopropyl Phosphotriester Modified Octanucleotides, (<i>Rp,Rp</i>)- and (<i>Sp,Sp</i>)-{d-[GGA(iPr)ATTCC]}₂and - {d- [GGAA(iPr)TTCC]}₂

Abstract

The DNA octamer (d-[GGAATTCC])2 and four alkylated analogues, (Rp)-(d-[GGA(iPr)ATTCC])2, (Sp)-(d-[GGA(iPr)ATTCC])2, (Rp)-(d-[GGAA(iPr)TTCC])2, and (Sp)-(d-[GGAA(iPr)TTCC])2 have been examined using 1H and 31PNMR spectroscopies. Duplex stability, as monitored by both NMR and optical measurements, is shown to be a function of both site and stereochemistry of the phosphotriester moiety. Chemical shift changes relative to the native octamer indicate that there are long-range perturbations in the isopropylated molecules. 1HNMR is shown to be a general means by which stereochemistry at phosphorous can be determined.