Theory for RNA Folding, Stretching, and Melting Including Loops and Salt

Abstract

Secondary structure formation of nucleic acids strongly depends on salt concentration and temperature. We develop a theory for RNA folding that correctly accounts for sequence effects, the entropic contributions associated with loop formation, and salt effects. Using an iterative expression for the partition function that neglects pseudoknots, we calculate folding free energies and minimum free energy configurations based on the experimentally derived basepairing free energies. The configurational entropy of loop formation is modeled by the asymptotic expression -clnm, where m is the length of the loop and c the loop exponent, which is an adjustable constant. Salt effects enter in two ways: first, we derive salt-induced modifications of the free energy parameters for describing basepairing, and second, we include the electrostatic free energy for loop formation. Both effects are modeled on the Debye-Hückel level including counterion condensation. We validate our theory for two different RNA sequences. For tRNA-phe, the resultant heat capacity curves for thermal denaturation at various salt concentrations accurately reproduce experimental results. For the P5ab RNA hairpin, we derive the global phase diagram in the three-dimensional space spanned by temperature, stretching force, and salt concentration and obtain good agreement with the experimentally determined critical unfolding force. We show that for a proper description of RNA melting and stretching, both salt and loop entropy effects are needed.

Rapid point-of-care detection of SARS-CoV-2 using reverse transcription loop-mediated isothermal amplification (RT-LAMP)

“…Using the Transwab swab type for direct analysis of patients’ pharyngeal swab samples without prior RNA extraction is crucial to the success of the here described RT-LAMP assay. High salt concentrations in different viral transport media for example, could interfere with nucleic acid folding and loop formation, inhibiting RT-LAMP reaction [ 23 ]. Just as specific components of every viral transport media, the different volumes of viral transport media in the different available swab types influence the feasibility and efficiency of the RT-LAMP assay.…”

Coil-helix transition of polypeptide at water-lipid interface

“…In a final note, we should like to draw the reader’s attention to a different set of applications, for which our statistical mechanical model and its extensions are likely to produce significant new insights. These applications investigate the statistical mechanics and the dynamics of DNA melting (thermal denaturation) [13, 14, 42, 43, 44, 45, 46, 47, 48] or the loop formation in RNA [49]. Of particular interest is the loop exponent in the configurational entropy of loop formation [14, 49], which is frequently used as an adjustable parameter.…”

Salt Dependent Mesoscopic Model for RNA with Multiple Strand Concentrations

“…Frayed states are intermediaries in zipping and unzipping processes and have been suggested to be important for the interactions of RNA with proteins, 29,30 are required for secondary structure rearrangements for riboswitch function, 31 and may be relevant for strand migration. 32 The effect of monovalent ions in RNA has been investigated with several theoretical methods, such as molecular dynamics (MD), 14,[33][34][35][36] , coarse-grained models, 37 Debye-Hückel models, 38 and tightly-bound ion theory. 16,39 For instance, MD simulations such as made by Beššeová et al 33 33,34 concluded that the force field and salt effects are sequence-dependent and the helix compactness is sensitive to the salt and water conditions.…”

“…40 Debye-Hückel models concluded that a decrease in salt concentration generally destabilize the folding of RNA and lowers its denaturation temperatures. 37,38 Mesoscopic modelling, based on the Peyrard-Bishop (PB) description, using experimental melting temperatures as input data, have been restricted to high sodium concentrations. 41 Existing RNA melting temperature data at lower sodium concentrations exists at varying strand concentrations, however the mesoscopic approach requires all temperatures to be at a single strand concentration.…”