Heats of the helix–coil transitions of the poly A–poly U complexes

Krakauer, Henry; Sturtevant, Julian M.

doi:10.1002/bip.1968.360060406

Cited by 240 publications

(155 citation statements)

References 21 publications

Supporting

Mentioning

128

Contrasting

Unclassified

Order By: Relevance

“…Our above fitted parameter Dh = 7 kcal/mol is also close to the previous experimental result Dh = 5 kcal/mol for a U d (A-U) base triple (Krakauer and Sturtevant 1968). The 2.0 kcal/mol À1 theory-experiment discrepancy (Dh = 7 kcal/mol versus 5 kcal/mol) is probably caused by the simplifying assumption that distinct nonprotonated base triples irrespective of structure are forced to be characterized by the same thermodynamic parameters.…”

Section: Energetic Parameters For Base Triplessupporting

confidence: 86%

See 1 more Smart Citation

Predicting loop–helix tertiary structural contacts in RNA pseudoknots

Cao¹,

Giedroc²,

Chen³

2010

RNA

View full text Add to dashboard Cite

Tertiary interactions between loops and helical stems play critical roles in the biological function of many RNA pseudoknots. However, quantitative predictions for RNA tertiary interactions remain elusive. Here we report a statistical mechanical model for the prediction of noncanonical loop-stem base-pairing interactions in RNA pseudoknots. Central to the model is the evaluation of the conformational entropy for the pseudoknotted folds with defined loop-stem tertiary structural contacts. We develop an RNA virtual bond-based conformational model (Vfold model), which permits a rigorous computation of the conformational entropy for a given fold that contains loop-stem tertiary contacts. With the entropy parameters predicted from the Vfold model and the energy parameters for the tertiary contacts as inserted parameters, we can then predict the RNA folding thermodynamics, from which we can extract the tertiary contact thermodynamic parameters from theory-experimental comparisons. These comparisons reveal a contact enthalpy (DH) of À14 kcal/mol and a contact entropy (DS) of À38 cal/mol/K for a protonated C + d (G-C) base triple at pH 7.0, and (DH = À7 kcal/mol, DS = À19 cal/mol/K) for an unprotonated base triple. Tests of the model for a series of pseudoknots show good theory-experiment agreement. Based on the extracted energy parameters for the tertiary structural contacts, the model enables predictions for the structure, stability, and folding pathways for RNA pseudoknots with known or postulated loop-stem tertiary contacts from the nucleotide sequence alone.

show abstract

Section: Energetic Parameters For Base Triplessupporting

confidence: 86%

“…In order to account for such looploop contact, we simply assign an interaction energy for a conventional Watson-Crick U7-A37 base pair. Using a Dh of À8 kcal/mol (Krakauer and Sturtevant 1968), the fitted Ds from the experimental melting curve (Fig. 4D) is À16 cal/mol/K.…”

Section: Energetic Parameters For Base Triplesmentioning

confidence: 99%

Predicting loop–helix tertiary structural contacts in RNA pseudoknots

Cao¹,

Giedroc²,

Chen³

2010

RNA

View full text Add to dashboard Cite

show abstract

“…For the cylindrical models of ss-, ds-, and tsRNA, Preferential interaction coefficients are the fundamental determinant of the effect of salt concentration on the thermodynamics of nucleic acid processes. We discuss experimental studies of RNA conformational transitions (23) as an example of application of Eq. 10 to thermodynamic calculations, because these reactions involve a wide range of RNA axial charge densities ( Х 2 Ϫ 6.5, b Х 1 Ϫ 3.2 Å) and radii (a ϭ 7.5 Ϫ 13 Å) and independently measured enthalpies of the transitions.…”

Section: Range Of Applicability Of Low [Salt] Expression For ⌫ Umentioning

confidence: 99%

“…The experimental values of ⌬⌫ u (27) are shown in the experimental range of salt concentration, 0.01-0.1 M, with the error of 15%. These error estimates assume average errors of 10% in ⌬H 0 (23) and in dT m ͞d log C b .…”

Section: Range Of Applicability Of Low [Salt] Expression For ⌫ Umentioning

confidence: 99%

Asymptotic solution of the cylindrical nonlinear Poisson–Boltzmann equation at low salt concentration: Analytic expressions for surface potential and preferential interaction coefficient

Shkel

Tsodikov

Record

2002

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

The analytic solution to the nonlinear Poisson-Boltzmann equation describing the ion distributions surrounding a nucleic acid or other cylindrical polyions as a function of polyion structural quantities and salt concentration ([salt]) has been sought for more than 80 years to predict the effect of these quantities on the thermodynamics of polyion processes. Here we report an accurate asymptotic solution of the cylindrical nonlinear Poisson-Boltzmann equation at low to moderate concentration of a symmetrical electrolyte (<0.1 M 1:1 salt). The approximate solution for the potential is derived as an asymptotic series in the small parameter ؊1 , where ϵ ؊1 ͞a, the ratio of the Debye length ( ؊1 ) to the polyion radius (a). From the potential at the polyion surface, we obtain the coulombic contribution to the salt-polyelectrolyte preferential interaction (Donnan) coefficient (⌫ u coul ) per polyion charge at any reduced axial charge density . ⌫ u coul is the sum of the previously recognized low-salt limiting value and a salt-dependent contribution, analytically derived here in the range of low-salt concentra- T he cylindrical nonlinear Poisson-Boltzmann (NLPB or PB) equation is widely used for calculating electrostatic potential around rod-like charged objects surrounded by mobile ions both in the theory of polyelectrolyte solutions (1, 2), in applications in plasma physics (3) and in colloid and surface sciences (4). In particular, the surface coulombic potential (and͞or its distance dependence) of a charged polyion in an electrolyte solution is required for calculations of such thermodynamic properties as electrostatic free energy (5, 6), polyion-ligand binding constant (7,8), and especially the fundamental thermodynamic quantity ⌫ u coul , the coulombic contribution to the preferential interaction coefficient (equivalent to the experimentally observable Donnan coefficient). This coefficient is required for interpretation of thermodynamic experiments on salt-polyion interactions and on effects of salt concentration ([salt], C b ) on polyion processes (1, 9). Numerical calculations of NLPB solution for the model of a long periodically charged polyion as an infinite charged cylinder characterized by only two structural quantities, reduced charge density § and radius a, are known to successfully describe experimentally measured thermodynamic properties of polyelectrolyte solutions (1). Monte Carlo simulations confirm the accuracy of the cylindrical PB equation in the presence of added univalent salt up to 0.1 M (10, 11). However, despite numerous studies devoted to solving the NLPB equation (2, 3), no sufficiently accurate analytic solution for the cylindrical NLPB equation was known at low-to moderate-salt concentration.Solution of cylindrical NLPB equation is more challenging at low-salt (LS) concentration than at high [salt], where several useful accurate approximations for the potential, electrostatic free energy and preferential interaction coefficient are known (4,(12)(13)(14). In the absence of added salt, the ...

show abstract

“…Triple helix formation In the triple-stranded structures proposed we have considered interactions known to be major determinants in the maintenance of tertiary structure in synthetic polyribonucleotides (26)(27)(28)(29)(30)(31)(32)(33) (29,31).…”

Section: Processing Mechanismsmentioning

confidence: 99%

Could poly(A) align the splicing sites of messenger RNA precursors?

Bina¹,

Feldmann²,

Deeley³

1980

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

In general, poly(A)mRNA appears to be derived from larger nuclear RNA precursors. The maturation of these precursors involves excision of sequences of variable length from within the molecule and splicing of the remaining structural and coding sequences. The mechanism by which this process occurs is not known. It does not appear to operate solely through the recognition of a defined primary sequence or through the formation of a consistent secondary structure. We propose an alternative model in which poly(A) facilitates the splicing event by promoting the formation of triple-stranded structures within the mRNA precursor.The structural genes of eukaryotes and viruses that specify polyadenylated § mRNA species are interrupted by nucleotide sequences not represented in the mature mRNA transcripts. Such sequences have been termed "intervening sequences" or "introns" (for review see refs. 1-3). The primary products of such transcription units are large mRNA precursors that include intervening sequences (4, 5). Present evidence indicates that, after the addition of a poly(A) tract to its 3' end, the mRNA precursor is processed within the nucleus or during transport to the cytoplasm to produce a mature mRNA molecule (5-8). Processing is accomplished by the successive excision of introns and splicing of conserved sequences. The only examples of eukaryotic mRNAs that are known not to follow such a processing pathway are those specifying histones. Those histone genes that have been examined do not contain intervening sequences (9), and histone mRNAs are predominantly not polyadenylated (10)(11)(12) The conservation of sequences spanning the splicing sites in RNA species from evolutionarily distant organisms points both to a common general mechanism for processing of polyadenylated RNA and to the possibility that, in a given organism, processing may be catalyzed by a single enzyme or enzyme complex. At the moment, a mechanism that allows the accurate removal of intervening sequences from a mRNA precursor and the precise ligation of the remaining structural sequences is unknown. It seems likely that if the order of structural sequences is to be conserved, the ends of an intervening sequence must be brought close to each other prior to endonucleolytic cleavage, so that ligation can take place without physical separation of the 3' and 5' ends of the structural sequences that are to be spliced. However, intervening sequences are variable in length and, with the exception of the border regions already mentioned, possess no marked homologies or symmetries of sequence. Attempts to draw the ends of an intervening sequence together by maximizing Watson-Crick base pairing do not generate structures in which donor and acceptor sites exhibit a reasonably constant configuration. A splicing mechanism based solely on the maintenance of a fixed secondary structure also seems unlikely for other reasons. For example, it has been shown that intervening sequences are free to change much more rapidly than structural sequences (16)(17)(...

show abstract

Heats of the helix–coil transitions of the poly A–poly U complexes

Cited by 240 publications

References 21 publications

Predicting loop–helix tertiary structural contacts in RNA pseudoknots

Predicting loop–helix tertiary structural contacts in RNA pseudoknots

Asymptotic solution of the cylindrical nonlinear Poisson–Boltzmann equation at low salt concentration: Analytic expressions for surface potential and preferential interaction coefficient

Could poly(A) align the splicing sites of messenger RNA precursors?

Contact Info

Product

Resources

About