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Biochemistry, Biophysics, and Structural Biology Commons

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Molecular Biology

Honors Theses

DNA polymerases

Publication Year

Articles 1 - 2 of 2

Full-Text Articles in Biochemistry, Biophysics, and Structural Biology

The Inner Workings Of The Dna Copying Nanomachine : Kinetic Studies Of Dna Polymerase I From The Thermophilic Bacterium Rhodothermus Marinus, Emily P. Kornberg Apr 2013

The Inner Workings Of The Dna Copying Nanomachine : Kinetic Studies Of Dna Polymerase I From The Thermophilic Bacterium Rhodothermus Marinus, Emily P. Kornberg

Honors Theses

DNA polymerase I from Rhodothermus marinus is a high-fidelity DNA polymerase capable of operating at high temperatures and incorporating 2´,3´-dideoxynucleotides. The R. marinus DNA Polymerase I active site contains an unusual proline in the middle of a mobile “O helix.” This proline residue is hypothesized to decrease the relative free energy of a kinetic checkpoint termed the ajar conformation, and thereby slow the incorporation of incorrect nucleotides. We aim to test the accuracy of a newly developed nucleotide incorporation model, in which the enzyme allows the template to interact with the bound dNTP in the ajar conformation, whether ...


Determination Of The Atomic Resolution Structure Of A Dna Polymerase I Isolated From Rhodothermus Marinus, Natalie S. Omattage Apr 2012

Determination Of The Atomic Resolution Structure Of A Dna Polymerase I Isolated From Rhodothermus Marinus, Natalie S. Omattage

Honors Theses

DNA polymerase I employs a multistep mechanism for sorting correctly paired nucleotides from mismatches. We aim to characterize reaction intermediates during nucleotide selection to better understand how this class of enzymes achieves high DNA replication fidelity. DNA polymerase I from R. marinus contains an unusual and disruptive proline in the mobile O helix near the active site. To characterize this enzyme, the structure of the large (5´-to-3´ exo-deficient) fragment of the R. marinus DNA polymerase I (RF) was solved to 2.95 Å (R = 0.234) using multi-wavelength anomalous dispersion. Alignment with ...