Principles of Nucleic Acid Structure

Saenger, Wolfram

doi:10.1007/978-1-4612-5190-3

Cited by 5,936 publications

(6,658 citation statements)

References 892 publications

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“…This is consistent with previous findings that the ribose in A-form RNA prefers the C3′-endo form but that outside regular helices, RNA riboses adopt C2′-endo conformations. 63,74 With respect to the average populated puckering mode, MD and REMD simulations show in general similar results for the stem and loop regions (Supporting Information, Table S1). However, compared to the MD simulation, more C2′-endo conformations are sampled in the bulge region during the REMD simulation, which may be due to better sampling by the latter approach.…”

Section: Resultssupporting

confidence: 54%

“…The 63 Corresponding plots for TAR-Arg, TAR-AcP, and TAR-NeoB structures are given in the Supporting Information ( Figures S2-S4).…”

Section: Resultsmentioning

confidence: 99%

“…Ranges of average backbone torsion angles of canonical A-form RNA structures (black lines) and syn and anti ranges of the glycosidic bond are indicated. 63 Essential Dynamics of Unbound and Bound TAR RNA Structures. Unbound TAR RNA can transiently sample distinct bound conformations according to experimental evidence.…”

Section: Resultsmentioning

confidence: 99%

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HIV-1 TAR RNA Spontaneously Undergoes Relevant Apo-to-Holo Conformational Transitions in Molecular Dynamics and Constrained Geometrical Simulations

Fulle

Christ

Kestner

et al. 2010

J. Chem. Inf. Model.

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We report all-atom molecular dynamics and replica exchange molecular dynamics simulations on the unbound human immunodeficiency virus type-1 (HIV-1) transactivation responsive region (TAR) RNA structure and three TAR RNA structures in bound conformations of, in total, ∼250 ns length. We compare the extent of observed conformational sampling with that of the conceptually simpler and computationally much cheaper constrained geometrical simulation approach framework rigidity optimized dynamic algorithm (FRODA). Atomic fluctuations obtained by replica-exchange molecular dynamics (REMD) simulations agree quantitatively with those obtained by molecular dynamics (MD) and FRODA simulations for the unbound TAR structure. Regarding the stereochemical quality of the generated conformations, backbone torsion angles and puckering modes of the sugar-phosphate backbone were reproduced equally well by MD and REMD simulations, but further improvement is needed in the case of FRODA simulations. Essential dynamics analysis reveals that all three simulation approaches show a tendency to sample bound conformations when starting from the unbound TAR structure, with MD and REMD simulations being superior with respect to FRODA. These results are consistent with the experimental view that bound TAR RNA conformations are transiently sampled in the free ensemble, following a conformation selection model. The simulation-generated TAR RNA conformations have been successfully used as receptor structures for docking. This finding has important implications for RNA-ligand docking in that docking into an ensemble of simulation-generated RNA structures is shown to be a valuable means to cope with large apo-to-holo conformational transitions of the receptor structure.

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Section: Resultssupporting

confidence: 54%

“…The 63 Corresponding plots for TAR-Arg, TAR-AcP, and TAR-NeoB structures are given in the Supporting Information ( Figures S2-S4).…”

Section: Resultsmentioning

confidence: 99%

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HIV-1 TAR RNA Spontaneously Undergoes Relevant Apo-to-Holo Conformational Transitions in Molecular Dynamics and Constrained Geometrical Simulations

Fulle

Christ

Kestner

et al. 2010

J. Chem. Inf. Model.

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“…Hydrogen bonding modulates recognition of DNA and RNA bases, and the interaction energy between two bonded complementary nucleobases is dependent on the intrinsic basicity of the acceptor atoms as well as on the acidity of donor NH groups [1,2]. In addition, understanding the intrinsic reactivity of nucleic bases can shed light on key biosynthetic mechanisms in which nucleobases are substrates [3][4][5][6][7][8].…”

mentioning

confidence: 99%

The acidity of uracil and uracil analogs in the gas phase: Four surprisingly acidic sites and biological implications

Kurinovich

Lee

2002

J. Am. Soc. Mass Spectrom.

160

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The gas phase acidities of a series of uracil derivatives (1-methyluracil, 3-methyluracil, 6-methyluracil, 5,6-dimethyluracil, and 1,3-dimethyluracil) have been bracketed to provide an understanding of the intrinsic reactivity of uracil. The experiments indicate that in the gas phase, uracil has four sites more acidic than water. Among the uracil analogs, the N1-H sites have ⌬H acid values of 331-333 kcal mol Ϫ1 ; the acidity of the N3 sites fall between 347-352 kcal mol Ϫ1 . The vinylic C6 in 1-methyluracil and 3-methyluracil brackets to 363 kcal mol Ϫ1 , and 369 kcal mol Ϫ1 in 1,3-dimethyluracil; the C5 of 1,3-dimethyluracil brackets to 384 kcal mol Ϫ1 . Calculations conducted at B3LYP/6-31ϩG* are in agreement with the experimental values. The bracketing of several of these sites involved utilization of an FTMS protocol to measure the less acidic site in a molecule that has more than one acidic site, establishing the generality of this method. In molecules with multiple acidic sites, only the two most acidic sites were bracketable, which is attributable to a kinetic effect. The measured acidities are in direct contrast to in solution, where the two most acidic sites of uracil (N1 and N3) are indifferentiable. The vinylic C6 site is also particularly acidic, compared to acrolein and pyridine. The biological implications of these results, particularly with respect to enzymes for which uracil is a substrate, are discussed. (J Am Soc Mass Spectrom 2002, 13, 985-995)

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“…There have been a number of different compilations of base pair types since the solution of early crystal structures revealed modes of interaction other than canonical Watson-Crick hydrogen bonding. These have been classifications based on base type [35][36] or by geometry [37][38]. Our method of representation is totally independent of how one classifies a structure as it directly compares the positions of atoms relative to one another.…”

Section: Validation Of the Methods: Planar Base-base Interactionsmentioning

confidence: 99%

Representation, searching and discovery of patterns of bases in complex RNA structures

Harrison

South

Willett

et al. 2003

Journal of Computer-Aided Molecular Design

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SummaryWe describe a graph theoretic method designed to perform efficient searches for substructural patterns in nucleic acid structural coordinate databases using a simplified vectorial representation. Two vectors represent each nucleic acid base and the relative positions of bases with respect to one another are described in terms of distances between the defined start and end points of the vectors on each base. These points comprise the nodes and the distances the edges of a graph, and a pattern search can then be performed using a subgraph isomorphism algorithm.The minimal representation was designed to facilitate searches for complex patterns but was first tested on simple, well-characterised arrangements of bases such as base pairs and GNRA-tetraloop receptor interactions. The method performed very well for these interaction types. A survey of side-by-side base interactions, of which the adenosine platform is the best known example also locates examples of similar base rearrangements that we consider to be 2 important in structural regulation. A number of examples were found, with GU platforms being particularly prevalent. A GC platform in the RNA of the Thermus thermophilus small ribosomal subunit is in an analogous position to an adenosine platform in other species. An unusual GG platform is also observed close to one of the substrate binding sites in Haloarcula marismortui large ribosomal subunit RNA.Abbreviations PDB Protein Databank 3D three-dimensional GNRA Guanine, N = any base, R = pyrimidine base, Adenine 3

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Principles of Nucleic Acid Structure

Cited by 5,936 publications

References 892 publications

HIV-1 TAR RNA Spontaneously Undergoes Relevant Apo-to-Holo Conformational Transitions in Molecular Dynamics and Constrained Geometrical Simulations

HIV-1 TAR RNA Spontaneously Undergoes Relevant Apo-to-Holo Conformational Transitions in Molecular Dynamics and Constrained Geometrical Simulations

The acidity of uracil and uracil analogs in the gas phase: Four surprisingly acidic sites and biological implications

Representation, searching and discovery of patterns of bases in complex RNA structures

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