Influence of netropsin's charges on the minor groove width of d(CGCGAATTCGCG)2. (Q38364221)

2 September 2017

title

Influence of netropsin's charges on the minor groove width of d(CGCGAATTCGCG)2. (English)

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2 September 2017

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2 September 2017

Wellenzohn B

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2 September 2017

Flader W

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2 September 2017

Winger RH

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2 September 2017

Hallbrucker A

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2 September 2017

Mayer E

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2 September 2017

publication date

1 January 2001

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2 September 2017

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2 September 2017

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2 September 2017

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2 September 2017

page(s)

276-286

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Recognition of nine base pairs in the minor groove of DNA by a tripyrrole peptide-Hoechst conjugate

2 September 2017

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Thermodynamics of base pairing

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Genetic medicine--when will it come to the drugstore?

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Binding of distamycin A and netropsin to the 12mer DNA duplexes containing mixed AT.GC sequences with at most five or three successive AT base pairs

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Normal mode calculation of a netropsin-DNA complex: effect of structural deformation on vibrational spectrum.

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Differential stabilization by netropsin of inducible B-like conformations in deoxyribo-, ribo- and 2′-deoxy-2′-fluororibo-adenosine containing duplexes of (dA)n(dT)nand (dA)n(dU)n

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Molecular structure of the netropsin-d(CGCGATATCGCG) complex: DNA conformation in an alternating AT segment

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The molecular origin of DNA-drug specificity in netropsin and distamycin

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Interaction of minor groove ligands to an AAATT/AATTT site: correlation of thermodynamic characterization and solution structure

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Evaluation of the influence of compound structure on stacked-dimer formation in the DNA minor groove

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A novel end-to-end binding of two netropsins to the DNA decamers d(CCCCCIIIII)2, d(CCCBr5CCIIIII)2and d(CBr5CCCCIIIII)2

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Complex of B-DNA with polyamides freezes DNA backbone flexibility

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The effect of crystal packing on oligonucleotide double helix structure

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Crystal lattice packing is important in determining the bend of a DNA dodecamer containing an adenine tract

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Crystal structure analysis of a complete turn of B-DNA

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The B-DNA dodecamer at high resolution reveals a spine of water on sodium

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Structure of the potassium form of CGCGAATTCGCG: DNA deformation by electrostatic collapse around inorganic cations

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Atomic-resolution crystal structures of B-DNA reveal specific influences of divalent metal ions on conformation and packing

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The solution conformation of a carbocyclic analog of the Dickerson-Drew dodecamer: comparison with its own X-ray structure and that of the NMR structure of the native counterpart

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Sodium and chlorine ions as part of the DNA solvation shell

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Localization of ammonium ions in the minor groove of DNA duplexes in solution and the origin of DNA A-tract bending

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Molecular dynamics simulations of an oligonucleotide duplex with adenine tracts phased by a full helix turn.

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Detection of alkali metal ions in DNA crystals using state-of-the-art X-ray diffraction experiments

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Sequence-specific binding of counterions to B-DNA.

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Absence of minor groove monovalent cations in the crosslinked dodecamer C-G-C-G-A-A-T-T-C-G-C-G

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Structure of a B-DNA dodecamer: conformation and dynamics

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A new crystal form for the dodecamer C-G-C-G-A-A-T-T-C-G-C-G: symmetry effects on sequence-dependent DNA structure

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Modeling DNA structures: molecular mechanics and molecular dynamics

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Calculations of nucleic acid conformations

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Structure and energetics in the complexes of a double-stranded B-DNA dodecamer with netropsin derivatives of a tricationic water-soluble porphyrin: a theoretical investigation

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Effect of periodic box size on aqueous molecular dynamics simulation of a DNA dodecamer with particle-mesh Ewald method

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Observation of the A-DNA to B-DNA transition during unrestrained molecular dynamics in aqueous solution

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Conformational and helicoidal analysis of 30 PS of molecular dynamics on the d(CGCGAATTCGCG) double helix: "curves", dials and windows.

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Refinement of netropsin bound to DNA: bias and feedback in electron density map interpretation

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Crystal structure of the DNA decamer d(CGCAATTGCG) complexed with the minor groove binding drug netropsin

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Molecular structure of the A-tract DNA dodecamer d(CGCAAATTTGCG) complexed with the minor groove binding drug netropsin

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Induced fit DNA recognition by a minor groove binding analogue of Hoechst 33258: fluctuations in DNA A tract structure investigated by NMR and molecular dynamics simulations

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Coupling of local folding to site-specific binding of proteins to DNA

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A novel DNA recognition mode by the NF-κB p65 homodimer

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The Dickerson-Drew B-DNA Dodecamer Revisited at Atomic Resolution

21 January 2018

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A “Hydrat-Ion” Spine in a B-DNA Minor Groove

21 January 2018

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Influence of drug binding on DNA flexibility: a normal mode analysis

21 January 2018

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Selective binding of synthetic polypeptides to DNA of varying composition and sequence: effect of minor groove binding drugs

21 January 2018

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Sequence and structural selectivity of nucleic acid binding ligands

21 January 2018

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Structure of a B-DNA dodecamer. II. Influence of base sequence on helix structure

21 January 2018

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Structure of a B-DNA dodecamer. III. Geometry of hydration

21 January 2018

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Binding of Net-Fla, a netropsin-flavin hybrid molecule, to DNA: molecular mechanics and dynamics studies in vacuo and in water solution

21 January 2018

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Effect of warmup protocol and sampling time on convergence of molecular dynamics simulations of a DNA dodecamer using AMBER 4.1 and particle-mesh Ewald method

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A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat

21 January 2018

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21 January 2018

Identifiers

DOI

10.1002/BIP.10156

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2 September 2017

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