Circular Dichroism of DNA G-Quadruplexes: Combining Modeling and Spectroscopy to Unravel Complex Structures

Alessio Terenzi, Giampaolo Barone, Antonio Monari, Alessio Terenzi, Hugo Gattuso, Xavier Assfeld

Risultato della ricerca: Articlepeer review

25 Citazioni (Scopus)

Abstract

We report on the comparison between the computational and experimental determination of electronic circular dichroism spectra of different guanine quadruplexes obtained from human telomeric sequences. In particular the difference between parallel, antiparallel, and hybrid structures is evidenced, as well as the induction of transitions between the polymorphs depending on the solution environment. Extensive molecular dynamics simulations (MD) are used to probe the conformational space of the different quadruplexes, and subsequently state-of-the-art hybrid quantum mechanics/molecular mechanics (QM/MM) techniques coupled with excitonic semiempirical Hamiltonian are used to simulate the macromolecular induced circular dichroism. The coupling of spectroscopy and molecular simulation allows an efficient one-to-one mapping between structures and optical properties, offering a way to disentangle the rich, yet complicated, quantity of information embedded in circular dichroism spectra. We show that our methodology is robust and efficient and allows us to take into account subtle conformational changes. As such, it could be used as an efficient tool to investigate structural modification upon DNA/drug interactions. (Graph Presented).
Lingua originaleEnglish
pagine (da-a)3113-3121
Numero di pagine9
RivistaJOURNAL OF PHYSICAL CHEMISTRY. B, CONDENSED MATTER, MATERIALS, SURFACES, INTERFACES & BIOPHYSICAL
Volume120
Stato di pubblicazionePublished - 2016

All Science Journal Classification (ASJC) codes

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  • ???subjectarea.asjc.2500.2508???
  • ???subjectarea.asjc.2500.2505???

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