Assessment of dynamic disorder in DNA oligonucleotides using low-frequency Raman spectroscopy

Abstract

The degree of DNA compaction in various regions of the cell nucleus determines whether the corresponding genes should be expressed, and whether other important cellular processes, such as DNA replication and repair, should take place. However, approaches to the experimental assessment of the compactness of DNA in cell nuclei, as well as its indicator, dynamic disorder — thermal fluctuations in the position and mutual orientation of molecular fragments — are practically not developed. In this paper, using single-stranded oligonucleotides guanine and cytosine, as well as their double-stranded combination as an example, we show that dynamic disorder in DNA can be estimated using low-frequency Raman spectroscopy. For the first time, the Raman spectra of oligonucleotides were measured in a wide range including the low-frequency and high-frequency regions. It was found that the low-frequency Raman intensity is maximal for single-stranded oligocytosine and minimal in double-stranded oligonucleotide, in full agreement with the magnitude of dynamic disorder estimated from the molecular dynamics simulations. The results obtained indicate the prospects of using low-frequency Raman spectroscopy to assess the dynamic disorder and compactness of DNA. It is expected that the use of such a technique should contribute to the understanding of key cellular processes and their underlying physical mechanisms, which is necessary for the development of advanced methods of molecular biophysics and cell biology.