Effects of Sequence and Base Composition on the CD and TDS Profiles of i‐DNA

Abstract

The i-motif DNA, also knowna si -DNA, is an oncanonical DNAs econdary structure formed by cytosine-rich sequences,c onsisting of two intercalated parallel-stranded duplexes held together by hemi-protonated cytosine-cytosine + (C:C + )base pairs.The growing interest in the i-DNAstructure as atarget in anticancer therapyincreases the need for tools for arapid and meaningful interpretation of the spectroscopic data of i-DNAsamples.Herein, we analyzed the circular dichroism (CD) and thermal difference UV-absorbance spectra (TDS) of 255 DNAs equences by means of multivariate data analysis, aiming at unveiling peculiar spectral regions that could be used as diagnostic features during the analysis of i-DNA-forming sequences.

Drivers of i-DNA Formation in a Variety of Environments Revealed by Four-Dimensional UV Melting and Annealing

“…To illustrate the procedure, the temperature dependent UV spectra at pH 6.0 of 44L1 are shown in Figures 3A-B. The temperaturedependent thermal difference spectra (TDS) 24 were obtained by subtracting the UV spectrum of fully unfolded species at the highest temperature (90 °C) from the spectra of fully or partially folded species at a lower temperature, between 5 and 90 °C (Figures 3C-D). The TDS positive peak around 240 nm and negative peak around 295 nm indicate the formation of i-DNA 53 .…”

“…As cytosine protonation at the N3 position is essential for formation of the hemi-protonated base pairs, stability and unfolding/folding rates of i-DNA depend on pH [9][10][11][12][13][14][15][16][17][18][19][20] . i-DNA stability is often modest under physiological conditions 11,13,21 , but some i-DNA structures have been shown to remain folded at neutral pH 11,[13][14][15][16][20][21][22][23][24][25][26] . In-cell NMR 20,27 and experiments with an i-DNA-specific antibody 28 recently demonstrated that i-DNAs are present in human cells.…”

“…those with shorter loops. 11,13,20,24 In addition to pH and temperature, cation type and concentration influence both stability and conformation: Na + , K + , Li + , NH 4 + , and Cu 2+ destabilize i-DNA, 5,38−40 whereas Ag + and Cu + stabilize this structure. 41−44 Moreover, i-DNA has been reported to be stabilized by macromolecular crowding conditions.…”

Synthesis and Characterization of Bis-Triazolyl-Pyridine Derivatives as Noncanonical DNA-Interacting Compounds

“…On the other hand, the Tel 23 G4 sequence showed a CD spectrum having two positive bands at 290 and 270 nm and a weak negative band at 240 nm, consistent with the formation of a hybrid [3+1] G4 folding topology. As for Bcl-2 iM, c-Myc iM , and hTeloC iM , all of them exhibited a CD spectrum with a positive band at 288 nm and a negative one at around 260 nm, which are characteristic values of iM formation [ 48 ], while the Hairpin showed a positive band at around 280 nm and a negative one at ~250 nm in the CD spectrum, confirming duplex formation ( Figure S4 ).…”

Conformational plasticity of DNA secondary structures: probing the conversion between i-motif and hairpin species by circular dichroism and ultraviolet resonance Raman spectroscopies

“…At pH 5.2, the CD spectra of both BCL2 and KRAS sequences exhibited the characteristic iM profile, i.e., a strong positive band at 288 nm and a negative one at 264 nm. 62 On increasing the pH to 6.6, a shift of the maximum to 285 nm was observed for both oligonucleotides, suggesting the formation of a certain amount of hairpin conformation. Upon further increase of the pH to 7.8, the CD spectra of both DNA sequences exhibited a significant intensity drop of the positive band along with the shift of the maximum to 280 nm.…”