Giedroc Group

Publications

Ribosomal Frameshifting

Frameshifting RNA pseudoknots: Structure and mechanism

Giedroc, D. P., & Cornish, P. V. (2008)
Vir. Res. Special Issue: Structural Motifs in RNA Viruses, in press (invited contribution)
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Simulating RNA folding kinetics on approximated energy landscapes

Tang, X., Thomas, S., Tapia, L., Giedroc, D. P., & Amato, N. M. (2008)
J. Mol. Biol., in the press
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Metal ions and the thermodynamics of RNA folding, In Metal Ion Interactions with Nucleic Acids (Hud, N., ed.).

Giedroc, D. P., & Grossoehme, N. E. (2008)
Royal Society of Chemistry (RSC) Publishing, Cambridge, UK, in press (invited monograph).
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The global structures of a wild-type and poorly functional plant luteoviral mRNA pseudoknot are essentially identical

Cornish, P. V., Stammler, S. N. & Giedroc, D. P. (2006)
RNA 12, 1959-1969.
View: PubMed

Pairwise coupling analysis of helical junction hydrogen bonding interactions in luteoviral RNA pseudoknots

Cornish, P. V. & Giedroc, D. P. (2006)
Biochemistry 45, 11162-11171.
View: PubMed

Dissecting non-canonical interactions in frameshift-stimulating mRNA pseudoknots

Cornish, P. V., Giedroc, D. P. & Hennig, M. (2006)
J. Biomol. NMR 35, 209-223.
View: PubMed

A Loop 2 Cytidine-Stem 1 Minor Groove Interaction as a Positive Determinant for Pseudoknot-Stimulated -1 Ribosomal Frameshifting.

Cornish, P.V., Hennig, M., & Giedroc, D. P. (2005)
Proc. Natl. Acad. Sci. USA 102, 12694-12699.
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Detection of Scalar Couplings Involving 2’-Hydroxyl Protons Across Hydrogen Bonds in a Frameshifting mRNA Pseudoknot.

Giedroc, D. P., Cornish, P. V., & Hennig, M. A. (2003)
J. Am. Chem. Soc 125, 4676-4677.
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Solution Structure of a Luteoviral P1-P2 Frameshifting mRNA Pseudoknot.

Nixon, P.L., Rangan, A., Kim, Y.-G., Rich, A., Hoffman, D. W., Hennig, M., & Giedroc, D.P. (2002)
J. Mol. Biol. 322, 621-633.
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Thermodynamic Analysis of Conserved Loop-Stem Interactions in P1-P2 Frameshifting mRNA Pseudoknots from Plant Luteoviridae.

Nixon, P.L., Cornish, P.V., Suram, S.V., & Giedroc, D.P. (2002)
Biochemistry 41, 10665-10674.
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Structure, Stability and Function of RNA Pseudoknots Involved in Ribosomal Frameshifting.

Giedroc, D.P., Theimer, C.A., & Nixon, P.L. (2000)
J. Mol. Biol. 298, 167-185 (invited review).
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Energetics of a Strongly pH Dependent RNA Tertiary Structure in a Frameshifting Pseudoknot.

Nixon, P.L., & Giedroc, D.P. (2000)
J. Mol. Biol. 296, 659-671.
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Contribution of the Intercalated Adenosine at the Helical Junction to the Stability of the gag-pro Frameshifting Pseudoknot from Mouse Mammary Tumor Virus.

Theimer, C.A. & Giedroc, D.P. (2000)
RNA 6, 409-421.
View: PubMed

Equilibrium Unfolding Pathway of an H-type RNA Pseudoknot which Promotes Programmed –1 Ribosomal Frameshifting.

Theimer, C.A. & Giedroc, D.P. (1999)
J. Mol. Biol. 289, 1283-1299.
View: PubMed

Thermodynamics of Stabilization of RNA Pseudoknots by Cobalt(III) Hexammine.

Nixon, P.L., Theimer, C.A., & Giedroc, D.P. (1999)
Biopolymers 50, 443-458.
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Equilibrium Unfolding (Folding) Pathway of a Model H-type Pseudoknotted RNA: The Role of Magnesium Binding in Stability.

Nixon, P.L., & Giedroc, D.P. (1998)
Biochemistry 37, 16116-16129.
View: PubMed

Non-Nearest Neighbor Effects on the Thermodynamics of Unfolding of a Model mRNA Pseudoknot.

Theimer, C.A., Wang, Y., Hoffman, D.W., Krisch, H.M., & Giedroc, D.P. (1998)
J. Mol. Biol. 279, 545-564.
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Base Pairings Within the RNA Pseudoknot Associated with the Simian Retrovirus-1 gag-pro Frameshift Site.

Du, Z., Holland, J.A., Hansen, M. R., Giedroc, D.P., & Hoffman, D.W. (1997)
J. Mol. Biol. 270, 464-470.
View: PubMed

Structure of the Autoregulatory Pseudoknot within the Gene 32 Messenger RNA of Bacteriophages T2 and T6: A Model for a Possible Family of Structurally Related RNA Pseudoknots.

Du, Z., Giedroc, D.P., & Hoffman, D.W. (1996)
Biochemistry 35, 4187-4198.
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Thermodynamics of Folding of the RNA Pseudoknot of the T4 Gene 32 Autoregulatory Messenger RNA.

Qiu, H., Kaluarachchi, K., Du, Z., Hoffman, D.W., & Giedroc, D.P. (1996)
Biochemistry 35, 4176-4186.
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