Abstract
Raman titration experiment with magnesium salt added gradually to aqueous solution of duplexes formed by RNA homopolynucleotides polyU and polyA was performed to reveal its effect on homopolynucleotide complexes. Statistical analysis of obtained spectral set has confirmed the effect already found by less structurally sensitive methods [Nucleic Acids Res.31(17) (2003), 5101–5107] that at sufficiently high concentrations magnesium causes transformation of polyU·polyA duplexes to polyU·polyA·polyU triplexes and single polyA strands. It was found that at relatively high polynucleotide concentrations used in Raman experiment, the threshold magnesium concentration for this effect is above the concentration of duplex basepairs in solution. Due to the strong spectral changes attributed to the varied percentages of duplexes, triplexes and single strands, it was not possible to register weaker direct Raman signs of the magnesium binding to polynucleotide strand.
Highlights
Nucleic acids (NA) are negatively charged poly-ions, which need extra-molecular positive charges in order to fold in different compact structures and to carry out their functions [2]
It was demonstrated by using UV spectroscopy, isothermal titration calorimetry, ultrasound velocimetry and densimetry that increased magnesium concentration in a mixed solution of polyuridylic acid (polyU) and polyadenylic acid (polyA) in 1:1 stoichiometric ratio can lead to decrease of duplexes concentration and at the same time appearance of triplexes
The singular value decomposition (SVD) analysis of magnesium titration data has shown that the factor dimension of the spectral set is only two
Summary
Nucleic acids (NA) are negatively charged poly-ions, which need extra-molecular positive charges in order to fold in different compact structures and to carry out their functions [2]. Magnesium is known as an alkaline earth metal playing an important role in stabilization of biomolecular structures including nucleic acids. It is the divalent ion with the highest intracellular concentration (concentration of free Mg2+ ions is approximately 1 mM) and is present in all DNA and RNA activation processes [1]. A few years ago Kankia published a complex study of magnesium effect on polyU·polyA duplexes [6] It was demonstrated by using UV spectroscopy, isothermal titration calorimetry, ultrasound velocimetry and densimetry that increased magnesium concentration in a mixed solution of polyU and polyA in 1:1 stoichiometric ratio can lead to decrease of duplexes concentration and at the same time appearance of triplexes. Our work represents results of Raman measurements on the mixed polyU·polyA 1:1 solvent with gradually increased magnesium concentration and analysis of the spectral set
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