Nucleic acids are biomolecules found in all living things in great abundance and are most commonly found in cells. The two principal nucleic acids are DNA and RNA. DNA’s primary function is to encode genetic information for amino acid sequences that make up proteins that are important in cell functions. RNA has various roles that include regulation and expression of genes.

MicroRNAs (miRNAs) are small RNAs, which range between 20 to 25 nucleotides, that bind to mRNA targets and regulate their translation. Circulating miRNAs are bound to various carriers, including nucleoprotein complexes, lipoproteins, exosomes and microvesicles. The carriers protect the miRNAs from degradation and are able to provide transportation to malignant cells where miRNAs may contribute to tumor progression and metastasis. Functional study of miRNAs and exploration of their utility as disease markers require miRNA extraction from biological samples, which contain large amounts of interfering compounds for downstream RNA identification and quantification.

Aptamers are short, single stranded oligonucleotides, usually around 30 to 50 nucleotides in length that bind to their targets with high affinity and specificity and are comparable to antibodies. Aptamers are discovered through a process known as systematic evolution of ligands by exponential enrichment (SELEX) and necessitates recovery of the ssDNA. An efficient recovery of ssDNA aptamers in SELEX is required to develop high affinity DNA aptamers capable of selectively binding a target molecule.

The most common extraction methods employ either silica columns or TRIzol reagent, but these approaches afford low recovery for small RNAs, possibly due to their short strand lengths. We fabricated the titanium dioxide nanofibers using electrospinning to facilitate DNA and miRNA extraction and developed the optimal buffer conditions to improve DNA and miRNA recovery from biological buffers, cell lysate, and serum. Improving the recovery of nucleic acids (NA) could result from the strong coordination between TiO2 and NA’s phosphate backbone. Our results demonstrated that TiO2 nanofibers can work as a valuable tool for extraction of NA from complex biological matrices with high recovery.

Simple cells in the primary visual cortex of all mammals are renown for having an ‘orientation preference’, meaning that they respond to a specific orientation of an elongated stimulus that lands on their spatial receptive field. Moreover, these cells respond to increments and decrements in luminance in slightly separate regions of their receptive fields, and the angle formed by the centers of these regions can predict their preferred orientation. Despite decades of research into the topic, the mechanism that gives rise to tuned simple cells and their receptive field structure remains an open question. Many models struggle to explain why the properties of simple cells are similar across mammals despite substantial inter-species differences in how simple cells are spatially organized across the cortex. For instance, in the primary visual cortex of cats and primates, vertical columns of cells have similar orientation preferences, and the preferences of these columns rotates smoothly, in a quasiperiodic fashion, as one moves horizontally across the cortex. In contrast, simple cells in mouse primary visual cortex with different tuning preferences are scattered randomly throughout the cortical tissue. Here I assess a mechanistic model of tuning asserting that a single mechanism can generate tuned cells that are either mapped out in an orderly manner across the cortex or arranged in a salt and pepper fashion. The two projects carried out in this thesis test a specific prediction made by the model and compare it to physiological data in mouse primary visual cortex and the thalamic afferents that innervate the cortex. Overall, the results corroborate the model and lend support to the notion that a universal, cross-species mechanism may be used to encode the orientation of a visual stimulus.

DNA methyltransferases (DNMTs) are enzymes responsible for establishing and maintaining DNA methylation in cells. DNMT inhibition is actively pursued in cancer treatment, dominantly through the formation of irreversible covalent complexes between small molecular compounds and DNMTs that suffers from low efficacy and high cytotoxicity, as well as no selectivity towards different DNMTs. Herein, we discover aptamers against the maintenance DNA methyltransferase, DNMT1, by coupling Asymmetrical Flow Field-Flow Fractionation (AF4) with Systematic Evolution of Ligands by EXponential enrichment (SELEX). One of the identified aptamers, Apt. #9, contains a stem-loop structure, and can displace the hemi-methylated DNA duplex, the native substrate of DNMT1, off the protein on sub-micromolar scale, leading for effective enzymatic inhibition. Apt. #9 shows no inhibition nor binding activity towards two de novo DNMTs, DNMT3A and DNMT3B. Intriguingly, it can enter cancer cells with over-expression of DNMT1, colocalize with DNMT1 inside the nuclei, and inhibit the activity of DNMT1 in cells. This study opens the possibility of exploring the aptameric DNMT inhibitors being a new cancer therapeutic approach, by modulating DNMT activity selectively through reversible interaction. The aptamers could also be valuable tools for study of the functions of DNMTs and the related epigenetic mechanisms.