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134 results on '"Noronha, Anne M."'

1. Structural basis of 3′-end poly(A) RNA recognition by LARP1

Author

Kozlov, Guennadi, primary, Mattijssen, Sandy, additional, Jiang, Jianning, additional, Nyandwi, Samuel, additional, Sprules, Tara, additional, Iben, James R, additional, Coon, Steven L, additional, Gaidamakov, Sergei, additional, Noronha, Anne M, additional, Wilds, Christopher J, additional, Maraia, Richard J, additional, and Gehring, Kalle, additional

Published
2022
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2. Accommodation of mispair aligned N(super 3)T-ethyl-N(super 3)T DNA interstrand cross link

Author

da Silva, Mateus Webba, Wilds, Christopher J., Noronha, Anne M., Colvin, O. Michael, Miller, Paul S., and Gamcsik, Michael P.

Subjects
Biochemistry -- Research, DNA -- Research, Biological sciences, Chemistry
Abstract

The structural properties underpinning the differences in the immediate environment of a N(super 3)T-ethyl-N(super 3)T interstrand cross link that is inserted into a scaffold wherein the cross link is mispair-aligned is described. Results demonstrate that the lesion defined by mismatch-aligned minor groove N(super 3)T-ethyl-N(super 3)T cross-linked thymine bases produces very localized distortions in a DNA stem that may be difficult to recognize by repair mechanisms that are not transcription-or-replication-coupled.

Published
2004

3. Mispair-aligned N(super 3)T-alkyl-N(super 3)T interstrand cross-linked DNA: synthesis and characterization of duplexes with interstrand cross-links of variable lengths

Author

Wilds, Christopher J., Noronha, Anne M., Robidoux, Sebastien, and Miller, Paul S.

Subjects
Nitrogen compounds -- Chemical properties, Nitrogen compounds -- Structure, DNA -- Research, Chemistry
Abstract

A cross-link that bridges the N(super 3) positions of a mismatched thymide base pair is synthesized, as a part of the studies on DNA duplexes that contain alkyl interstrand cross-links. Fully cross-linked duplexes were synthesized using an orthogonal approach to selectively remove protecting groups that allowed construction of the cross-linked duplex via conventional solid-phase oligonucleotide synthesis.

Published
2004

5. Solution structure of a DnA duplex containing mispair-aligned N(sup)4C-Ethyl-N(sup)4C interstrand cross-linked cytosines

Author

da Silva, Mateus Webba, Noronha, Anne M., Noll, David M., Miller, Paul S., Colvin, O. Michael, and Gamcsik, Michael P.

Subjects
DNA, Crosslinked polymers -- Analysis, DNA repair -- Physiological aspects, Structure-activity relationships (Biochemistry), Biological sciences, Chemistry
Abstract

Results show that the cross-link N(sup)4C-Ethyl-N(sup)4C interstrand in the undecamer deoxyoligonucleotide imitates the BCNU-induced G-C cross-link and the C-C cross-link, rendering this DNA duplex recognizable by different DNA repair mechanisms.

Published
2002

6. N(sup)4C-Alkyl-N(sup)4C cross-linked DNA: bending deformations in duplexes that contain a -CNG- interstand cross-link

Author

Noronha, Anne M., Wilds, Christopher J., and Miller, Paul S.

Subjects
DNA -- Analysis, Plasticity -- Analysis, Nucleotide sequence -- Influence, DNA-ligand interactions -- Analysis, Biological sciences, Chemistry
Abstract

Results indicate that bending deformations in the helix involving the -CNG- sequence cross-linked DNA duplexes may be controlled by varying the cross-link length. Data show that the cross-link containing 2,4,or 7 methylene groups joins the C residues of a -CNG- sequence in the DnA duplex.

Published
2002

7. N(sup)4C--ethyl--N(sup)4C cross-linked DNA: synthesis and characterization of duplexes with interstrand cross-links of different orientations

Author

Noronha, Anne M., Noll, David M., Wilds, Christopher J., and Miller, Paul S.

Subjects
DNA, Crosslinked polymers -- Analysis, Hydrogen bonding -- Analysis, Chemical structure -- Analysis, Biological sciences, Chemistry
Abstract

This articles describes the synthesis of N(sup)4C--ethyl--N(sup)4C interstrand cross-linked DNA duplexes employing N(sup)4C--ethyl--N(sup)4C phosphoramidite reagent. The ligated oligomers containing staggered cross-links exhibit differences in structure and stability with -GC- staggered cross-links disrupt hydrogen bonding and affecting helix stability by perturbing adjacent base pairs.

Published
2002

9. Synthesis and biophysical properties of arabinonucleic acids (ANA): circular dichroic spectra, melting temperatures, and ribonuclease H susceptibility of ANA . RNA hybrid duplexes

Author

Noronha, Anne M., Wilds, Christopher J., Lok, Chun-Nam, Viazovkina, Katya, Arion, Dominique, Parniak, Michael A., and Damha, Masad J.

Subjects
Biochemistry -- Research, Biophysics -- Analysis, Acids -- Analysis, Melting points -- Analysis, Ribonuclease -- Research, RNA -- Research, Biological sciences, Chemistry
Abstract

Research has been conducted on the arabinonucleic acid (ANA) which is the 2'-epimer of RNA. The synthesis of the ANA from the arabinonucleoside building blocks is described.

Published
2000

12. Cross-link structure affects replication-independent DNA interstrand cross-link repair in mammalian cells

Author

Hlavin, Erica M., Smeaton, Michael B., Noronha, Anne M., Wilds, Christopher J., and Miller, Paul S.

Subjects
DNA -- Structure, DNA -- Chemical properties, DNA repair -- Analysis, Gene expression -- Analysis, Luciferase -- Chemical properties, Genetic transcription -- Analysis, Biological sciences, Chemistry
Abstract

A study was conducted to understand the cross-link structure of DNA interstrand that affects the repair in nonreplicating reporter plasmids that contain a mispaired [N.sup.4]C-ethyl-[N.sup.4]C (C-C), N3T-ethyl-N3T (T-T), or N1I-ethyl-N3T (I-T) ICL. The insertion of both, C and G residues at the C-C cross-link site without any need for Rev1 for repair indicated that replicative or other translesion polymerases could bypass the C-C remnant.

Published
2010

13. Repair of [O.sup.6]-G-alkyl-[O.sup.6]-G interstand cross-links by human [O.sup.6]-alkylguanine-DNA alkyltransferase

Author

Qingming Fang, Noronha, Anne M., Murphy, Sebastian P., Wilds, Christopher J., Tubbs, Julie L., Tainer, John A., Chowdhury, Gautam, Guengerich, F. Peter, and Pegg, Anthony E.

Subjects
DNA repair -- Research, Oligonucleotides -- Structure, Oligonucleotides -- Chemical properties, Transferases -- Chemical properties, Biological sciences, Chemistry
Abstract

The ability of [O.sup.6]-alkylguanine-DNA alkyltransferase to repair interstrand cross-link DNA damage is investigated. The butane cross-links present in the oligodeoxiribonucleotides of DNA are found to hinder the repair mechanism.

Published
2008

14. Distortion-dependent unhooking of interstrand cross-links in mammalian cell extracts

Author

Smeaton, Michael B., Hlavin, Erica M., Mason, Tracey McGregor, Noronha, Anne M., Wilds, Christropher J., and Miller, Paul S.

Subjects
DNA replication -- Research, Proteins -- Crosslinking, Proteins -- Research, Cell research, Biological sciences, Chemistry
Abstract

Interstrand cross-linked (ICL) linear DNA duplexes are used to examine cross-link processing in mammalian whole-cell extracts. The results have shown that in DNA not undergoing transcription or replication, distortions induced by the presence of an ICL has contributed to initial cross-link recognition and processing.

Published
2008

15. Structure, flexibility, and repair of two different orientations of the same alkyl interstrand DNA cross-links

Author

Noll, David M., Silva, Mateus Webba da, Noronha, Anne M., Wilds, Christopher J., Colvin, O. Michael, Miller, Paul S., and Gamesik, Michael P.

Subjects
Atomic force microscopy -- Analysis, Molecular dynamics -- Analysis, DNA -- Structure, DNA -- Research, Biological sciences, Chemistry
Abstract

A study characterizes the repair, structure, and flexibility of DNA that contains N4C-ethyl-N4C interstand DNA cross-link in two different orientations. A combination of (super 1)H nuclear magnetic resonance (NMR), restrained molecular dynamics simulations, and atomic force microscopy (AFM) was used to examine the structure and flexibility of DNA containing these cross-links.

Published
2005

18. Altering Residue 134 Confers an Increased Substrate Range of Alkylated Nucleosides to the E. coli OGT Protein.

Author

Schoonhoven, Nadia M., O'Flaherty, Derek K., McManus, Francis P., Sacre, Lauralicia, Noronha, Anne M., Kornblatt, M. Judith, and Wilds, Christopher J.

Subjects
MUTAGENS, GUANINE, BASE pairs, THYMINE, OLIGONUCLEOTIDES
Abstract

O6-Alkylguanine-DNA alkyltransferases (AGTs) are proteins responsible for the removal of mutagenic alkyl adducts at the O6-atom of guanine and O4-atom of thymine. In the current study we set out to understand the role of the Ser134 residue in the Escherichia coli AGT variant OGT on substrate discrimination. The S134P mutation in OGT increased the ability of the protein to repair both O6-adducts of guanine and O4-adducts of thymine. However, the S134P variant was unable, like wild-type OGT, to repair an interstrand cross-link (ICL) bridging two O6-atoms of guanine in a DNA duplex. When compared to the human AGT protein (hAGT), the S134P OGT variant displayed reduced activity towards O6-alkylation but a much broader substrate range for O4-alkylation damage reversal. The role of residue 134 in OGT is similar to its function in the human homolog, where Pro140 is crucial in conferring on hAGT the capability to repair large adducts at the O6-position of guanine. Finally, a method to generate a covalent conjugate between hAGT and a model nucleoside using a single-stranded oligonucleotide substrate is demonstrated. [ABSTRACT FROM AUTHOR]

Published
2017
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20. Synthesis and Characterization of Oligonucleotides Containing an O6-2′-Deoxyguanosine-Alkyl-O6-2′-Deoxyguanosine Interstrand Cross-Link in a 5′-GNC Motif and Repair by Human O6-Alkylguanine-DNA Alkyltransferase

Author

McManus, Francis P., Fang, Qingming, Booth, Jason D. M., Noronha, Anne M., Pegg, Anthony E., and Wilds, Christopher J.

Subjects
Alkylating Agents, DNA Repair, Cell Survival, Deoxyguanosine, CHO Cells, DNA, Nucleic Acid Denaturation, Article, O(6)-Methylguanine-DNA Methyltransferase, Cricetulus, Cricetinae, Mutation, Animals, Humans, Sulfonic Acids, Busulfan
Abstract

O(6)-2'-Deoxyguanosine-alkyl-O(6)-2'-deoxyguanosine interstrand DNA cross-links (ICLs) with a four and seven methylene linkage in a 5'-GNC- motif have been synthesized and their repair by human O6-alkylguanine-DNA alkyltransferase (hAGT) investigated. Duplexes containing 11 base-pairs with the ICLs in the center were assembled by automated DNA solid-phase synthesis using a cross-linked 2'-deoxyguanosine dimer phosphoramidite, prepared via a seven step synthesis which employed the Mitsunobu reaction to introduce the alkyl lesion at the O(6) atom of guanine. Introduction of the four and seven carbon ICLs resulted in no change in duplex stability based on UV thermal denaturation experiments compared to a non-cross-linked control. Circular dichroism spectra of these ICL duplexes exhibited features of a B-form duplex, similar to the control, suggesting that these lesions induce little overall change in structure. The efficiency of repair by hAGT was examined and it was shown that hAGT repairs both ICL containing duplexes, with the heptyl ICL repaired more efficiently relative to the butyl cross-link. These results were reproducible with various hAGT mutants including one that contains a novel V148L mutation. The ICL duplexes displayed similar binding affinities to a C145S hAGT mutant compared to the unmodified duplex with the seven carbon containing ICLs displaying slightly higher binding. Experiments with CHO cells to investigate the sensitivity of these cells to busulfan and hepsulfam demonstrate that hAGT reduces the cytotoxicity of hepsulfam suggesting that the O(6)-2'-deoxyguanosine-alkyl-O(6)-2'-deoxyguanosine interstrand DNA cross-link may account for at least part of the cytotoxicity of this agent.

Published
2010

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