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Nucleic Acid Biophysics
Aromatic Ring Transforms DNA Binding Modes of an Octahedral Ruthenium Complex
Möller, G.B., McCauley, M.J., Price, L.J., Ferris, G.E., Rouzina, I., Núñez, M.E., Williams, M.C.
Biophys. J. 125 (2026) 1623-1636.
https://doi.org/10.1016/j.bpj.2026.02.029
A Method for the Sensitive Detection of Base Pairing and Stacking Energies for Damaged and Noncanonical Sequences from Single Molecule Unfolding Experiments.
McCauley, M.J., Rouzina, I., Núñez, M.E., Williams, M.C.
In: Zuccheri, G., ed. DNA Nanotechnology. Methods in Molecular Biology 2901. (2025) Humana, New York, NY. pp. 251-268.
https://doi.org/10.1007/978-1-0716-4394-5_19
Assessing the Potential for DNA Quadruplex Formation in the Predatory Bacterium Bdellovibrio bacteriovorus.
Tsao, L.H.,* Shepardson-Fungairiño, S.,* Murayama, H.,* Cecere, A.,* Wren, E.,* and Núñez, M.E.
Biochemistry 61, (2022) 2073-2087. (PMCID: PMC9536305) DOI: 10.1021/acs.biochem.2c00443
Significant Differences in RNA Structure Destabilization by HIV-1 GagDp6 and NCp7 Proteins.
McCauley, M., Rouzina, I., Li, J.,* Núñez, M.E., and Williams, M.C.
Viruses 15, (2020) 484-503. (PMCID: PMC7290599) DOI: 10.3390/v12050484
Quantifying the Stability of Oxidatively Damaged DNA by Single-Molecule DNA Stretching.
McCauley, M.J., Furman, L.,* Dietrich, C.A.,* Rouzina, I., Núñez, M.E., Williams, M.C.
Nucleic Acids Research 46 , (2018) 4033-4043. (PMCID: PMC5934642) doi: 10.1093/nar/gky148
Effect of the Spiroiminodihydantoin Lesion on Nucleosome Stability and Positioning.
Norabuena, E.; Barnes Williams, S.; Klureza, M.;* Goehring, L.;* Gruessner, B.; Radhakrishnan, M.; Jamieson, E.R.; Núñez, M.E.
Biochemistry 55, (2016) 2411-2421. (PMCID: PMC6299323)DOI: 10.1021/acs.biochem.6b00093
Base Pair Opening in a Deoxynucleotide Duplex Containing a cis-syn Thymine Cyclobutane Dimer Lesion.
Wenke, B.B.*, Huiting, L.H.*, Frankel, E.B.*, Lane, B.F., Núñez, M.E.
Biochemistry 52, (2013) 9275-9285. (PMCID: PMC3912563) DOI: 10.1021/bi401312r
Hidden in Plain Sight: Subtle Effects of the 8-Oxoguanine Lesion on the Structure, Dynamics, and Thermodynamics of a 15-Base-Pair Oligodeoxynucleotide Duplex.
Crenshaw, C.M., Wade, J.E.*, Arthenari, H., Frueh, D., Lane, B.F., Núñez, M.E.
Biochemistry 50, (2011) 8463-8477. (PMCID: PMC3188433) DOI: 10.1021/bi201007t
Thymine Dimer-Induced Structural Changes to the DNA Duplex Examined with Reactive Probes.
Rumora, A.E.*, Kolodziejczak, K.M.*, Malhowski, A.M.*, Núñez, M.E.
Biochemistry 47, (2008) 13026-13035. (PMCID: PMC2891882) DOI: 10.1021/bi801417u
Thermodynamics of Zero-Force and Force-Dependent DNA Intercalation from Single Molecule Stretching.
Vladescu, I., McCauley, M., Núñez, M.E., Rouzina, I., Williams, M.C.
Nature Meth. 4, (2007) 517-522. (PMID: 17468764) DOI: 10.1038/nmeth1044
Exploring the Interaction of Ruthenium(II) Polypyridyl Complexes with DNA Using Single-Molecule Techniques.
Mihailovic, A.*, Vladescu, I., McCauley, M., Ly, E.*, Williams, M.C., Spain, E.M., Núñez, M.E.
Langmuir 22, (2005) 4699-4709. (PMCID: PMC2519805) DOI: 10.1021/la053242r
Bacterial Biophysics
AFM Force Mapping Elucidates Pilus Deployment and Key Lifestyle-Dependent Surface Properties in Bdellovibrio bacteriovorus.
Volle, C.B., Núñez, M.E, Spain, E.M., Hart, B.C.*, Wengen, M.B.*, Lane, S.*, Criollo, A.*, Mahoney, C.A.*, and Ferguson, M.
Langmuir 39, (2023) 4233-4244. (PMID: 36926913) DOI: 10.1021/acs.langmuir.2c03134
Extracellular Polymeric Substance Protects Some Cells in an Escherichia coli Biofilm from the Biomechanical Consequences of Treatment with Magainin 2.
Greer, H.M.,* Overton, K.,* Ferguson, M.A., Spain, E.M., Darling, L.E.O., Núñez, M.E., and Volle, C.B.
Microorganisms 9, (2021) 976-993. (PMCID: PMC8147140). DOI: 10.3390/microorganisms9050976
Qualitative and Quantitative Changes to Escherichia coli during Treatment with Magainin 2 Observed in Native Conditions by Atomic Force Microscopy.
Overton, K.,* Greer, H.M.,* Ferguson, M.A., Spain, E.M., Elmore, D.E., Núñez, M.E., Volle, C.B.
Langmuir 36, (2020) 650-659. (PMCID: PMC7430157). DOI: 10.1021/acs.langmuir.9b02726
Identification and Differential Production of Ubiquinone-8 in the Bacterial Predator Bdellovibrio bacteriovorus.
Spain, E.M., Núñez, M.E., Kim, H.-J.,* Taylor, R.*; Wengen, M.*, Dalleska, N., Bromley, J.*, Schemerhorn, M.*, Ferguson, M.
Res. Microbiol. 167, (2016) 413-423. (PMID 27106259) DOI: 10.1016/j.resmic.2016.04.003
Spatially Organized Films from Bdellovibrio bacteriovorus Prey Lysates.
Ferguson, M.A., Núñez, M.E., Kim, H.-J.*, Goffredi, S., Shamskhou, E.*, Faudree, L.*, Landry, R.; Ma, A.*, Choi, D.-E.*, Thomas, N.*; Schmitt, J.*, Spain, E.M.
App. Env. Microbiol. 80, (2014) 7405-14 (PMCID: PMC4249199) DOI: 10.1128/AEM.02423-14
Characterizing the Adhesion of Biofilm-Forming E. coli to Surfaces using Atomic Force Microscopy.
Xu, H.*, Murdaugh, A., Chen, W., Aidala, K., Ferguson, M., Spain, E., Núñez, M.E.
Langmuir 29, (2013) 3000-3011. (PMCID: PMC3590879) DOI: 10.1021/la304745s
Quantitative Changes in the Elasticity and Adhesive Properties of E.coli ZK1056 Prey Cells During Predation by Bdellovibrio bacteriovorus 109J.
Volle, C.B.*, Ferguson, M.A., Aidala, K.E., Spain, E.M., Núñez, M.E.
Langmuir 24, (2008) 8102-8110. (PMID: 18572929) DOI: 10.1021/la8009354
Spring Constants and Adhesive Properties of Native Bacterial Biofilm Cells Measured by Atomic Force Microscopy.
Volle, C.B.*, Ferguson, M.A., Aidala, K.E., Spain, E.M., Núñez, M.E.
Coll. Surf. B: Biointerfaces 67, (2008) 32-40. (PMID: 18815013) DOI: 10.1016/j.colsurfb.2008.07.021
Rapid Isolation of Host-Independent Bdellovibrio bacteriovorus.
Ferguson, M.A., Schmitt, J.*, Sindhurakar, A.R.*, Volle, C.B.*, Núñez, M.E., Spain, E. M.
J. Microbiol. Meth. 73, (2008) 279-281. (PMID: 18410974) DOI: 10.1016/j.mimet.2008.02.023
Investigating a Bacterial Killer Using Atomic Force Microscopy.
Núñez, M.E., Spain, E.M.
Atomic Force Microscopy of Bacterial Communities.
Núñez, M.E., Martin, M.O., Chan, P.*, Duong, L. *, Sinhurakar, A.*, Spain, E.M.
Meth. Enzymol. 397, (2005) 256-268. (PMID: 16260296) DOI: 10.1016/S0076-6879(05)97015-8
Predation, Death, and Survival in a Biofilm: Investigating Bdellovibrio by Atomic Force Microscopy.
Núñez, M.E., Martin, M.O., Chan, P.*, Spain, E.M.
Coll. Surf. B: Biointerfaces 42, (2005) 263-271. (PMID: 15893228) DOI: 10.1016/j.colsurfb.2005.03.003
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