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

Optimization Of Non-Natural Nucleotides For Selective Incorporation Opposite Damaged Dna, Diana Vineyard, Xuemei Zhang, Alison Donnelley, Irene Lee, Anthony J. Berdis Oct 2007

Optimization Of Non-Natural Nucleotides For Selective Incorporation Opposite Damaged Dna, Diana Vineyard, Xuemei Zhang, Alison Donnelley, Irene Lee, Anthony J. Berdis

Chemistry Faculty Publications

The promutagenic process known as translesion DNA synthesis reflects the ability of a DNA polymerase to misinsert a nucleotide opposite a damaged DNA template. To study the underlying mechanism of nucleotide selection during this process, we quantified the incorporation of various non-natural nucleotide analogs opposite an abasic site, a non-templating DNA lesion. Our kinetic studies using the bacteriophage T4 DNA polymerase reveal that the π-electron surface area of the incoming nucleotide substantially contributes to the efficiency of incorporation opposite an abasic site. A remaining question is whether the selective insertion of these non-hydrogen-bonding analogs can be achieved through optimization of ...


The Use Of Non-Natural Nucleotides To Probe Template-Independent Dna Synthesis, Anthony J. Berdis, David Mccutcheon Aug 2007

The Use Of Non-Natural Nucleotides To Probe Template-Independent Dna Synthesis, Anthony J. Berdis, David Mccutcheon

Chemistry Faculty Publications

The vast majority of DNA polymerases use the complementary templating strand of DNA to guide each nucleotide incorporation. There are instances, however, in which polymerases can efficiently incorporate nucleotides in the absence of templating information. This process, known as translesion DNA synthesis, can alter the proper genetic code of an organism. To further elucidate the mechanism of template-independent DNA synthesis, we monitored the incorporation of various nucleotides at the “blunt-end” of duplex DNA by the high-fidelity bacteriophage T4 DNA polymerase. Although natural nucleotides are not incorporated at the blunt-end, a limited subset of non-natural indolyl analogues containing extensive π-electron surface ...


Curriculum Vitae, Donald Dudley Clarke Phd Jan 2007

Curriculum Vitae, Donald Dudley Clarke Phd

Chemistry Faculty Publications

Curriculum vitae of Donald Clarke, PhD, professor of chemistry at Fordham University, Rose Hill campus


Effect Of N-Halosucinimides On 5-, 7- And 5,7-8-Quinolinol Sulfonic Acids / Herman Gershon, Muriel Gershon, And Donald D. Clark Harding Laboratory, The New York Botanical Garde, Fordham University, Bronx, New York 10458, Usa, Herman Gershon, Muriel Gershon, Donald Dudley Clarke Phd Jan 2007

Effect Of N-Halosucinimides On 5-, 7- And 5,7-8-Quinolinol Sulfonic Acids / Herman Gershon, Muriel Gershon, And Donald D. Clark Harding Laboratory, The New York Botanical Garde, Fordham University, Bronx, New York 10458, Usa, Herman Gershon, Muriel Gershon, Donald Dudley Clarke Phd

Chemistry Faculty Publications

8-Quinolinol 5-, 7- and 5,7-sulfonic acids were treated with N-halosuccinimides (NXS) where the halogen atom was chlorine, bromine or iodine under different conditions of solvent, temperature and time. Under neutral or basic conditions the sulfonic acid group was retained while in dilute acid the S03H group was largely displaced by halogen. Excess NXS caused additional electrophilic substitution. Mild hydrolysis of 5-iodo-8-quinolinol- 7-sulfonic acid and 7-iodo-8-quinolinol-5-sulfonic acid with 15% sulfuric acid in acetic acid formed the 5- and 7-iodo-8-quinolinol respectively in high yield