The influence of Ni<sup>2+</sup> and other ions on the trigonal structure of DNA

Acosta-Reyes, F.J.; Pagán, M.; Fonfría-Subirós, Elsa; Saperas, Núria; Subirana, Juan A.; Campos, J. Lourdes

doi:10.1002/bip.23397

Cited by 4 publications

(1 citation statement)

References 42 publications

(49 reference statements)

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“…This issue has also been addressed by dodecamers and other length DNA duplexes being crystallized in a variety of space groups. For example, duplex packing in the trigonal space group P 3 2 which is sometimes observed when co-crystallized with nickel (2 + ) ions involves end-to-end pseudo-stacked helices running through the crystal structures, such as that of d(CGAATTAATTCG) ( 22 ). This arrangement releases the base pairs near to the helix termini to be free from any potential crystal packing constraints.…”

Section: The Double Helix Visualized By Single-crystal Studiesmentioning

confidence: 99%

Beyond the double helix: DNA structural diversity and the PDB

Neidle

2021

Journal of Biological Chemistry

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Section: The Double Helix Visualized By Single-crystal Studiesmentioning

confidence: 99%

Beyond the double helix: DNA structural diversity and the PDB

Neidle

2021

Journal of Biological Chemistry

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Experimental detection of conformational transitions between forms of DNA: problems and prospects

Zubova,

Strelnikov

2023

Biophys Rev

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Crystal structure of the HMGA AT-hook 1 domain bound to the minor groove of AT-rich DNA and inhibition by antikinetoplastid drugs

Nué-Martinez,

Maturana,

Lagartera

et al. 2024

Sci Rep

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High mobility group (HMG) proteins are intrinsically disordered nuclear non-histone chromosomal proteins that play an essential role in many biological processes by regulating the expression of numerous genes in eukaryote cells. HMGA proteins contain three DNA binding motifs, the “AT-hooks”, that bind preferentially to AT-rich sequences in the minor groove of B-form DNA. Understanding the interactions of AT-hook domains with DNA is very relevant from a medical point of view because HMGA proteins are involved in different conditions including cancer and parasitic diseases. We present here the first crystal structure (1.40 Å resolution) of the HMGA AT-hook 1 domain, bound to the minor groove of AT-rich DNA. In contrast to AT-hook 3 which bends DNA and shows a larger minor groove widening, AT-hook 1 binds neighbouring DNA molecules and displays moderate widening of DNA upon binding. The binding affinity and thermodynamics of binding were studied in solution with surface plasmon resonance (SPR)-biosensor and isothermal titration calorimetry (ITC) experiments. AT-hook 1 forms an entropy-driven 2:1 complex with (TTAA)2-containing DNA with relatively slow kinetics of association/dissociation. We show that N-phenylbenzamide-derived antikinetoplastid compounds (1–3) bind strongly and specifically to the minor groove of AT-DNA and compete with AT-hook 1 for binding. The central core of the molecule is the basis for the observed sequence selectivity of these compounds. These findings provide clues regarding a possible mode of action of DNA minor groove binding compounds that are relevant to major neglected tropical diseases such as leishmaniasis and trypanosomiasis.

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The influence of Ni²⁺ and other ions on the trigonal structure of DNA

Cited by 4 publications

References 42 publications

Beyond the double helix: DNA structural diversity and the PDB

Beyond the double helix: DNA structural diversity and the PDB

Experimental detection of conformational transitions between forms of DNA: problems and prospects

Crystal structure of the HMGA AT-hook 1 domain bound to the minor groove of AT-rich DNA and inhibition by antikinetoplastid drugs

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The influence of Ni2+ and other ions on the trigonal structure of DNA

Cited by 4 publications

References 42 publications

Beyond the double helix: DNA structural diversity and the PDB

Beyond the double helix: DNA structural diversity and the PDB

Experimental detection of conformational transitions between forms of DNA: problems and prospects

Crystal structure of the HMGA AT-hook 1 domain bound to the minor groove of AT-rich DNA and inhibition by antikinetoplastid drugs

Contact Info

Product

Resources

About

The influence of Ni²⁺ and other ions on the trigonal structure of DNA