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).

Gattuso, H., Spinello, A., Terenzi, A., Assfeld, X., Barone, G., Monari, A. (2016). Circular Dichroism of DNA G-Quadruplexes: Combining Modeling and Spectroscopy to Unravel Complex Structures. JOURNAL OF PHYSICAL CHEMISTRY. B, CONDENSED MATTER, MATERIALS, SURFACES, INTERFACES & BIOPHYSICAL, 120(12), 3113-3121 [10.1021/acs.jpcb.6b00634].

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

Spinello, A.
Membro del Collaboration Group
;
Terenzi, A.
Membro del Collaboration Group
;
BARONE, Giampaolo
Membro del Collaboration Group
;
2016-01-01

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).
2016
Settore CHIM/03 - Chimica Generale E Inorganica
Gattuso, H., Spinello, A., Terenzi, A., Assfeld, X., Barone, G., Monari, A. (2016). Circular Dichroism of DNA G-Quadruplexes: Combining Modeling and Spectroscopy to Unravel Complex Structures. JOURNAL OF PHYSICAL CHEMISTRY. B, CONDENSED MATTER, MATERIALS, SURFACES, INTERFACES & BIOPHYSICAL, 120(12), 3113-3121 [10.1021/acs.jpcb.6b00634].
File in questo prodotto:
File Dimensione Formato  
JPCB_2016_120_3113.pdf

Solo gestori archvio

Tipologia: Versione Editoriale
Dimensione 1.16 MB
Formato Adobe PDF
1.16 MB Adobe PDF   Visualizza/Apri   Richiedi una copia

I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.

Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/10447/225795
Citazioni
  • ???jsp.display-item.citation.pmc??? 8
  • Scopus 39
  • ???jsp.display-item.citation.isi??? 37
social impact