A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation

Lü, Zhi; Turner, Douglas H.; Mathews, David H.

doi:10.1093/nar/gkl472

Cited by 126 publications

(217 citation statements)

References 81 publications

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“…Therefore, the enthalpy contribution for group I single-nucleotide bulge loops is just the average of the measured values (13.4 6 9.4 kcal/mol). As noted previously, the standard error for enthalpy measurements is much larger than for free energy measurements (Lu et al 2006). The enthalpy for the group II bulges is slightly larger than the enthalpy for group I bulges (14.1 6 9.2 kcal/mol) (Blose et al 2007).…”

Section: Resultsmentioning

confidence: 70%

“…The enthalpy for the group II bulges is slightly larger than the enthalpy for group I bulges (14.1 6 9.2 kcal/mol) (Blose et al 2007). The enthalpy values presented in Table 3 can be used in conjunction with the free energy and enthalpy parameters for other nearest-neighbor motifs to determine the stability of RNA structures at temperatures other than 37°C (Lu et al 2006); however, the range of enthalpic values makes this extrapolation problematic.…”

Section: Resultsmentioning

confidence: 99%

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Non-nearest-neighbor dependence of the stability for RNA group II single-nucleotide bulge loops

McCann¹,

Lim²,

Manni³

et al. 2010

RNA

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Thirty-one RNA duplexes containing single-nucleotide bulge loops were optically melted in 1 M NaCl, and the thermodynamic parameters DH°, DS°, DG°3 7 , and T M for each sequence were determined. The bulge loops were of the group II variety, where the bulged nucleotide is identical to one of its nearest neighbors, leading to ambiguity as to the exact position of the bulge. The data were used to develop a model to predict the free energy of an RNA duplex containing a single-nucleotide bulge. The destabilization of the duplex by the bulge was primarily related to the stability of the stems adjacent to the bulge. Specifically, there was a direct correlation between the destabilization of the duplex and the stability of the less stable duplex stem. Since there is an ambiguity of the bulge position for group II bulges, several different stem combinations are possible. The destabilization of group II bulge loops is similar to the destabilization of group I bulge loops, if the second least stable stem is used to predict the influence of the group II bulge. In-line structure probing of the group II bulge loop embedded in a hairpin indicates that the bulged nucleotide is the one positioned farther from the hairpin loop.

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Section: Resultsmentioning

confidence: 70%

Section: Resultsmentioning

confidence: 99%

Non-nearest-neighbor dependence of the stability for RNA group II single-nucleotide bulge loops

McCann¹,

Lim²,

Manni³

et al. 2010

RNA

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show abstract

“…This does not have to be the case, however. Base-pairing is typically much weaker in mesophilic than thermophilic functional RNAs (Galtier and Lobry 1997;Lu et al 2006), and strong tertiary interactions can hold together intrinsically unstable helices (Stein and Crothers 1976a;Blose et al 2007). Thus, it is possible that secondary and tertiary structure could melt simultaneously leading to partial or full unfolding cooperativity.…”

Section: Discussionmentioning

confidence: 99%

Molecular crowders and cosolutes promote folding cooperativity of RNA under physiological ionic conditions

Strulson

Boyer

Whitman

et al. 2014

RNA

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Folding mechanisms of functional RNAs under idealized in vitro conditions of dilute solution and high ionic strength have been well studied. Comparatively little is known, however, about mechanisms for folding of RNA in vivo where Mg 2+ ion concentrations are low, K + concentrations are modest, and concentrations of macromolecular crowders and low-molecular-weight cosolutes are high. Herein, we apply a combination of biophysical and structure mapping techniques to tRNA to elucidate thermodynamic and functional principles that govern RNA folding under in vivo-like conditions. We show by thermal denaturation and SHAPE studies that tRNA folding cooperativity increases in physiologically low concentrations of Mg 2+ (0.5-2 mM) and K + (140 mM) if the solution is supplemented with physiological amounts (∼20%) of a water-soluble neutral macromolecular crowding agent such as PEG or dextran. Low-molecular-weight cosolutes show varying effects on tRNA folding cooperativity, increasing or decreasing it based on the identity of the cosolute. For those additives that increase folding cooperativity, the gain is manifested in sharpened two-state-like folding transitions for full-length tRNA over its secondary structural elements. Temperaturedependent SHAPE experiments in the absence and presence of crowders and cosolutes reveal extent of cooperative folding of tRNA on a nucleotide basis and are consistent with the melting studies. Mechanistically, crowding agents appear to promote cooperativity by stabilizing tertiary structure, while those low molecular cosolutes that promote cooperativity stabilize tertiary structure and/or destabilize secondary structure. Cooperative folding of functional RNA under physiological-like conditions parallels the behavior of many proteins and has implications for cellular RNA folding kinetics and evolution.

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“…The enthalpic contributions due to a group III bulge loops are not statistically different than the value obtained for group I or group II bulge loops (16.5 kcal/mol), so all of the enthalpic values for group I, II, and III bulge loops can be combined for an average value of 16.0 kcal/mol. The enthalpic values can be used in conjunction with the free energy parameters to determine the stability of RNA structures at temperatures other than 37°C (Lu et al 2006). …”

Section: Enthalpic Contributions Of Group III Single Nucleotide Bulgementioning

confidence: 99%

Non-nearest-neighbor dependence of stability for group III RNA single nucleotide bulge loops

Kent

McCann

Phillips

et al. 2014

RNA

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Thirty-five RNA duplexes containing single nucleotide bulge loops were optically melted and the thermodynamic parameters for each duplex determined. The bulge loops were of the group III variety, where the bulged nucleotide is either a AG/U or CU/G, leading to ambiguity to the exact position and identity of the bulge. All possible group III bulge loops with Watson-Crick nearestneighbors were examined. The data were used to develop a model to predict the free energy of an RNA duplex containing a group III single nucleotide bulge loop. The destabilization of the duplex by the group III bulge could be modeled so that the bulge nucleotide leads to the formation of the Watson-Crick base pair rather than the wobble base pair. The destabilization of an RNA duplex caused by the insertion of a group III bulge is primarily dependent upon non-nearest-neighbor interactions and was shown to be dependent upon the stability of second least stable stem of the duplex. In-line structure probing of group III bulge loops embedded in a hairpin indicated that the bulged nucleotide is the one positioned further from the hairpin loop irrespective of whether the resulting stem formed a Watson-Crick or wobble base pair. Fourteen RNA hairpins containing group III bulge loops, either 3 ′ or 5 ′ of the hairpin loop, were optically melted and the thermodynamic parameters determined. The model developed to predict the influence of group III bulge loops on the stability of duplex formation was extended to predict the influence of bulge loops on hairpin stability.

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A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation

Cited by 126 publications

References 81 publications

Non-nearest-neighbor dependence of the stability for RNA group II single-nucleotide bulge loops

Non-nearest-neighbor dependence of the stability for RNA group II single-nucleotide bulge loops

Molecular crowders and cosolutes promote folding cooperativity of RNA under physiological ionic conditions

Non-nearest-neighbor dependence of stability for group III RNA single nucleotide bulge loops

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