PubMed HealthSearch

PubMed · 6198621

An RNA folding rule.

Abstract

The folding of single-stranded RNA into its secondary structure is postulated to be equivalent to the simple rule that the next double-helical region (stem) to form is the one with the largest equilibrium constant. The rule is tested and shown to give results consistent with the enzyme cleavage data of several sequences. Computational time complexity is of order NxN for a sequence of N bases. A modification of the rule provides for the probabilistic choice of the next stem among those having an equilibrium constant within a specified range of the largest. Populations of competing structures are thus generated for detecting common characteristics and for assessing the applicability of the simple rule.

Explore related subjects

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

H M Martinez. 1984-01-11. An RNA folding rule.. https://doi.org/10.1093/nar%2F12.1part1.323

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related citations

Correlation between multiple hydrogen bonding and alteration of the oxidation potential of the bacteriochlorophyll dimer of reaction centers from Rhodobacter sphaeroides.

The electronic absorption and vibrational Raman spectra of mutant reaction centers from Rhodobacter sphaeroides bearing multiple site-specific mutations near the primary electron donor (P), a bacteriochlorophyll dimer, are reported. These mutations bear double and triple combinations of single-point mutations that alter the H-bonding interactions between histidine residues and the C2- and C9-conjugated carbonyl groups of the primary donor [Mattioli, T.A., Williams, J.C., Allen, J.P., & Robert, B. (1994) Biochemistry 33, 1636-1643] and change the donor redox midpoint potential from 410 to 765 mV compared to 505 mV for wild type [Lin, X., Murchison, H.A., Nagarajan, V., Parson, W.W., Williams, J.C., & Allen, J.P. (1994) Proc. Natl. Acad. Sci. U.S.A. 91, 10265-10269]. Near-infrared Fourier transform Raman spectroscopy was used to determine the changes in H-bonding interactions of the primary donor in these multiple mutants. The Fourier transform Raman spectra of the mutants exhibit the predicted changes in hydrogen bond interactions of the P carbonyl groups with the protein, and they are consistent with the designed mutations. Moreover, the Raman data verify that the H-bonds formed or broken in the multiple mutants are similar in strength to those observed in the corresponding single mutants. A correlation was observed between the change in P/P.+ redox midpoint potential and the total change in H-bonding interaction energy (from -207 to 364 meV relative to wild type) as gauged by the estimated enthalpy of each H-bond formed or broken on the four conjugated carbonyls of the primary donor. Only minor changes were observed in the optical spectra of the mutant reaction centers, indicating that the addition of H-bonds from histidines has little effect in destabilizing the first electronic excited state of the dimer relative to the ground state. However a blue shift in the dimer absorption band at ca. 890 nm at 20 K was associated with the removal of the H-bond to the C2 acetyl carbonyl group via His L168. A red shift of the oxidized dimer band at ca. 1250 nm was associated with the formation of each H-bond to the C9 keto carbonyl groups.

Hydrogen Bonding

The helix-coil transition in polypeptides: a microscopic approach. II.

In the framework of an earlier constructed model [N.S. Ananikyan et al. (1990) Biopolymers, Vol. 30, pp. 357-367], some analytical estimates for the correlation length and degree of helicity near the transition point were obtained in the case of an arbitrary topology of hydrogen bond closing (delta). It was shown that the Zimm-Bragg cooperativity parameter sigma is determined by the set of (delta-1) amino acid residues and so is nonlocal. An analytic expression for cooperativity parameters in a heteropolypeptide chain was obtained and numerical calculations showed that in case of heteropolypeptide with random primary structure the nonlocality of cooperativity parameter influenced the temperature dependence of helicity degree.

Hydrogen Bonding