Unfolding and Conformational Variations of Thrombin-Binding DNA Aptamers: Synthesis, Circular Dichroism and Molecular Dynamics Simulations

ChemMedChem ◽  
2014 ◽  
Vol 9 (5) ◽  
pp. 993-1001 ◽  
Author(s):  
Lidan Sun ◽  
Hongwei Jin ◽  
Xiaoyang Zhao ◽  
Zhenming Liu ◽  
Yifu Guan ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Circular Dichroism ◽  
Molecular Dynamics Simulations ◽  
Dna Aptamers ◽  
Conformational Variations ◽  
Dynamics Simulations ◽  
Circular Dichroïsm

scholarly journals Electronic Circular Dichroism Spectra of DNA Quadruple Helices Studied by Molecular Dynamics Simulations and Excitonic Calculations Including Charge Transfer States

Molecules ◽  
2021 ◽  
Vol 26 (16) ◽  
pp. 4789
Author(s):  
Haritha Asha ◽  
James A. Green ◽  
Lara Martinez-Fernandez ◽  
Luciana Esposito ◽  
Roberto Improta
Keyword(s):  
Molecular Dynamics ◽  
Circular Dichroism ◽  
Charge Transfer ◽  
Molecular Dynamics Simulations ◽  
Thermal Fluctuations ◽  
Telomeric Sequence ◽  
Quadruple Helix ◽  
Electronic Circular Dichroism ◽  
Dynamics Simulations ◽  
Circular Dichroïsm

We here investigate the Electronic Circular Dichroism (ECD) Spectra of two representative Guanine-rich sequences folded in a Quadruple helix (GQ), by using a recently developed fragment diabatisation based excitonic model (FrDEx). FrDEx can include charge transfer (CT) excited states and consider the effect of the surrounding monomers on the local excitations (LEs). When applied to different structures generated by molecular dynamics simulations on a fragment of the human telomeric sequence (Tel21/22), FrDEx provides spectra fully consistent with the experimental one and in good agreement with that provided by quantum mechanical (QM) method used for its parametrization, i.e., TD-M05-2X. We show that the ECD spectrum is moderately sensitive to the conformation adopted by the bases of the loops and more significantly to the thermal fluctuations of the Guanine tetrads. In particular, we show how changes in the overlap of the tetrads modulate the intensity of the ECD signal. We illustrate how this correlates with changes in the character of the excitonic states at the bottom of the La and Lb bands, with larger LE and CT involvement of bases that are more closely stacked. As an additional test, we utilised FrDEx to compute the ECD spectrum of the monomeric and dimeric forms of a GQ forming sequence T30695 (5’TGGGTGGGTGGGTGGG3’), i.e., a system containing up to 24 Guanine bases, and demonstrated the satisfactory reproduction of the experimental and QM reference results. This study provides new insights on the effects modulating the ECD spectra of GQs and, more generally, further validates FrDEx as an effective tool to predict and assign the spectra of closely stacked multichromophore systems.

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