ArticleBiophysical journal2001
Conformational analysis of DNA-trinucleotide-hairpin-loop structures using a continuum solvent model.
Article in Biophysical journal, 2001. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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14 citing papers in PubMed.
- Structure and target interaction of a G-quadruplex RNA-aptamer.RNA biology · 2016Article
- RAID3--An interleukin-6 receptor-binding aptamer with post-selective modification-resistant affinity.RNA biology · 2015Article
- Role of the closing base pair for d(GCA) hairpin stability: free energy analysis and folding simulations.Nucleic acids research · 2011Article
- Maturation of the 5S rRNA 5' end is catalyzed in vitro by the endonuclease tRNase Z in the archaeon H. volcanii.RNA (New York, N.Y.) · 2008Article
- Magnitude and direction of DNA bending induced by screw-axis orientation: influence of sequence, mismatches and abasic sites.Nucleic acids research · 2008Article
- Folding of a DNA hairpin loop structure in explicit solvent using replica-exchange molecular dynamics simulations.Biophysical journal · 2007Article
- Closing loop base pairs in RNA loop-loop complexes: structural behavior, interaction energy and solvation analysis through molecular dynamics simulations.Journal of molecular modeling · 2004Article
- Influence of a fluorobenzene nucleobase analogue on the conformational flexibility of RNA studied by molecular dynamics simulations.Nucleic acids research · 2004Article
- Simulation of the folding equilibrium of alpha-helical peptides: a comparison of the generalized Born approximation with explicit solvent.Proceedings of the National Academy of Sciences of the United States of America · 2003Article
- Insights into nucleic acid conformational dynamics from massively parallel stochastic simulations.Biophysical journal · 2003Article
- Sequence context dependence of tandem guanine:adenine mismatch conformations in RNA: a continuum solvent analysis.Biophysical journal · 2003Article
- DNA tri- and tetra-loops and RNA tetra-loops hairpins fold as elastic biopolymer chains in agreement with PDB coordinates.Nucleic acids research · 2003Article
- Biopolymer Chain Elasticity: A novel concept and a least deformation energy principle predicts backbone and overall folding of DNA TTT hairpins in agreement with NMR distances.Nucleic acids research · 2003Article
- Modelling ion binding to AA platform motifs in RNA: a continuum solvent study including conformational adaptation.Nucleic acids research · 2001Article
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1 author.
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Abstract
A number of trinucleotide sequences in DNA can form compact and stable hairpin loops that may have significance for DNA replication and transcription. The conformational analysis of these motifs is important for an understanding of the function and design of nucleic acid structures. Extensive conformational searches have been performed on three experimentally known trinucleotide hairpin loops (AGC, AAA, and GCA) closed by a four-base-pair stem. An implicit solvation model based on the generalized Born method has been employed during energy minimization and conformational search. In addition, energy-minimized conformers were evaluated using a finite-difference Poisson-Boltzmann approach. For all three loop sequences, conformations close to experiment were found as lowest-energy structures among several thousand alternative energy minima. The inclusion of reaction-field contributions was found to be important for a realistic conformer ranking. Most generated hairpin loop structures within approximately 5 kcal x mol(-1) of the lowest-energy structure have a similar topology. Structures within approximately 10 kcal x mol(-1) could be classified into about five structural families representing distinct arrangements of loop nucleotides. Although a large number of backbone torsion angle combinations were compatible with each structural class, some specific patterns could be identified. Harmonic mode analysis was used to account for differences in conformational flexibility of low-energy sub-states. Class-specific differences in the pattern of atomic fluctuations along the sequence were observed; however, inclusion of conformational entropy contributions did not change ranking of structural classes. For an additional loop sequence (AAG) with no available experimental structure, the approach suggests a lowest-energy loop topology overall similar to the other three loop sequences but closed by a different non-canonical base-pairing scheme.
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