Effect of the length of DNA sequences (G4C2), (G4C2)2 and (G4C2)4 on formation of liquid crystalline phases

V magistrski nalogi obravnavamo vpliv dolžine linearnih agregatov, ki jih tvorijo z gvaninom bogati oligonukleotidi treh različnih DNK zaporedij (G4C2), (G4C2)2 in (G4C2)4 na nastanek tekočekristalnih faz. Omenjena zaporedja imajo sposobnost tvorbe DNK kvadrupleksov in so povezana z nastankom nekaterih nevrodegenerativnih bolezni, kot sta amiotrofična lateralna skleroza in frontotemporalna demenca. Meritve so bile izvedene z eksperimentalnima metodama dinamično sipanje svetlobe in polarizacijska optična mikroskopija. V magistrskem delu predstavimo pripravo vzorcev DNK zaporedij za izvedbo meritev z obema metodama, postavitev eksperimenta in potek meritev. V prvem delu meritev smo z dinamičnim sipanjem merili intenziteto sipane svetlobe v odvisnosti od časa. Opazili smo dva difuzijska načina, hitrega in počasnega. Predpostavljamo, da hitri difuzijski način opisuje dinamiko kvadrupleksnih agregatov in iz izračunanih difuzijskih koeficientov določimo dolžine agregatov posameznih raztopin DNK zaporedij. Difuzijski koeficient za zaporedje (G4C2) je 0,2∙10^(-10) m^2/s, kar pomeni, da zaporedje tvori izjemno dolge agregate, z dolžinami več kot 80 nm. Za zaporedje (G4C2)2 so značilni kratki kvadrupleksi (≈3 nm), saj je difuzijski koeficient bistveno večji in znaša 1,2∙10^(-10) m^2/s. Zaporedje (G4C2)4 tvori srednje dolge agregate, z dolžino približno 10 nm, difuzijski koeficient pa znaša 0,8∙10^(-10) m^2/s. V drugem delu meritev smo se posvetili iskanju ustreznih pogojev za nastanek in opazovanje tekočekristalnih faz zaporedij (G4C2), (G4C2)2 in (G4C2)4. S pomočjo polarizacijske optične mikroskopije smo ugotovili, da vsa tri zaporedja pri dovolj visokih koncentracijah kažejo kromonično tekočekristalno obnašanje z nematsko in kolumnarno heksagonalno fazo. Ugotovili smo, da je za formiranje agregatov in tekočekristalnih faz značilen zapleten strukturni polimorfizem. Kljub podobni kemijski strukturi naših DNK zaporedij smo opazili tvorbo različno dolgih agregatov, kar se opazi tudi pri različnih teksturah nastalih kromoničnih faz.In the master\u27s thesis, we discuss effect of the length of the linear aggregates formed by guanine-rich oligonucleotides of three different DNA sequences (G4C2), (G4C2)2 and (G4C2)4 on the formation of liquid crystalline phases. The mentioned sequences have the ability to form DNA quadruplexes and are associated with the progression of certain neurodegenerative diseases, such as amyotrophic lateral sclerosis and frontotemporal dementia. The measurements were made using the experimental methods of dynamic light scattering and polarization optical microscopy. In the master\u27s thesis, we present the preparation of DNA sequence samples for the measurements of both methods, the experimental setup, and the measurement procedure. In the first part of the measurements, we used dynamic light scattering to measure the intensity of the scattered light as a function of time. We observed two diffusion modes, the fast and the slow. We assume that the fast diffusion mode describes the dynamics of quadruplex aggregates. From the calculated diffusion coefficients, we determine the aggregate lengths of each solution of DNA sequences. The diffusion coefficient of the (G4C2) sequence is 0,2∙10^(-10) m^2/s, which means that the sequence forms extremely long aggregates, with lengths of more than 80 nm. The sequence (G4C2)2 is characterized by short quadruplexes (≈3 nm) since the diffusion coefficient is significantly higher and amounts to 1,2∙10^(-10) m^2/s. The sequence (G4C2)4 forms medium-long aggregates, with a length of about 10 nm, and a diffusion coefficient of 0,8∙10^(-10) m^2/s. In the second part of the measurements, we devoted ourselves to finding suitable conditions for the formation and observation of liquid crystalline phases of the sequences (G4C2), (G4C2)2 and (G4C2)4. Using polarizing optical microscopy, we found that all three sequences at sufficiently high concentrations show chromonic liquid crystal behaviour with nematic and columnar hexagonal phases. We found that the formation of aggregates and liquid crystalline phases is characterized by complex structural polymorphism. Despite the similar chemical structure of the sequences, we observed the formation of aggregates of different lengths, which is also reflected in the different textures of the formed chromonic phases