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Full-Text Articles in Physical Sciences and Mathematics
Application And Development Of Computational Methods In Conformational Studies Of Bio-Molecules, Aleksandra Karolak
Application And Development Of Computational Methods In Conformational Studies Of Bio-Molecules, Aleksandra Karolak
USF Tampa Graduate Theses and Dissertations
The work presented in my dissertation focuses on the conformational studies of bio-molecules including proteins and DNA using computational approaches. Conformational changes are important in numerous molecular bioprocesses such as recognition, transcription, replication and repair, etc. Proteins recognize specific DNA sequences and upon binding undergo partial or complete folding or partial unfolding in order to find the optimal conformational fit between molecules involved in the complex. In addition to sequence specific recognition, proteins are able to distinguish between subtle differences in local geometry and flexibility associated with DNA that may further affect their binding affinities. Experimental techniques provide high-resolution details …
Structural Changes In Dna Upon Binding In A 2:1 Motif To A Polyamide Minor Groove Binder: F -Ipp In 5'-Tagcta-3', Alexandra Kwit
Structural Changes In Dna Upon Binding In A 2:1 Motif To A Polyamide Minor Groove Binder: F -Ipp In 5'-Tagcta-3', Alexandra Kwit
Senior Honors Projects
Polyamide minor groove binders are known to disrupt cellular function when bound to DNA. In this project, the structural changes of the sequence 5'-TAGCTA-3', an important binding site for regulatory proteins in the EGFR pathway, were investigated when bound to f-IPP using molecular dynamics simulations. Changes in base-pair and base-pair-step parameters of slide, twist, and roll varied when f-IPP was added to the 5'-TAGCTA-3' system, causing the DNA backbone to stretch and increase in flexibility. Additionally, changes in dihedral angles of the DNA phosphate backbone upon binding impacted global features of the DNA in that the minor groove narrowed following …
Synthetic Oligodeoxynucleotide Purification Via Catching By Polymerization, Suntara Fueangfung
Synthetic Oligodeoxynucleotide Purification Via Catching By Polymerization, Suntara Fueangfung
Dissertations, Master's Theses and Master's Reports - Open
Large quantities of pure synthetic oligodeoxynucleotides (ODNs) are important for preclinical research, drug development, and biological studies. These ODNs are synthesized on an automated synthesizer. It is inevitable that the crude ODN product contains failure sequences which are not easily removed because they have the same properties as the full length ODNs. Current ODN purification methods such as polyacrylamide gel electrophoresis (PAGE), reversed-phase high performance liquid chromatography (RP HPLC), anion exchange HPLC, and affinity purification can remove those impurities. However, they are not suitable for large scale purification due to the expensive aspects associated with instrumentation, solvent demand, and high …
Dna Aptamers Selected Against Wild-Type Helix 69 Ribosomal Rna And Their Implications In Combating Antibiotic Resistance, Sakina Miriam Hill
Dna Aptamers Selected Against Wild-Type Helix 69 Ribosomal Rna And Their Implications In Combating Antibiotic Resistance, Sakina Miriam Hill
Wayne State University Dissertations
Outbreaks of advanced antibiotic-resistant strains of microbes have hastened the need to identify new viable molecular targets for the development of novel anti-infectives. For this purpose, helix 69 (H69, or m3a 19-nucleotide (nt) hairpin motif that is highly conserved throughout phylogeny and rich in modified nucleotides, including pseudouridine () and 3-methylpseudouridine (m3) was chosen as a potential target. Helix 69, which is located in domain IV of Escherichia coli 23S ribosomal RNA (rRNA), undergoes conformational changes when in close proximity to the decoding region of 16S rRNA and transfer RNAs (tRNAs) in the peptidyl-transferase center (PTC). Functionally, the exact biological …