Studies on the conformation of protonated DNA

Abstract

Experiments were made to demonstrate the predominant protonation effects and structural changes of the ordered double helical DNA structure and denatured state of DNA. Spectrophotometric titrations performed at different wavelengths indicate that cytosine can be protonated in the DNA double helical molecule to a high extent without breakdown of the secondary structure. With DNA heat-denatured under severe conditions the protonation of cytosine can be measured at 280, 295, and 300 mμ: the apparent pK value obtained was ∼4.6. The protonated double helical conformation of the DNA molecule differs from the unprotonated state, which follows from the decrease of the thermal stability and from changes in the ORD curves. The ORD of a GC-rich DNA indicates a novel Cotton effect with positive rotations at ∼260 mμ in 0.02M KCl below pH 4.0 to pH 3.3. The occurrence of the new peak parallels the extent of protonated cytosine measured by the spectrophotometric titrations. It is concluded that the protonated cytosine in the double helical structure is responsible for the difference between the protonated DNA conformation and the native state at neutral pH.

The unique protonated conformation of poly D (G−C) as detected by circular dichroism studies

“…The appearance of a small second positive band at 257 nm on protonation of many natural DNA samples have been reported in several studies [ 15,171. Guschlbauer et The CD spectrum of the neutral form of poly d (G-C) is comparable to that expected for the 'C' form of a double stranded polynucleotide [ 191, and hence might differ only in the magnitude of the tilt of the bases while the conformation of the bases themselves are the same as in DNA.…”

Does DNA acid fixation produce left‐handed Z structure?

“…However, it is worth mentioning that earlier studies led to the suggestion that N-3 of cytosine is the initial site of protonation, due to the fact that cytosine has the highest pKa [29,30], while recent spectroscopic investigations propose the formation of Hoogsteen-type G-C base pairs, which results from protonation of guanine N-7 site and the subsequent anti to syn conformational transition and share the proton with N-3 of cytosine base [21,27]. Recent NMR study of oligonucleotide suggests the protonation of the cytosine N-3 resulting in an anti parallel orientation in syn conformation and forming two bonds with guanine base [31].…”

Molecular aspects on the interaction of protoberberine, benzophenanthridine, and aristolochia group of alkaloids with nucleic acid structures and biological perspectives

“…[48][49][50][51][52][53][54][55][56][57][58] In natural DNA, protonation was suggested to induce some non-specific conformational change that eventually led to acid denaturation. 50 Guscshlbauer et al 48,49 proposed the first protonation sites to be the N7 of guanines in DNA from absorption spectroscopic and circular dichroic studies. A subsequent Raman spectroscopic study on calf thymus DNA, on the otherhand, proposed the first protonation sites in DNA to be adenines and cytosines suggesting the formation of a C-type conformation.…”