Low resolution three-dimensional models of the 7SL RNA of the signal recognition particle, based on an intramolecular cross-link introduced by mild irradiation with ultraviolet light.

A number of intramolecular RNA-RNA cross-links were introduced into the human 7SL RNA by mild irradiation of a reconstituted signal recognition particle with ultraviolet light. Synthesis of radioactively labeled RNA was initiated in vitro from the T7 promoter. Smaller cross-linked complexes were generated by digestion of the RNA with RNase H in the presence of complementary deoxyoligonucleotides. Cross-linked complexes were separated from noncross-linked fragments by two-dimensional polyacrylamide gel electrophoresis. A close proximity between the stemloop around position 200 and the nucleotides at positions 67 to 76 was revealed by the absence of a characteristic oligonucleotide from the fingerprint of one of the complexes, suggesting a close spatial neighborhood between these two regions of the RNA. This and previous results, which described two different conformers of the RNA, were used to deduce two preliminary three-dimensional structure models of the 7SL RNA. The models differ in the base pairing scheme of the conserved core of the 7SL RNA.