A technique for relating long-range base pairing on single-stranded DNA and eukaryotic RNA processing

Our previous results have shown that after photochemical crosslinking with psoralens in solutions of different concentrations of NaCl, short (100-300 base pairs) hairpins can be stabilized on denatured Simian virus 40 (SV40) DNA for electron microscope visualization. Six major hairpins were mapped. This study has been extended by crosslinking single stranded SV40 linear molecules, EcoRI-SV40 and Bgl I-SV40, in the presence of magnesium ions. After the reaction, in addition to the hairpins detected before, seven DNA hairpins, and hairpin loops with sizes from 300 to nearly 2000 nucleotides are observed. These loops are located at specific regions on the SV40 genome; at the EcoRI map positions (0.16 ± 0.02) (0.26 ± 0.03), (0.33 ± 0.03) (0.39 ± 0.03), (0.51 ± 0.03) (0.57 ± 0.03) (0.72 ± 0.03) (0.78 ± 0.04), (0.74 ± 0.03) (0.85 ± 0.03), (0.77 ± 0.05) (0.94 ± 0.03), and at (0.74 ± 0.04) (0.09 ± 0.07). At least three of these loops are found in regions thought to be involved in splicing of the early and late SV40 transcripts: (0.51 ± 0.03) (0.57 ± 0.03), (0.72 ± 0.03) (0.78 ± 0.04), (0.77 ± 0.05) (0.94 ± 0.03). These loop structures are most likely to arise from base pairing between distant regions of the single-stranded DNA, RNA transcribed from the double-stranded DNA template is expected to behave in a similar way, possibly providing recognition sites for processing (splicing) enzymes.