# Electronic Circular Dichroism Spectra of DNA Quadruple Helices Studied by Molecular Dynamics Simulations and Excitonic Calculations including Charge Transfer States

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## Abstract

**:**

## 1. Introduction

## 2. Methods

#### Computational Details

**Electronic calculations:**For our DFT/TD-DFT calculations, necessary to parametrize FrDEx and to provide the reference QM and FHC spectra, we selected the M05-2X functional [41], using a 6-31G(d) basis set, implemented within the Gaussian 16 package [42]. This functional can reliably describe CT transitions in stacked systems, as shown also by our previous studies on oligonucleotides [43]. Solvent effects of waTer have been included by the Polarizable Continuum Model (PCM) [44]. This approach has been already profitably used to the study the photoactivated behavior of oligonucleotides [43], including GQ [13,45,46,47,48]. The electronic couplings for the FHC approach were calculated using the ‘EET’ option within Gaussian, which utilises a transition density based approach to calculate the Coulombic couplings between LEs [22]. We also made selected test calculations with another functional, M06-2X [41], and a larger basis set to ensure that the ECD spectra are not qualitatively affected by these changes. These results are shown in the Supplementary Information, Figure S3.

**QM/MM:**For T30695, our reference QM results utilise a QM/MM model, applied to a structure obtained from PDB code 2LE6, without any further geometry optimization [36]. The QM region contains 12 G bases plus two inner Na${}^{+}$ ions for both the monomeric and the interface species and is described at the M05-2X/6-31G(d) level. The rest of the system is computed at the Molecular Mechanics (MM) level (amber force field parm96.dat) [49] and both regions are coupled using the ONIOM interface [50] as implemented in Gaussian [42]. The whole system is embedded in implicit water using PCM. An illustration of the QM/MM model is shown in the Supplementary Information, Figure S2.

**MD simulations:**Classical MD simulations in explicit solvent have been performed on Tel21 and Tel22 sequences by using the Amber16 package [51] and the OL15 [52] DNA force field. The GQ was solvated in a truncated octahedral box with a minimal distance of 10 Å of solute from the box border. We used SPC/E water model [53] and a 0.15 M excess NaCl. Two Na${}^{+}$ ions were manually inserted between the tetrads. Joung and Cheatham (JC) parameters for the ions were used [54]. The model 1 of the NMR structure with pdb code 143D [55] was chosen as starting structure for the simulations. The equilibration of the starting structure by using standard protocols was followed by a 1 microsec long single production run. Eleven structures extracted every 100 ns from the trajectory were selected for the ECD spectra calculations. The stacking interactions between G bases were assessed by calculating the distance between centres of mass of the bases as well as by evaluating the overlap areas of planar projections of the ring and exocyclic atoms in consecutive bases. The latter calculations have been performed by 3DNA software [56].

**FrDEx:**For all the FrDEx calculations, the sugar backbone and inner ions are removed from the GQ structures. For the majority of the computations, only the guanine bases are considered, where the guanine geometries from the PDB/MD are replaced by a 9-methyl-guanine, geometry optimised at the M05-2X/6-31G(d)/PCM(water) level of theory, by minimising the RMSD between them. We also made some tests by using directly the G structures provided by MD simulations. Analogously, in the study of the contribution of the loops, adenine and thymine are replaced by geometry optimised 9-methyladenine and 1-methylthymine, respectively.

## 3. Results

#### 3.1. Tel21

#### 3.1.1. Assessment of the FrDEx Options

#### 3.1.2. Guanine Internal Geometry

#### 3.1.3. Including Loop Bases

#### 3.1.4. Considering Thermal Fluctuations

#### 3.2. Monomeric and Dimeric Forms of T30695

## 4. Concluding Remarks

## Supplementary Materials

## Author Contributions

## Funding

## Data Availability Statement

## Conflicts of Interest

## Sample Availability

## References

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**Figure 1.**Schematic drawing of (

**a**) Hoogsteen bonding arrangement of four guanines within a tetrad and the guanine quadruplex structures of (

**b**) Tel21/22 (antiparallel) and (

**c**) T30695 (parallel dimer). Only the guanine bases are numbered and labelled for T30695, both for monomers A and B. The adenine and thymine bases are numbered in addition to the guanines for Tel21/22, with Tel21 not including the 5${}^{\prime}$ terminal adenine A0. The two lateral loops (LL1 and LL2) are also indicated, as well as the diagonal loop (DL).

**Figure 2.**Computed ECD spectra of (

**a**) Tel21 NMR structure by TD-DFT and FrDEx with 4 or 12 CT states, compared to experiment [59]. Panels (

**b**,

**c**) show computed spectra of Tel21 from MD snapshots at 100 and 300 ns, respectively, using TD-DFT and FrDEx with 4 CT states. All panels use pairs as the SC to calculate ${H}_{\mathrm{inter}}$, panel (

**a**) uses a strand as SC to calculate ${H}_{\mathrm{intra}}$, whilst panels (

**b**,

**c**) use different sizes of SC indicated in the captions. In panel (

**a**), the intensity of peak I is normalised to a value of 1 for both the experimental spectrum and the TD-DFT spectrum of the NMR structure, with the FrDEx spectra normalised using the same scaling factor as the TD-DFT spectrum. The spectra in panels (

**b**,

**c**) are not normalised. All calculated spectra are shifted by −0.85 eV.

**Figure 3.**Computed ECD spectra of Tel21 GQ at 100 ns using as a geometry for G either the optimized structure of G monomer (black) or the geometry directly extracted from MD simulations (red). FrDEx spectra are reported as dashed lines and the full QM spectra as solid lines. All FrDEx calculations use pairs as the SC to calculate ${H}_{\mathrm{inter}}$ and strands for ${H}_{\mathrm{intra}}$. All spectra shifted by −0.85 eV.

**Figure 4.**Computed ECD spectra of Lateral Loop 1 (LL1), Lateral Loop 2 (LL2) and Diagonal Loop (DL) in conf. 2 of the Tel21 100 ns structure and DL conf. 1 from Tel22 MD stucture at 100 ns. All spectra include only adenine and thymine bases, solid lines report TD-DFT spectra and dashed lines FrDEx spectra.

**Figure 5.**FrDEx computed ECD spectra including all adenine and thymine bases in the LLs and DL, and all G bases of Tel21 100 ns structure GQ with DL in conf. 2 (solid black) and Tel22 100 ns structure with DL in conf. 1 (solid red). Dashed lines indicate the spectra without the contributions from the loops, i.e., with only the G bases. We have not considered A0 base of Tel22 GQ. All FrDEx calculations use pairs as the SC to calculate ${H}_{\mathrm{inter}}$ and ${H}_{\mathrm{intra}}$. All calculated spectra are shifted by −0.85 eV.

**Figure 6.**Computed ECD spectra of Tel21 GQ at the NMR structure and different time points on the MD Trajectory, as well as the average spectrum from the MD snapshots. All FrDEx calculations use strand as the SC to calculate ${H}_{\mathrm{intra}}$ and pair as the SC to calculate ${H}_{\mathrm{inter}}$. All calculated spectra are shifted by −0.85 eV.

**Figure 7.**(

**a**) Total overlap area between immediately stacked bases in adjacent tetrads, (

**b**) rotational strengths of each excitonic state for each calculation of Figure 6 (

**c**) coefficients of the L${}_{\mathrm{a}}$/L${}_{\mathrm{b}}$ states of the different G’s for excitonic state 1 (

**d**) coefficients of the L${}_{\mathrm{a}}$/L${}_{\mathrm{b}}$ states of the different G’s for excitonic state 13.

**Figure 8.**(

**a**) Percentage involvement of CT states in the lowest 24 excitonic states for Tel21 in the NMR structure and MD snapshots; contribution of pairs of guanines to the CT states in excitonic state (

**b**) 1 and (

**c**) 13.

**Figure 9.**ECD spectra of the parallel GQ dimer T30695 from experiment [37] and computed by FrDEx, with low energy peaks normalised to 1. We also show the T30695 GQ “monomer” A, and the interface consisting of 1 tetrad of A and 2 of B (int 1A2B) computed by FrDEx and PCM/MM/TD-M05-2X/6-31G(d), both of which are normalised using the same value as the FrDEx spectrum of the dimer.

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**MDPI and ACS Style**

Asha, H.; Green, J.A.; Martinez-Fernandez, L.; Esposito, L.; Improta, R. Electronic Circular Dichroism Spectra of DNA Quadruple Helices Studied by Molecular Dynamics Simulations and Excitonic Calculations including Charge Transfer States. *Molecules* **2021**, *26*, 4789.
https://doi.org/10.3390/molecules26164789

**AMA Style**

Asha H, Green JA, Martinez-Fernandez L, Esposito L, Improta R. Electronic Circular Dichroism Spectra of DNA Quadruple Helices Studied by Molecular Dynamics Simulations and Excitonic Calculations including Charge Transfer States. *Molecules*. 2021; 26(16):4789.
https://doi.org/10.3390/molecules26164789

**Chicago/Turabian Style**

Asha, Haritha, James A. Green, Lara Martinez-Fernandez, Luciana Esposito, and Roberto Improta. 2021. "Electronic Circular Dichroism Spectra of DNA Quadruple Helices Studied by Molecular Dynamics Simulations and Excitonic Calculations including Charge Transfer States" *Molecules* 26, no. 16: 4789.
https://doi.org/10.3390/molecules26164789