Vibrational dynamics of thin films of salt deoxyribonucleic acid

Abstract

U ovoj doktorskoj disertaciji istraživan je utjecaj natrijevih i magnezijevih iona na strukturu i dinamiku deoksiribonukleinske kiseline (DNA) primjenom infracrvene spektroskopije s Fourierovom transformacijom na tankim filmovima DNA. Tanki filmovi DNA pripravljeni su iz niza otopina stalne koncentracije genomske DNA: Na-DNA (DNA s intrinsičnim kationima natrija) u čistoj vodi, 10 mM natrijevom kloridu i magnezijevom kloridu različitih ionskih jakosti, a Mg-DNA (DNA s intrinsičnim kationima magnezija) u čistoj vodi i magnezijevom kloridu različitih ionskih jakosti. Ovakav izbor uzoraka omogućio je istraživanje utjecaja, s jedne strane koncentracije dodane soli, a s druge strane kompeticije intrinsičnih i dodanih protuiona, na strukturu i konformaciju DNA. Pripravom tankih filmova iz otopina izbjegnut je utjecaj vibracija vode na spektar DNA u području baza. Spektri tankih filmova dobivenih iz Na-DNA u otopini natrijevog klorida te Na-DNA u čistoj vodi pokazali su da je konformacija dvostruke uzvojnice (ds) ostala sačuvana nakon provođenja protokola sušenja pa je za referentni spektar uzet spektar tankog filma dobiven iz čiste vodene otopine Na-DNA. U cilju razumijevanja utjecaja kationa magnezija na strukturu DNA istraživana su vibracijska svojstva tankih filmova Na-DNA u MgCl2 u širokom rasponu omjera koncentracija kationa i fosfata, [Mg]/[P], od 0,0067 do 30. Dobiveni rezultati pokazali su da kationi magnezija već pri niskim koncentracijama ostvaruju interakciju s fosfatnim skupinama, a s daljnjim povećanjem koncentracije i s bazama DNA preko dugodosežnih elektrostatskih sila. Pri najvećim omjerima [Mg]/[P] diskutiran je prijelaz DNA iz konformacije dvostruke uzvojnice u kompaktnu formu na osnovu eksperimentalnih rezultata, ali i teorijski predviđene neutralizacije fosfatnih skupina dobivene Manningovim dvoparametarskim modelom. Istraživana su i vibracijska svojstva tankih filmova Mg-DNA u čistoj vodi i Mg-DNA u MgCl2 u intervalu omjera [Mg]/[P] od 0,0067 do 10 te su rezultati uspoređeni s rezultatima dobivenim za Na-DNA u istom koncentracijskom rasponu. Spektri tankih filmova Mg-DNA u čistoj vodi pokazali su nešto drugačija vibracijska svojstva u odnosu na Na-DNA u čistoj vodi te je uočen znatno veći udio B forme DNA. Pri niskim koncentracijama magnezijevih iona ([Mg]/[P] < 1) spektri tankih filmova Na-DNA u MgCl2 i Mg-DNA u MgCl2 su različiti što se može pripisati utjecaju intrinsičnih natrijevih iona i intrinsičnih magnezijevih iona na DNA. S druge strane, pri višim koncentracijama magnezijevih iona, Na-DNA u MgCl2 i Mg-DNA u MgCl2 pokazuju slična vibracijska svojstva.In this doctoral thesis, the impact of sodium and magnesium ions on the structure and dynamics of deoxyribonucleic acid (DNA) was investigated utilizing Fourier transform infrared spectroscopy on DNA thin films. DNA thin films were obtained from a series of genomic DNA solutions of constant DNA concentration: Na-DNA (DNA with intrinsic sodium counterions) in pure water, 10 mM sodium chloride and magnesium chloride of various ionic strengths, and Mg-DNA (DNA with intrinsic magnesium counterions) in pure water and magnesium chloride of various ionic strengths. Such a choice of samples allowed the research of the effect of the concentration of the added salt as well as of the competition of intrinsic and added counterions on DNA structure and conformation. By preparation of thin films from solutions the influence of vibrational bands of bulk water that would impede the proper detection of DNA vibrational bands in the base region was avoided. Spectra of thin films obtained from Na-DNA in solution of sodium chloride and Na-DNA in pure water have shown that DNA retains its double helical structure (ds) under drying protocol so the spectrum of Na-DNA in pure water was chosen as a reference. In order to address how the behaviour of DNA evolves upon progressive addition of Mg2+ cations, an extensive investigation of infrared vibrational properties of Na-DNA in a broad range of added magnesium chloride salt concentration with cation to phosphate ratio, [Mg]/[P], between 0.0067 and 30 was performed. The obtained results revealed that at low magnesium concentrations the magnesium cations interact with the phosphate groups of the DNA, while with the further increase of magnesium concentration they interact with the base sites as well, via long-range electrostatic interactions. At highest [Mg]/[P] ratios the possibility of structural transition into a more compact form is discussed based on both the experimental results and calculations of DNA charge neutralization by Manning’s two variable condensation theory. The vibrational properties of Mg-DNA in pure water and Mg-DNA in a broad range of added magnesium chloride salt concentrations with cation to phosphate ratio, r=[Mg]/[P], between 0.0067 and 10 were investigated and compared with the results of Na-DNA in the same concentration range. The spectra of thin films Mg-DNA in pure water showed slightly different vibrational properties then Na-DNA in pure water and a significantly higher portion of B form DNA was observed. At low concentrations of magnesium ions (r < 1) spectra of Na-DNA in MgCl2 and Mg-DNA in MgCl2 show substantial differences which were attributed to the influence of the intrinsic sodium and magnesium ions on DNA. On the other hand, Na-DNA in MgCl2 and Mg-DNA in MgCl2 at higher concentrations of magnesium ions show similar vibrational properties