One-and two-dimensional NMR investigation of the chemically synthesized DNA d(GGGTACCC)2

Abstract

One- and two-dimensional proton NMR studies were reported on the self-complementary d(GGGTACCC) duplex. The resonances of the exchangeable protons were assigned by one-dimensional NOE difference spectra and the melting behavior of these imino protons was observed with line broadening and chemical shift change. The resonance of nearly all of the nonexchangeable protons of octamer duplex in solution were assigned by proton two-dimensional nuclear Overhauser enhancement spectroscopy(NOESY) and J-correlated spectroscopy (COSY). We obtained complete assignment for the adenine H8, guanine H8, cytosine H6 and H5, thymine H6 and $CH_3$, and the deoxyribose H1``, H2``, H2", H3``, H4`` resonances. These assignment were required for the analysis of two dimensional NOE and J-coupled data in terms of the solution structure of oligonucleotides. A set of short ($<4.5$) proton-proton distances defined for complementary d (GGGTACCC) octamer duplex were estimated from NOESY data set recorded as a function of mixing time. The conformation and dynamics of the selfcomplementary DNA octamer d (GGGTACCC) duplex was studied by means of 1H NMR and distance constraints.