Data on secondary structures and ligand interactions of G-rich oligonucleotides that defy the classical formula for G4 motifs

The data provided in this article are related to the research article "The expanding repertoire of G4 DNA structures" [1]. Secondary structures of G-rich oligonucleotides (ONs) that represent “imperfect” G-quadruplex (G4) motifs, i.e., contain truncated or interrupted G-runs, were analyzed by optical methods. Presented data on ON structures include circular dichroism (CD) spectra, thermal difference spectra (TDS) and UV -melting curves of the ONs; and rotational relaxation times (RRT) of ethidium bromide (EtBr) complexes with the ONs. TDS, CD spectra and UV-melting curves can be used to characterize the topologies and thermal stabilities of the ON structures. RRTs are roughly proportional to the hydrodynamic volumes of the complexes and thus can be used to distinguish between inter- and intramolecular ON structures. Presented data on ON interactions with small molecules include fluorescence emission spectra of the G4 sensor thioflavin T (ThT) in complexes with the ONs, and CD-melting curves of the ONs in the presence of G4-stabilizing ligands N-methylmesoporphyrin IX (NMM) and pyridostatin (PDS). These data should be useful for comparative analyses of classical G4s and “defective”G4s, such as quadruplexes with vacancies or bulges.

(NMM) and pyridostatin (PDS). These data should be useful for comparative analyses of classical G4s and "defective"G4s, such as quadruplexes with vacancies or bulges. & 2017 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

Subject area
Molecular biology; Physical chemistry More specific subject area

DNA secondary structures
Type of data Data allow one to evaluate sensitivities of G4s with defects towards known G4-stabilizing ligands (NMM and PDS) and a popular ligh-up probe (ThT).
Data can be compared with the previously published data on G4s with vacancies or bulges and used for developing improved G4-predicting algorithms.

Data
The dataset of this article provides information on G-rich ONs that defy the consensus G 3 þ N L1 G 3 þ N L2 G 3 þ N L3 G 3 þ formula for G4 motifs and may form "imperfect" quadruplex structures (imGQs) with bulges between G-tetrads or vacancies/mismatches in the tetrads [2,3]. Table 1 contains MS data on imGQ ONs and control (GQ) ONs. GQ ONs are "perfect" G4s that comply with the The ON set includes both genomic and model sequences.  [4] and PDS [5] effects on thermal stabilities of GQs and imGQs, respectively. Fig. 5 shows ThT [6] fluorescence in complexes with GQs and imGQs.
ON synthesis, HPLC purification and MALDI TOF MS analysis (Table 1) were performed as previously described [8]. Absorption, CD, and fluorescence emission spectra were recorded using a Chirascan spectrophotometer (Applied Photophysics, UK). Molar CD per nucleotide residue (Figs. 1A and 2A) was calculated as follows: Δε ¼ θ/(32.982 Â C Â l Â n), where θ is ellipticity (degree), C is ON concentration (M); l is optical pathlength (cm) and n is the number of nucleotide residues in the ON. In the melting experiments (Figs. 1B and 2B), ON absorbance at 295 nm was registered every 1°C across the 20-90°C temperature range (see Table 2 in [1] for Tm values). The heating rate was 1°C /min. Rotational relaxation times (RRT) of ethidium bromide (EtBr) complexes with the ONs (Figs. 1C and 2C) were estimated using the PerrineWeber equation [9,10]: RRT¼3τ(1/P 0 À 1/3)/(1/P À 1/P 0 ), where P is observed polarization, P 0 ¼ 41 7 1% is its limiting value in the absence of rotational depolarization, and τ is fluorescence lifetime of EtBr in complexes with the ONs. The fluorescence polarization P was calculated as previously described [9]: P¼(I || ÀI ┴ )/(I || þI ┴ ). The vertical (I || ) and horizontal (I ┴ ) components of EtBr fluorescence intensity at emission maximum (610 nm) were measured with Cary Eclipse spectrofluorometer at 4°C upon excitation at 540 nm by the vertically polarized light. Concentration of EtBr was 1 μM, and ON concentration was 5 μM. The fluorescence lifetime (τ) was evaluated using Easy Life V. Fluorescence decay was registered through a RG610 long pass filter at  excitation LED 525 nm. Thermal difference spectra (TDS, Figs. 1D and 2D) were obtained by subtracting ON absorption spectra recorded at 20°C from the spectra recorded at 90°C. In the melting experiments with NMM and PDS (Figs. 3 and 4), the ligands were added to preannealed ON solutions, and ON CD at 265/295 nm was registered every 1°C across the 20-90°C temperature range. The heating rate was 1°C /min. The melting temperatures of GQs/imGQs were defined by performing a fitting procedure using the two-state model for monomolecular melting [11]   in DataFit 9. PDS was obtained from ApexBio, and NMM was obtained from Frontier Scientific. Fluorescence emission spectra of ThT in complexes with the ONs (Fig. 5) were recorded using a Chirascan spectrophotometer (Applied Photophysics) upon excitation at 425 nm at 20°C. ThT was obtained from Abcam.