Chen, Guangju

Wang, Yan

Yue, Hongwei

Zhu, Yanyan

BMC Structural Biology

English

PubMed

Abstract
          
            Background
            Copper nucleases as a famous class of artificial metallonucleases have attracted considerable interest in relation to their diverse potentials not only as therapeutic agents but also in genomic researches. Copper nucleases present high efficient oxidative cleavage of DNA, in which DNA strand scission occurs generally after hydrogen atom abstracted from a sugar moiety. In order to achieve the selective cleavage of DNA sequences by copper nucleases, the DNA specific recognition agents of the Dervan-type hairpin and cyclic polyamides can be considered as proper carriers of copper nucleases. Investigation of the DNA cleavage selectivity of copper nucleases assisted by the hairpin and cyclic polyamides at the molecular level has not yet been elucidated.
          
          
            Results
            We carried out a series of molecular dynamics simulations for the nuclease [Cu(BPA)]2+ or [Cu(IDB)]2+ bound to the hairpin/cyclic polyamide and associated with DNA to investigate the selective DNA cleavage properties of Cu(II)-based artificial nucleases. The simulated results demonstrate that the DNA cleavage selectivity of the two nucleases assisted by the hairpin polyamide is improved efficiently. The [Cu(BPA)]2+ or [Cu(IDB)]2+ nuclease with a substrate OOH- bound to the hairpin polyamide can be stably located at the minor groove of DNA, and possibly abstracts H atom from the sugar of DNA. However, the DNA cleavage properties of the two nucleases assisted by the cyclic polyamide are significantly poor due to the rigidity of linking region between the cyclic polyamide and nuclease. With introduction of the flexible linker -CH2CH2CH2NH2, the modified cyclic polyamide can assist the two copper nucleases to improve the selective DNA cleavage properties efficiently.
          
          
            Conclusion
            A flexible linker and a proper binding site of the polyamide-type recognition agents play an important role in improving the DNA cleavage selectivity of copper nucleases. Current investigations provide an insight into the DNA cleavage specificities of chemical nucleases assisted by an appropriate nucleic acid recognition agent.
          </jats:sec

Hongwei Yue

Yanyan Zhu

Yan Wang

Guangju Chen

Crossref

Investigation and improvement of DNA cleavage models of polyamide + Cu(II) nuclease + OOH- ligands bound to DNA

Aldrich-Wright JR: Polyamide platinum anticancer complexes designed to target specific DNA sequences. Inorg Chem

Aldrich-Wright JR: Synthesis of DNAsequence-selective hairpin polyamide platinum complexes. Chem Eur J

AM: Oxygen-dependent cleavage of DNA by the 1,10-phenanthroline-cuprous complex.

Carbon-hydrogen bonds of DNA sugar units as targets for chemical nucleases and drugs. Angew Chem Int Ed Engl

CG: A three-point method for evaluations of AMBER force field parameters: an application to copper-based artificial nucleases. Theor Chem Account

Chem Rev

CL: Targeted chemical nucleases. Acc Chem Res

Cowan JA: DNA cleavage by copper-ATCUN complexes. factors influencing cleavage mechanism and linearization of dsDNA.

DC: Structural effects of DNA sequence on T·A recognition by hydroxypyrrole/pyrrole pairs in the minor groove.

DE: Design of a G·Cspecific DNA minor groove-binding peptide. Science

DE: NMR structure of a cyclic polyamide-DNA complex.

Dervan PB: Cycle polyamide motif for recognition of the minor groove of DNA.

Dervan PB: Cyclic pyrroleimidazole polyamides targeted to the androgen response element. JA m Chem Soc

Dervan PB: Discrimination of 5’-GGGG-3’,5 ’-GCGC-3’, and 5’-GGCC-3’ sequences in the minor groove of DNA by eight-ring hairpin polyamides.

Dervan PB: Hairpin peptide motif. a new class of oligopeptides for sequence-specific recognition in the minor groove of double-helical DNA.

Dervan PB: Hydroxybenzamide/pyrrole pair distinguishes T·A from A·T base pairs in the minor groove of DNA. JA m Chem Soc

Dervan PB: Optimization of the hairpin polyamide design for recognition of the minor groove of DNA.

Dervan PB: Recognition of the four Watson-Crick base pairs in the DNA minor groove by synthetic ligands. Nature

Designed sequence-specific minor groove ligands. Annu Rev Biophys Biomol Struct

Development and testing of a general Amber force field.

Diercksen G: Self-consistent perturbation theory. II. extension to open shells.

Dinuclear copper(II) complexes of a polybenzimidazole ligand: their structures and inductive roles in DNA condensation. Inorg Chem

Distinguish protein decoys by using a scoring function based on a new AMBER force field, short molecular dynamics simulations, and the generalized Born solvent model. Proteins: Structure, Function, and Bioinformatics

DL: A 5-nanosecond molecular dynamics trajectory for B-DNA: analysis of structure, motions, and solvation.

DL: Intrusion of counterions into the spine of hydration in the minor groove of B-DNA: fractional occupancy of electronegative pockets.

DM: Chemical nucleases. Chem Rev

EC: Ni(II)·Xaa-Xaa-His induced DNA cleavage: deoxyribose modification by a common “activated” intermediate derived from KHSO5, MMPP, or H2O2. J Am Chem Soc

Edelson BS: Recognition of the DNA minor groove by pyrroleimidazole polyamides. Curr Opin Struct Biol

Edelson BS: Regulation of gene expression by synthetic DNA-binding ligands. Top Curr Chem

Efficient and specific strand scission of DNA by a dinuclear copper complex: comparative reactivity of complexes with linked tris(2-pyridylmethyl)amine moieties.

Efficient inorganic deoxyribonucleases greater than 50-million-fold rate enhancement in enzyme-like DNA cleavage.

et al: A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations.

et al: AMBER9.

GJ: Evaluation of AMBER force field parameters for copper(II) with pyridylmethyl-amine and benzimidazolylmethyl-amine ligands: a quantum chemical study. Chem Phys Letter

GJ: Molecular docking studies on the metallonucleases and polyamides with double-strand DNA molecules.

GJ: Molecular dynamics simulations on binding models of Dervan-type polyamide + Cu(II) nuclease ligands to DNA.

GJ: Systematic characterization on electronic structures and spectra for a series of complexes,

Greenberg MM: Model studies indicate that copper phenanthroline induces direct strand breaks via β-elimination of the 2’-deoxyribonolactone intermediate observed in enediyne mediated DNA damage.

K: Crystal structures of nucleosome core particles in complex with minor groove DNA-binding ligands.

Lippard SJ: Unwinding of supercoiled DNA by platinumethidium and related complexes.

McNett KM: Photoprocesses of copper complexes that bind to DNA. Chem Rev

Mechanisms of DNA cleavage by copper complexes of 3-Clip-Phen and of its conjugate with a distamycin analogue. Nucleic Acids Res

Nesbet RK: Self-consistent orbitals for radicals.

New developments in molecular orbital theory. Rev Modern Phys

Nonenzymic cleavage and ligation of DNA at a three A·T base pair site. A two-step pseudohydrolysis of DNA.

NV: Hydrogen peroxide and dioxygen activation by dinuclear copper complexes in aqueous solution: hydroxyl radical production initiated by internal electron transfer.

Ornstein RL: 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.

Reagents for the site-specific cleavage of megabase DNA.

Recognition and reaction of metallointercalators with DNA. Chem Rev

Recognition and strand scission at junctions between single- and double-stranded DNA by a trinuclear copper complex.

Rokita SE: Changing selectivity of DNA oxidation from deoxyribose to guanine by ligand design and a new binuclear copper complex.

Rokita SE: Oxidative strand scission of nucleic acids by a multinuclear copper(II) complex.

Rokita SE: Selective DNA strand scission with binuclear copper complexes: implications for an active Cu2-O2 species.

Rokita SE: Targeted guanine oxidation by a dinuclear copper(II) complex at single stranded/double stranded DNA junctions. Inorg Chem

Rokita SE: Targeted strand scission of DNA substrates by a tricopper(II) coordination complex.

SETTLE: an analytical version of the SHAKE and RATTLE algorithm for rigid water models. J Comput Chem

Sigman DS: Cleavage of DNA by coordination complexes. superoxide formation in the oxidation of 1,10-phenanthroline-cuprous complexes by oxygen - relevance to DNAcleavage reaction.

Sun HZ: DNA hydrolysis promoted by di- and multi-nuclear metal complexes. Coord Chem Rev

TDP: Structure and spectroscopy of copper-dioxygen complexes. Chem Rev

Tullius TD:

Tullius TD: Oxidative strand scission of nucleic acids: routes initiated by hydrogen abstraction from the sugar moiety. Chem Rev

Unni Nair B: A new dinuclear biphenylene bridged copper(II) complex: DNA cleavage under hydrolytic conditions. Biochim Biophy Acta

ZJ: Oxidative DNA cleavage promoted by multinuclear copper complexes:

ZW: Cleavage of double-strand DNA by linear and triangular trinuclear copper complexes.

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Investigation and improvement of DNA cleavage models of polyamide + Cu(II) nuclease + OOH- ligands bound to DNA

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