Publications

Zhao, Y.; Knee, J.L.; Baranger, A.M. "Characterization of Two Adenosine Analogs as Fluorescence Probes in RNA" Bioorg. Chem., accepted for publication.

Anunciado, D.; Agumeh, M.; Kormos, B.L.; Beveridge, D.L.; Knee, J.L.; Baranger, A.M. "Characterization of the Dynamics of an Essential Helix in the U1A Protein by Time-Resolved Fluorescence Measurements", J. Phys. Chem. B., 2008, 112, 6122-6130

Benitex, Y.; Baranger, A.M. "Recognition of Essential Purines by the U1A Protein", BMC Biochemistry, 2007, 8:22

Yan, Z.; Ramisetty, S.R.; Bolton, P.H.; Baranger, A.M. "Selective Recognition of RNA Helices Containing Dangling Ends by a Quinoline Derivative" ChemBioChem, 2007, 8, 1658.

Yan, Z.; Sikri, S.: Beveridge, D.L.; Baranger, A.M. "Identification of an Aminoacridine Derivative that Binds to RNA Tetraloops" J. Med. Chem., 2007, 50, 4096-4104.

Kormos, B.L.; Benitex, Y.; Baranger, A.M.; Beveridge, D.L. "Affinity and Specificity of Protein U1A-RNA Complex Formation Based on an Additive Component Free Energy Model" J. Mol. Biol., 2007, Vol. 371. Issue 5, 1405-1419.

Kormos, B.L; Baranger, A.M.; Beveridge, D.L. "A Study of Collective Atomic Fluctuations and Cooperativity in a U1A-RNA Complex Based on Molecular Dynamics Simulations" J. Struct. Biol., 2007, 157, 500.

Beveridge, D.L.; Dixit, S.B.; Kormos, B.L.; Baranger, A.M.; Jayaram, B.. "Molecular Dynamics Simulations and Free Energy Calculations on Protein-Nucleic Acid Complexes." In Computational Studies of DNA and RNA.Eds., J. Sponer and F. Lankas. Springer: New York. 2006.

Kormos, B.L; Baranger, A.M.; Beveridge, D.L. "Do Collective Atomic fluctuations Account for Cooperative Effects? Molecular Dynamics Studies of the U1A-RNA Complex", J. Am. Chem. Soc. 2006 , 128 , 8992.

Zhao, Y.; Kormos, B.L.; Beveridge, D.L.; Baranger, A.M. "Molecular Dynamics Simulation Studies of a Protein-RNA Complex with a Selectively Modified Binding Interface" Biopolymers , 2006 , 81 , 256.

Yan, Z.; Baranger, A.M. "Binding of an Aminoacridine Derivative to a Tetraloop RNA" Bioorganic and Medicinal Chemistry Letters , 2004 , 14 , 5889.

Zhao, Y.; Baranger, A.M. "Design of an Adenosine Analog that Selectively Improves the Affinity of a Mutant U1A Protein for RNA", J. Am. Chem. Soc. , 2003 , 125 , 2480.

Tuite, J.B.; Shiels, J.C.; Baranger, A.M. "Substitution of an Essential Adenine in the U1A-RNA Complex with a Non-polar Isostere", Nucleic Acids Res. , 2002 , 30 , 5269, cover article.

Gayle, A.Y.; Baranger, A.M. "Inhibition of the U1A-RNA Complex by an Aminoacridine Derivative", Bioorg. Med. Chem. Lett. , 2002 , 12 , 2839-2842.

Pitici, F.; Baranger, A.M., Beveridge, D.L. "Molecular Dynamics Simulation Studies of Induced Fit and Conformational Capture in U1A-RNA Binding: Do Molecular Substates Code for Specificity?", Biopolymers , 2002 , 65 , 424.

Shiels, J.C.; Tuite, J.B.; Nolan, S.J.; Baranger, A.M. "Investigation of a Conserved Stacking Interaction in Target Site Recognition by the U1A Protein", Nucleic Acids Res. , 2002 , 30 , 550-558.

Shiels, J.C.; Jerkovic, B.; Baranger, A.M.; Bolton, P.H. "RNA-DNA Hybrids Containing Damaged DNA are Substrates for RNase H", Bioorg. Med. Chem. Lett. , 2001 , 11 , 2623.

Blakaj, D.M.; McConnell, K.J.; Beveridge, D.L.; Baranger, A.M. "Molecular Dynamics and Thermodynamics of a Protein-RNA Complex: Mutation of a Conserved Aromatic Residue Modifies Stacking Interactions and Structural Adaptation in the U1A-stem Loop 2 RNA Complex" J. Am. Chem. Soc. , 2001 , 123 , 2548.

Luchansky, S.; Nolan, S.J.; Baranger, A.M. "Contribution of RNA Conformation to the Stability of a High-Affinity RNA-Protein Complex", J. Am. Chem. Soc. 2000 , 122 , 7130.

Nolan, S.J.; Shiels, J.C.; Tuite, J.B.; Cecere, K.L.; Baranger, A.M. "Recognition of an Essential Adenine at a Protein-RNA Interface: Comparison of the Contributions of Hydrogen Bonds and a Stacking Interaction", J. Am. Chem. Soc. , 1999 , 121 , 8951.