An improved NOESY simulation program for partially relaxed spectra: BIRDER.

An improved 2D NOESY simulation program, BIRDER (back-calculation considering incomplete recovery and differential external relaxation), has been developed. BIRDER has the following features: (1) It allows for differential external relaxation rates for protons with different chemical environments, (2) it automatically accounts for incomplete recovery of z magnetization between scans, and (3) it incorporates anisotropic tumbling motional modes for nonspherical molecules. It was found that a lower R factor is obtained if differential external relaxation rates are used in the NOESY spectrum simulation. The method for experimentally determining these external relaxation rates is discussed. In practice, the ability to account for incomplete recovery of z magnetization is very useful in the quantitative analysis of 2D NOESY spectra of spin systems with long longitudinal relaxation times (T1). For example, the T1's of some protons in RNA duplexes are approximately 4-6 s. Thus, a more than 15 s relaxation delay is needed to allow the z magnetization to return to thermal equilibrium between scans, requiring more than a week to obtain a single NOESY spectrum. Unless incomplete recovery of z magnetization is explicitly considered, distance errors may arise when shorter relaxation delays are used. The situation is further complicated in studies of DNA:RNA hybrid or DNA-RNA chimeric duplexes in which the DNA protons relax much faster than the RNA protons. It is shown that BIRDER successfully corrects for the incomplete recovery of z magnetization and makes it possible to save spectrometer time by using shorter relaxation delays without introducing serious errors. The nonsymmetrical nature of NOESY spectra when the spin system is not fully relaxed is discussed.(ABSTRACT TRUNCATED AT 250 WORDS)