Calculation of folding energies of single-stranded nucleic acid sequences: conceptual issues.

Calculation of folding energies of single-stranded nucleic acid sequences: conceptual issues. Research Abstract Details 

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Calculation of folding energies of single-stranded nucleic acid sequences: conceptual issues. Abstract Text:

Donald R Forsdyke,

The stability of a folded single-stranded nucleic acid depends on the composition and order of its constituent bases and may be assessed by taking into account the pairing energies of its constituent dinucleotides. To assess the possible biological significance of a computed structure, Maizel and coworkers in the 1980s compared the energy of folding of a natural single-stranded RNA sequence with the energies of several versions of the same sequence produced by shuffling base order. However, in the 2000s many took as self-evident the view that shuffling at the mononucleotide level (single bases) was conceptual wrong and should be replaced by shuffling at the level of dinucleotides (retaining pairs of adjacent bases). Folding energies then became indistinguishable from those of corresponding shuffled sequences and doubt was cast on the importance of secondary structures. Nevertheless, some continued productively to employ the single base shuffling approach, the justification for which is the topic of this paper. Because dinucleotide pairing energies are needed to calculate structure, it does not follow that shuffling should not disrupt dinucleotides. Base shuffling allows determination of the relative contributions of base composition and base order to total folding energy. The potential for secondary structure arises from pressures acting at both DNA and RNA levels, and is abundant throughout genomes-with a probable primary role in recombination. Within a gene the potential can often be accommodated, and base order and composition work together (values have the same negative sign) in contributing to total folding energy. But sometimes protein-coding pressure on base order conflicts with the pressure for secondary structure and the values have opposite signs. Total folding energy can be deemed of potential biological significance when the average of several readings is significantly less than zero.

Calculation of folding energies of single-stranded nucleic acid sequences: conceptual issues. Publishing Authors By Initials

DR Forsdyke,

For similar nucleic acids, nucleotides, and nucleosides: nucleic acids: rna research abstracts see: nucleic acids, nucleotides, and nucleosides: nucleic acids: rna research

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Calculation of folding energies of single-stranded nucleic acid sequences: conceptual issues. Journal Published:

PUBLICATION TYPE: Review

Journal: Journal of theoretical biology

VOLUME: 248

Page Numbers: 745-53

Journal Abbreviation: J. Theor. Biol.

ISSN: 0022-5193

DAY: 18

MONTH: 07

YEAR: 2007

Calculation of folding energies of single-stranded nucleic acid sequences: conceptual issues. Information

Number of References: 66

LANGUAGE: eng

NlmUniqueID: 376342

Calculation of folding energies of single-stranded nucleic acid sequences: conceptual issues. Keywords Mesh Terms:

KEYWORDS: RNA

MESH TERMS: genetics

Chemical & Substance for Abstract: Calculation of folding energies of single-stranded nucleic acid sequences: conceptual issues. Information

Substance Name: RNA

Registry Number: 63231-63-0

Grant and Affiliation Information for Calculation of folding energies of single-stranded nucleic acid sequences: conceptual issues.

AFFILIATION: Department of Biochemistry, Queen's University, Kingston, Ontario, Canada K7L3N6. forsdyke@queensu.ca

Country: Netherlands

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MEDLINETA: J Theor Biol

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