A QM/MM refinement of an experimental DNA structure with metal-mediated base pairs.
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Summary
This investigation shows that the application of QM/MM models to generate additional constraints to be used during NMR structural refinements represents an elegant approach to obtaining high-resolution NMR structures.
- Type
- dissertation
- Published
- 2013-10-01
- Cited by
- 62
- References
- 60
- Access
- Open access
- OpenAlex
- https://openalex.org/W23622950
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:42918535
Keywords
Humanities, Political science, Philosophy
References
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- Metal‐Ion‐Mediated Base Pairs in Nucleic Acids (Eur. J. Inorg. Chem. 24/2008)
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- Direct conductance measurement of individual metallo-DNA duplexes within single-molecule break junctions.
- Comparison of simple potential functions for simulating liquid water
- 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures.
- A comparison of metallophilic interactions in group 11[X–M–PH3]n (n = 2–3) complex halides (M = Cu, Ag, Au; X = Cl, Br, I) from density functional theory
- The structure of B-DNA in oriented fibers.
- Spectrophotometric, potentiometric, and density gradient ultracentrifugation studies of the binding of silver ion by DNA
- Reversible bond formation enables the replication and amplification of a crosslinking salen complex as an orthogonal base pair.
- Mechanism of the Reaction of Polynucleotides and HgII
- Assessment of Weak Intermolecular Interactions Across QM/MM Noncovalent Boundaries
- A NEW ONIOM IMPLEMENTATION IN GAUSSIAN98. PART I. THE CALCULATION OF ENERGIES, GRADIENTS, VIBRATIONAL FREQUENCIES AND ELECTRIC FIELD DERIVATIVES
- Metal-mediated aggregation of DNA comprising 2,2'-bipyridine nucleoside, an asymmetrically substituted chiral bidentate ligand.
- MOLMOL: a program for display and analysis of macromolecular structures.
- Quantum Mechanics/Molecular Mechanics Strategies for Docking Pose Refinement: Distinguishing between Binders and Decoys in Cytochrome c Peroxidase
- A Discrete Self-Assembled Metal Array in Artificial DNA
- Revised Basis Sets for the LANL Effective Core Potentials.
- Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density.
- 2,6-Bis(functionalized) purines as metal-ion-binding surrogate nucleobases that enhance hybridization with unmodified 2'-O-methyl oligoribonucleotides.
Cited by
- 4-(2′-Pyridyl)imidazole as an artificial nucleobase in highly stabilizing Ag(I)-mediated base pairs
- A theoretical study of the interaction between DNA/RNA and the noble metal atoms of gold and silver - Ground-state properties
- Metal complexes of 6-pyrazolylpurine derivatives as models for metal-mediated base pairs.
- A Metal-Mediated Base Pair with a [2+1] Coordination Environment
- Mononuclear 1,3-Dideazaadenine-AgI-Thyminate Base Pairs† ‡
- Structures, physicochemical properties, and applications of T-Hg(II)-T, C-Ag(I)-C, and other metallo-base-pairs.
- DFT study and topological analysis of the bonding in DNA Hoogsteen-type base pairs
- Ein hochgradig stabilisierendes Silber(I)‐vermitteltes Basenpaar in paralleler DNA
- A tridentate "click" nucleoside for metal-mediated base pairing.
- Crystal structure of metallo DNA duplex containing consecutive Watson-Crick-like T-Hg(II)-T base pairs.
- Second generation silver(I)-mediated imidazole base pairs
- The structure of metallo-DNA with consecutive thymine–HgII–thymine base pairs explains positive entropy for the metallo base pair formation
- A highly stabilizing silver(I)-mediated base pair in parallel-stranded DNA.
- A density-based adaptive quantum mechanical/molecular mechanical method.
- High-Resolution Crystal Structure of a Silver(I)-RNA Hybrid Duplex Containing Watson-Crick-like C-Silver(I)-C Metallo-Base Pairs.
- A family of "click" nucleosides for metal-mediated base pairing: unravelling the principles of highly stabilizing metal-mediated base pairs.
- Direct detection of the mercury-nitrogen bond in the thymine-Hg(II)-thymine base-pair with (199)Hg NMR spectroscopy.
- Unprecedented dinuclear silver(I)-mediated base pair involving the DNA lesion 1,N(6)-ethenoadenine.
- Sequence-Dependent Duplex Stabilization upon Formation of a Metal-Mediated Base Pair.
- Formation of Silver Nanoclusters from a DNA Template Containing Ag(I)-Mediated Base Pairs
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