Theoretical studies focusing on the nature of landscapes that correlate molecular sequences to molecular function have mainly been carried out in silico due to the vast amounts of data that are needed for analysis. In vitro selections of aptamers are a good model system to study theoretical questions at a experimental level. With the introduction of robotic platforms that conduct in vitro selections, it is now capable of producing significant amounts of data in a short time, making theoretical modeling with real experimental data attainable. I will be using a Biomek 2000 Laboratory Automation Workstation to carry out multiple in vitro nucleic acid selections in parallel. I will explore the sequence space to examine whether existing in vitro selection systems are optimal at isolating the best winning species. New methods will be introduced that will allow for the selection of identical targets with identical pools free of cross contamination on the open robotic system. This will open the doors to further conduct selections against other identical or highly similar targets, such as complex cellular targets. Finally, I will investigate the methods to improve the effectiveness at isolating aptamers against the highly complex lung cancer cell lines. These targets are highly challenging for isolating specific aptamers because of the great diversity of biomarkers found among them. Moreover, their highly morphological similarity of the cultured cells makes selections for specific aptamers very difficult. I explore the different methods that will allow for the generation of aptamers that can distinguish between non-small cell lung cancer and small cell lung cancer, and between non-small cell lung cancer and normal lung cells. Fine-tuning of this process is essential at transferring this process to automated platforms for large-scale generation of biosensors against tumor biomarkers.

Nucleic acids and proteins, some of the building blocks of life, are not static structures but highly dynamic entities that need to interact with one another to meet cellular demands. The work presented in this thesis focuses on the application of highly sensitive fluorescence methods, both at ensemble and single-molecule level, to determine the dynamics and structure of specific biomolecular interactions with nanometer resolution and in temporal scales from nanoseconds to minutes, which includes most biologically relevant processes. The main aims of my PhD can be classified in three areas: i) exploring new fluorescent sensors with increased specificity for certain nucleic acid structures; ii) understanding how some of these nucleic acids sense the presence of small molecules in the cellular environment and trigger gene regulation by altering their structure; and iii) understanding how certain molecular machines, such as helicase proteins, are able to unwind the DNA double helix by using chemical energy in the form of ATP hydrolysis.

The theoretical part assembles methodological starting points for the research - the content and meaning of curricula documents for science education; the contemporary scientific knowledge about selected molecularly biological topics taught at secondary schools; the characteristics of student preconceptions and misconceptions, their diagnosis and importance. The practical part contains the setting of research problems and aims related to their object, presented as the content analysis of curriculum and the teaching methods concerning molecularly biological topics at a selected secondary school; the diagnosis of preconceptions regarding the term "nucleic acids" with pupils (first, third and fourth grade) studying at a selected secondary school (ninety- five respondents) that served to the determination of overall character of stated preconception (genesis, modification and conceptual change during the study at a secondary school). The incorporation of new laboratory exercises with the topic of nucleic acids to the education in the fourth grade and the assessment of their impact on the shape of the preconception has been also the part of the project. The evaluation was done by comparing of success in solving the tasks involved in the didactic test for pupils in the first and third grade and pupils...