Phosphorescence and optically detected magnetic resonance of HIV-1 nucleocapsid protein complexes with stem-loop sequences of the genomic Psi-recognition element

The binding of NCp7, the nucleocapsid protein of human immunodeficiency vir us type I, to oligonucleotide stem-loop (SL) sequences of the genomic Psi - recognition element has been studied using fluorescence, phosphorescence, a nd optically detected magnetic resonance (ODMR). RNA SL2, SL3, and SL4 cons tructs bind with higher affinity than the corresponding DNAs. G to I substi tutions in the SL3 DNA loop sequence lead to reduced binding affinity and s ignificant changes in the triplet state properties of Trp37 of NCp7, implic ating these bases in contacts with aromatic amino acid residues of the zinc finger domains of NCp7, in agreement with the NMR structure of the 1:1 com plex of NCp7 and SL3 RNA [DeGuzman, R. N., Wu, Z. R., Stalling, C. C., Papp aladro, L., Borer, P. N., and Summers, M. F. (1998) Science 279, 384-388]. The NCp7 to SL binding stoichiometry is 2:1 for intact SL sequences but is reduced to 1:I for SL variants with an abasic or hydrocarbon loop. It is pr oposed that DeltaD/DeltaE(0),(0) where DeltaD is the change in the zero-fie ld splitting D parameter and DeltaE(0,0) is the shift of the tryptophan pho sphorescence origin, provides a measure of aromatic stacking interactions w ith nucleic acid bases. Values on the order of 10(-5) indicate significant stacking interactions, while values closer to 10(-6) result from interactio ns not involving aromatic stacking. Binding of NCp7 to oligonucleotide subs trates produces shortened Trp37 triplet state lifetimes by enhancement of k (x) and an increase of the relative value of P-x, the intersystem crossing rate to the T-x sublevel. These effects are attributed to a reduction in th e degree of electronic symmetry of Trp37 in the complexes. Guanine and aden ine triplet states produced by optical pumping of SL3 DNA are characterized . We find, as with tryptophan, that /D/ < 3/E/.