DNA Polymorphism: A Comparison of Force Fields for Nucleic Acids

Reddy, Swarnalatha Y.; Leclerc, Fabrice; Karplus, Martin

doi:10.1016/s0006-3495(03)74957-1

Cited by 78 publications

(70 citation statements)

References 71 publications

(103 reference statements)

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“…50,54,58 The overall distribution of water and cations in the (AATT) 2 and in the AT/AT fragments is similar to that reported on the basis of considerably shorter simulations in another paper, 59 also using the CHARMM27 force field. The binding of the charged amino group in the region of high electronegative density is also similar to the results we have obtained in studies of polyamine-DNA interactions.…”

supporting

confidence: 83%

H4 histone tail mediated DNA–DNA interaction and effects on DNA structure, flexibility, and counterion binding. A molecular dynamics study

Korolev

Nordenskiöld

2007

Biopolymers

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All-atom molecular dynamics (MD) simulations were performed during 30-45 ns for a system of three identical DNA 22-mers, 14 short fragments of the charged H4 histone tail peptide fragment (amino acids 5-12, KGGKGLGK) with K(+) counterions, and explicit water. The simulation setup mimics the crowded conditions of DNA in eukaryotic chromatin. To assess the influence of tail fragments on DNA structure and dynamics, a "control" 20 ns MD simulation was carried for a system with the same DNA and water content but in the absence of oligopeptides. Results of DNA interaction with the histone tail fragments, K(+), and water is presented. DNA structure and dynamics and its interplay with the histone tail fragments binding are described. The charged side chains of the lysines play a major role in mediating DNA-DNA attraction by forming bridges and coordinating to phosphate groups and electronegative sites in the minor groove. Binding of all species to DNA is dynamic. Some of the tail fragments while being flexible and mobile in each of its functional groups remain associated near certain locations of the DNA oligomer. The present work allows capturing typical features of the histone tail-counterion-DNA structure, interaction, and dynamics.

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supporting

confidence: 83%

H4 histone tail mediated DNA–DNA interaction and effects on DNA structure, flexibility, and counterion binding. A molecular dynamics study

Korolev

Nordenskiöld

2007

Biopolymers

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“…This contains two main variants for modelling DNA: the older CHARMM22 force field, [26] and a more refined CHARMM27. [27] There have been a number of comparisons of how well these two force fields reproduce the behaviour of DNA, [28] and the general consensus is that the CHARMM27 force field is much better. In particular, it correctly predicts B-DNA to be the stable conformation in low ionic strength solvents at normal temperatures, whereas the CHARMM22 force field tends to cause the DNA to adopt an A-like form.…”

Section: Methodsmentioning

confidence: 99%

“…Equilibration followed a similar protocol to that used by other research groups. [23,28,37] The DNA atoms were tethered to their original positions with a harmonic force constant of 100 kcal mol À1 À2 and an NVT MD simulation performed for 10 ps at 310 K. A further five 10 ps simulations were then performed successively in which the tethering force constant was 50, 25, 10, 5 and 1 kcal mol À1…”

Section: Docking (Steps 1 and 2)mentioning

confidence: 99%

Simulations of DNA Coiling around a Synthetic Supramolecular Cylinder That Binds in the DNA Major Groove

Khalid

Hannon

Rodger

et al. 2006

Chemistry A European J

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In this work we present the results of a molecular simulation study of the interaction between a tetracationic bis iron(II) supramolecular cylinder, [Fe2(C25H20N4)3]4+, and DNA. This supramolecular cylinder has been shown to bind in the major groove of DNA and to induce dramatic coiling of the DNA. The simulations have been designed to elucidate the interactions that lead the cylinder to target the major groove and that drive the subsequent DNA conformational changes. Three sets of multi-nanosecond simulations have been performed: one of the uncomplexed d(CCCCCTTTTTCC) d(GGAAAAAGGGGG) dodecamer; one of this DNA complexed with the cylinder molecule; and one of this DNA complexed with a neutralised version of the cylinder. Coiling of the DNA was observed in the DNA-cylinder simulations, giving insight into the molecular level nature of the supramolecular coiling observed experimentally. The cylinder charge was found not to be essential for the DNA coiling, which implies that the DNA response is moderated by the short range interactions that define the molecular shape. Cylinder charge did, however, affect the integrity of the DNA duplex, to the extent that, under some circumstances, the tetracationic cylinder induced defects in the DNA base pairing at locations adjacent to the cylinder binding site.

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“…DNA is a structurally polymorphic molecule that can adopt a variety of conformations, which show significant deviation from canonical right-handed DNA (B-DNA) depending on the nucleotide sequence and environmental conditions. 3,[16][17][18][19][20][21][22] The main family of DNA forms identified based on crystallographic analysis of deoxyoligonucleotides are the right-handed A-and B-forms, 16 and the left-handed Z-form. 17,18 A schematic representation of the A-, B-, and Z-form structures of DNA is given in Figure 2.…”

Section: S T R U C T U R a L A N D F U N C T I O N A L A S P E C T mentioning

confidence: 99%

Molecular aspects on the interaction of protoberberine, benzophenanthridine, and aristolochia group of alkaloids with nucleic acid structures and biological perspectives

Maiti

Kumar

2006

Medicinal Research Reviews

161

103

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Alkaloids occupy an important position in chemistry and pharmacology. Among the various alkaloids, berberine and coralyne of the protoberberine group, sanguinarine of the benzophenanthridine group, and aristololactam-beta-d-glucoside of the aristolochia group have potential to form molecular complexes with nucleic acid structures and have attracted recent attention for their prospective clinical and pharmacological utility. This review highlights (i) the physicochemical properties of these alkaloids under various environmental conditions, (ii) the structure and functional aspects of various forms of deoxyribonucleic acid (DNA) (B-form, Z-form, H(L)-form, protonated form, and triple helical form) and ribonucleic acid (RNA) (A-form, protonated form, and triple helical form), and (iii) the interaction of these alkaloids with various polymorphic DNA and RNA structures reported by several research groups employing various analytical techniques like absorbance, fluorescence, circular dichroism, and NMR spectroscopy; electrospray ionization mass spectrometry, thermal melting, viscosity, and DNase footprinting as well as molecular modeling and thermodynamic studies to provide detailed binding mechanism at the molecular level for structure-activity relationship. Nucleic acids binding properties of these alkaloids are interpreted in relation to their biological activity.

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DNA Polymorphism: A Comparison of Force Fields for Nucleic Acids

Cited by 78 publications

References 71 publications

H4 histone tail mediated DNA–DNA interaction and effects on DNA structure, flexibility, and counterion binding. A molecular dynamics study

H4 histone tail mediated DNA–DNA interaction and effects on DNA structure, flexibility, and counterion binding. A molecular dynamics study

Simulations of DNA Coiling around a Synthetic Supramolecular Cylinder That Binds in the DNA Major Groove

Molecular aspects on the interaction of protoberberine, benzophenanthridine, and aristolochia group of alkaloids with nucleic acid structures and biological perspectives

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