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Nucleic Acid Biophysics
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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