The G-Triplex DNA

Authors

  • Dr. Vittorio Limongelli,

    1. Department of Pharmacy, University of Naples “Federico II”, Via D. Montesano, 49, 80131 Naples (Italy)
    2. Department of Chemistry and Applied Biosciences, ETH Zurich
    3. Facoltà di Informatica, Istituto di Scienze Computazionali (ICS), Università della Svizzera Italiana, Via Giuseppe Buffi 13, 6900 Lugano (Switzerland)
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    • These authors contributed equally to this work.

  • Stefano De Tito,

    1. Department of Pharmacy, University of Naples “Federico II”, Via D. Montesano, 49, 80131 Naples (Italy)
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    • These authors contributed equally to this work.

  • Dr. Linda Cerofolini,

    1. Magnetic Resonance Center (CERM), University of Florence, 50019 Sesto Fiorentino, Florence (Italy)
    2. Department of Chemistry, University of Florence, 50019 Sesto Fiorentino, Florence (Italy)
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  • Dr. Marco Fragai,

    1. Magnetic Resonance Center (CERM), University of Florence, 50019 Sesto Fiorentino, Florence (Italy)
    2. Department of Chemistry, University of Florence, 50019 Sesto Fiorentino, Florence (Italy)
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  • Dr. Bruno Pagano,

    1. Department of Pharmacy, University of Naples “Federico II”, Via D. Montesano, 49, 80131 Naples (Italy)
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  • Dr. Roberta Trotta,

    1. Department of Pharmacy, University of Naples “Federico II”, Via D. Montesano, 49, 80131 Naples (Italy)
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  • Dr. Sandro Cosconati,

    1. Department of Pharmacy, University of Naples “Federico II”, Via D. Montesano, 49, 80131 Naples (Italy)
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  • Dr. Luciana Marinelli,

    1. Department of Pharmacy, University of Naples “Federico II”, Via D. Montesano, 49, 80131 Naples (Italy)
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  • Prof. Ettore Novellino,

    1. Department of Pharmacy, University of Naples “Federico II”, Via D. Montesano, 49, 80131 Naples (Italy)
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  • Prof. Ivano Bertini,

    1. Magnetic Resonance Center (CERM), University of Florence, 50019 Sesto Fiorentino, Florence (Italy)
    2. Department of Chemistry, University of Florence, 50019 Sesto Fiorentino, Florence (Italy)
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  • Prof. Antonio Randazzo,

    Corresponding author
    1. Department of Pharmacy, University of Naples “Federico II”, Via D. Montesano, 49, 80131 Naples (Italy)
    • Antonio Randazzo, Department of Pharmacy, University of Naples “Federico II”, Via D. Montesano, 49, 80131 Naples (Italy)===

      Claudio Luchinat, Magnetic Resonance Center (CERM), University of Florence, 50019 Sesto Fiorentino, Florence (Italy)===

      Michele Parrinello, Department of Chemistry and Applied Biosciences, ETH Zurich===

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  • Prof. Claudio Luchinat,

    Corresponding author
    1. Magnetic Resonance Center (CERM), University of Florence, 50019 Sesto Fiorentino, Florence (Italy)
    2. Department of Chemistry, University of Florence, 50019 Sesto Fiorentino, Florence (Italy)
    • Antonio Randazzo, Department of Pharmacy, University of Naples “Federico II”, Via D. Montesano, 49, 80131 Naples (Italy)===

      Claudio Luchinat, Magnetic Resonance Center (CERM), University of Florence, 50019 Sesto Fiorentino, Florence (Italy)===

      Michele Parrinello, Department of Chemistry and Applied Biosciences, ETH Zurich===

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  • Prof. Michele Parrinello

    Corresponding author
    1. Department of Chemistry and Applied Biosciences, ETH Zurich
    2. Facoltà di Informatica, Istituto di Scienze Computazionali (ICS), Università della Svizzera Italiana, Via Giuseppe Buffi 13, 6900 Lugano (Switzerland)
    • Antonio Randazzo, Department of Pharmacy, University of Naples “Federico II”, Via D. Montesano, 49, 80131 Naples (Italy)===

      Claudio Luchinat, Magnetic Resonance Center (CERM), University of Florence, 50019 Sesto Fiorentino, Florence (Italy)===

      Michele Parrinello, Department of Chemistry and Applied Biosciences, ETH Zurich===

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  • We acknowledge Anh Tuân Phan for providing an optimized JR HMBC sequence, Roman Reshetnikov and Janez Plavec for useful discussions. Furthermore, we acknowledge that the results of this research have been achieved using the PRACE Research Infrastructure resource JUGENE based in Germany at Forschungszentrum Juelich. This work was supported by the Gabriele Charitable Foundation, Italian Institute of Technology (IIT), Italian M.U.R.S.T., P.R.I.N. 2009, Biologia Strutturale Meccanicistica, Italian Association for Cancer Research (A.I.R.C.), EU FP7, ERC Advanced Grant No. 247075, and a grant from the Swiss National Supercomputing Centre (CSCS) under project ID s386.

Abstract

original image

Triplex with a twist: Through metadynamics calculations, the thrombin binding aptamer (TBA) has been shown to adopt a stable G-triplex structural motif, in addition to the usual G-quadruplex (see scheme). An 11-mer oligonucleotide was also shown to form a stable G-triplex, whose structural and thermodynamic properties have been characterized.

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