Numerical simulations of Raman spectra of guanine‐cytosine Watson–Crick and protonated Hoogsteen base pairs

Abstract

Large changes in the Raman spectra of calf thymus DNA are observed upon lowering the pH. In order to gain a better insight into these effects, several simulations of the Raman spectra of the guanine-cytosine (GC) Watson-Crick and Hoogsteen base pairs are performed. By comparing the Raman bands of GC base pairs in calf thymus DNA at high and low pH with the theoretical simulations of GC base pairs, it is found that the intensity changes in the theoretical bands located between 400 and 1000 cm(-1) are small compared to the experimental ones. The behavior of the cytosine band at 1257 cm(-1) upon lowering the pH is not reproduced in the GC theoretical spectra. The bands located above 1300 cm(-1) in the theoretical spectra display intensity changes that are similar to those found for GC base pairs in calf thymus DNA spectra.

From Democritus to Schrödinger: a reflection on quantum molecular modeling

“…Figure 26 shows the modification of Raman spectrum of (GC) base pair after alkylation by the sulfur (HD) or by nitrogen (HN 2 ) mustard [95]. Our computed Raman spectrum is in agreement with the interval 1200-1600 cm -1 reported by Langlais et al [116], Duguid et al [117], and is similar to bands computed by Morari and Muntean [118] at the level B3LYP/6-31G(d). The most intense peak we observe for the (G-C) base pair band is m 61 = 1480.4 cm -1 , which corresponds to the stretch N7-C8 in the Guanine ring (see Fig.…”

DNA structure at low pH values, in the presence of Mn2+ ions: a Raman study

“…3,4 In supercoiled plasmids, protonated nuclease sensitive states persist under neutral pH conditions, suggesting that protonated structures may play a role in the transcriptional activity of the living cell. 3,4 The S 1 nuclease sensitivity was attributed to alterations in sugar phosphate backbone torsion angles necessary to accommodate protonated GÐCH C Hoogsteen pairs in a double helix 5 that also contains AT Watson-Crick pairs; low pH stabilizes such a conformation. 6 Hence, Hoogsteen syn dG : dCH C base pairs might be implied in the mechanism of S 1 recognition in eukaryotic cells.…”

“…The most apparent application would be the formation of initiating signals by Hoogsteen pairs for DNA or RNA polymerase. 3,5 There is no consensus on the precise nature of the changes in DNA conformation that occur when pH is lowered. It seems that a subtle interplay between chemical parameters (pH, ion type and concentration) may result in appreciable changes in DNA conformation.…”

Robust IR‐based detection of stable and fractionally populated G‐C+ and A‐T Hoogsteen base pairs in duplex DNA

“…107 Early calculations 104 typically found shifts in the opposite direction to those observed in experiment. This prompted a few studies 105--107 that investigated the effects of anharmonicity on the vibrational density of states of Watson-Crick and Hoogsteen bps.…”

“…Previous studies have performed theoretical investigations of the Raman [104][105][106][107] and IR spectra [106,107] of G-C + Hoogsteen bps [107]. Early calculations [104] typically found shifts in the opposite direction to those observed in experiment. This prompted a few studies [105][106][107] that investigated the effects of anharmonicity on the vibrational density of states of Watson-Crick and Hoogsteen bps.…”