Long ssRNA undergoes continuous compaction in the presence of polyvalent cations.

Ana Luisa Duran-Meza, Liya Oster, Richard Sportsman, Martin Phillips, Charles M Knobler, William M Gelbart

Journal: Biophysical journal 2023;122(17):3469-3475

PMID: 37501368

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Abstract

In the presence of polyvalent cations, long double-stranded DNA (dsDNA) in dilute solution undergoes a single-molecule, first-order, phase transition ("condensation"), a phenomenon that has been documented and analyzed by many years of experimental and theoretical studies. There has been no systematic effort, however, to determine whether long single-stranded RNA (ssRNA) shows an analogous behavior. In this study, using dynamic light scattering, analytical ultracentrifugation, and gel electrophoresis, we examine the effects of increasing polyvalent cation concentrations on the effective size of long ssRNAs ranging from 3000 to 12,000 nucleotides. Our results indicate that ssRNA does not undergo a discontinuous condensation as does dsDNA but rather a "continuous" decrease in size with increasing polyvalent cation concentration. And, instead of the 10-fold decrease in size shown by long dsDNA, we document a 50% decrease, as demonstrated for a range of lengths and sequences of ssRNA.

Address: Department of Chemistry and Biochemistry, UCLA, Los Angeles, California.; Department of Chemistry and Biochemistry, UCLA, Los Angeles, California. Electronic address: [email protected].; Department of Chemistry and Biochemistry, UCLA, Los Angeles, California; Molecular Biology Institute, UCLA, Los Angeles, California; California NanoSystems Institute, UCLA, Los Angeles, California.

DOI: 10.1016/j.bpj.2023.07.022

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MeSH Terms: RNA, Cations, DNA