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<p>The use of small molecules as fluorescent DNA markers has been extensively explored since the mid-1960s, revealing limitations in designing selective probes due to the largely missing relationship between probe structure and DNA conformation. Here, we present a multistep computational protocol applied to a recently proposed fluorescent marker, QCy(MeBT)₃, capable of simultaneously recognizing both B-DNA and G-quadruplex DNA through distinct emission signatures. Our protocol identifies the conformations that enable selective probe–DNA binding and predicts a remarkably high affinity. Moreover, these same conformations are responsible for the different absorption and fluorescence shifts observed experimentally upon binding to B-DNA or G-quadruplex. Overall, we establish a fundamental principle for predicting the performance of fluorescent probes in complex biological environments: the properties of specific molecular conformations determine their photobiophysical fate upon binding to a given DNA sequence, and thus their ability to recognize a particular DNA topology.</p><p></p>

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A fluorescent probe under the microscope showing dual recognition of B-DNA and G-quadruplex DNA

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年3月10日

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  • Lorenzo Gramolini,
  • Richard López-Corbalán,
  • Marco Marazzi,
  • Cristina García-Iriepa

摘要

The use of small molecules as fluorescent DNA markers has been extensively explored since the mid-1960s, revealing limitations in designing selective probes due to the largely missing relationship between probe structure and DNA conformation. Here, we present a multistep computational protocol applied to a recently proposed fluorescent marker, QCy(MeBT)₃, capable of simultaneously recognizing both B-DNA and G-quadruplex DNA through distinct emission signatures. Our protocol identifies the conformations that enable selective probe–DNA binding and predicts a remarkably high affinity. Moreover, these same conformations are responsible for the different absorption and fluorescence shifts observed experimentally upon binding to B-DNA or G-quadruplex. Overall, we establish a fundamental principle for predicting the performance of fluorescent probes in complex biological environments: the properties of specific molecular conformations determine their photobiophysical fate upon binding to a given DNA sequence, and thus their ability to recognize a particular DNA topology.