Publications, Grants, & Presentations

Publications at Mt. Holyoke

*undergraduate authors

10. Crenshaw, C.M., Wade, J.E.*, Arthanari, H., Frueh, D., Lane, B.F.,Núñez, M.E. (2011) Hidden in Plain Sight: Subtle Effects of the 8-Oxoguanine Lesion on the Structure, Dynamics, and Thermodynamics of a 15-Base Pair Oligodeoxynucleotide Duplex, Biochemistry 50, 8463-8477.

9. Rumora, A.E.*, Kolodziejczak, K.M.*, Malhowski Wagner, A.M.*,Núñez, M.E. (2008) Thymine Dimer-Induced Structural Changes to the DNA Duplex Examined with Reactive Probes, Biochemistry 47, 13026-13035.

8. Volle, C.B.*, Ferguson, M.A., Aidala, K.E., Spain, E.M., Núñez, M.E.(2008) Spring Constants and Adhesive Properties of Native Bacterial Biofilm Cells Measured by Atomic Force Microscopy. Coll. Surf. B: Biointerfaces 67,32-40.

7. Volle, C.B.*, Ferguson, M.A., Aidala, K.E., Spain, E.M., Núñez, M.E.(2008) Quantitative Changes in the Elasticity and Adhesive Properties of E. coli ZK1056 Prey Cells During Predation by Bdellovibrio bacteriovorus 109J.Langmuir 24, 8102-8110.

6. Ferguson, M.A., Schmitt, J.*, Sindhurakar, A.R.*, Volle, C.B.*, Núñez, M.E, Spain, E. M. (2008) Rapid Isolation of Host-Independent Bdellovibrio bacteriovorus. J. Microbiol. Meth. 73, 279-281.

5. Vladescu, I.D., McCauley, M.J., Núñez, M.E., Rouzina, I., Williams, M.C. (2007) Quantifying Force-Dependent and Zero-Force DNA Intercalation by Single-Molecule Stretching. Nature Meth. 4, 517-522 .

4. Núñez, M.E., Spain, E.M. (2006) Investigating a Bacterial Killer Using Atomic Force Microscopy. Microbiol. Today 33, 100-103.

3. Mihailovic, A.*, Vladescu, I., McCauley, M., Ly, E.*, Williams, M.C., Spain, E.M., Núñez, M.E.(2006) Exploring the Interaction of Ruthenium(II) Polypyridyl Complexes with DNA Using Single-Molecule Techniques.Langmuir 22, 4699-4709.

2. Núñez, M.E., Martin, M.O., Chan, P.H.*, Spain, E.M. (2005) Predation, Death, and Survival in a Biofilm: Investigating Bdellovibrio by Atomic Force Microscopy. Coll. Surf. B: Biointerfaces 42, 263-271.

1. Núñez, M.E., Martin, M.O., Chan, P. H.*, Duong, L.K.*, Sindhurakar, A.R.*, Spain, E.M. (2005) Atomic Force Microscopy of Bacterial Communities. Meth. Enzymol. 397, 256-268.

Prior Publications

12. Núñez, M.E., Martin, M.O., Duong, L.K.*, Ly, E.*, Spain, E.M. (2003) Investigations into the Life Cycle of the Bacterial Predator Bdellovibrio bacteriovorus 109J at an Interface by Atomic Force Microscopy. Biophys. J. 84, 3379-3388.

11. Núñez, M.E., Noyes, K.T.*, Barton, J. K. (2002) Oxidative Charge Transport in Nucleosome Core Particles. Chem. & Biol. 9, 403-415

10. Núñez, M. E., Holmquist, G.P., Barton, J. K. (2001) Evidence for Charge Transport in the Nucleus. Biochemistry 40, 12465-12471.

9. Núñez, M.E., Noyes, K.T.*, Gianolio, D., McLaughlin, L.W., Barton, J.K. (2000) Long-Range Guanine Oxidation in DNA Restriction Fragments by a Triplex-Directed Naphthalene Diimide Intercalator. Biochemistry 39, 6190-6199.

8. Núñez, M. E., Barton, J.K. (2000) Probing DNA Charge Transport with Metallointercalators. Curr. Op. Chem. Biol. 4, 199-206.

7. Núñez, M.E., Rajski, S.R., Barton, J.K. (2000). Damage to DNA by Long-Range Charge Transport. Meth. Enzymol. 319, 165-188.

6. Vicic, D.A., Odom, D.T., Núñez, M.E., Gianolio, D., Mc. Laughlin, L.W., Barton, J.K. (2000) Oxidative Repair of a Thymine Dimer in DNA from a Distance by a Covalently Linked Organic Intercalator. J. Am. Chem. Soc 122, 8603-8611.

5. Núñez, M.E., Hall, D.B., Barton, J.K. (1999) Long-Range Oxidative Damage to DNA: Effects of Distance and Sequence. Chem. & Biol. 6, 85-97.

4. Dandliker, P. J., Núñez, M. E., Barton, J. K. (1998) Oxidative Charge Transfer to Repair Thymine Dimers and Damage Guanine Bases in DNA Assemblies Containing Tethered Metallointercalators. Biochemistry 37, 6491-6502.

3. Núñez, M.*, Ferguson, J.E.*, Machecek, D., Jacob, G., Oda, R. P., Lawson, G., Landers, J. (1995) Detection of Hypoglycemic Drugs in Human Urine Using Micellar Electrokinetic Chromatography. Anal. Chem. 67, 3668-3675.

2. Ji, A., Núñez, M.*, Machecek, D., Ferguson, J.*, Iossi, M.*, Kao, P., Landers, J. (1995) Separation of Urinary Estrogens by Micellar Electrokinetic Chromatography. J. Chromatogr. 669, 15-26.

1. Strausbauch, M. A., Xu, S.J., Ferguson, J.E.*, Nuñez, M. E.*, Machecek, D., Lawson, G. M., Wettstein, P.J., Landers, J. (1995) Concentration and Separation of Hypoglycemic Drugs Using Solid-Phase Extraction-Capillary Electrophoresis. J. Chromatogr. 717, 279-291.

Grants, Fellowships, and Awards

Mount Holyoke College Faculty Award for Teaching (2012)

Henry Dreyfus Teacher-Scholar Award (2012)

Co-PI, National Institutes of Health (NCI) AREA program "Effect of the Spiroiminodihydantoin Lesion on DNA Helix Stability and Structure" (2011-2014)

Co-PI, NSF Research at Undergraduate Institutions, "RUI: Surface and Analytical Chemistry to Elucidate Fundamental Biofilm Properties and Mechanisms of Biofilm Control" (2009-2013)

Co-PI, NSF Major Research Instrumentation Grant, "MRI: Acquisition of a 500 MHz NMR Spectrometer" at Smith College (2009-2012)

PI, National Institutes of Health (NIGMS) AREA program "Effect of Base Lesions on the DNA Duplex" (2008-2012). Also awarded an ARRA Supplement (2009-2010).

Co-PI, Howard Hughes Medical Institute, Undergraduate Science Education Award (2008-2011)

Radcliffe Institute Fellow, Radcliffe Institute for Advanced Study at Harvard University (2006-2007)

Co-PI, NSF Research at Undergraduate Institutions, "RUI: Interfacial Chemistry of the Bacterial Predator Bdellovibrio" (2005-2009)

Co-PI, NSF Major Research Instrumentation Grant, "MRI: Acquisition of Genomics Instrumentation at Mount Holyoke College" (2005-2007)

Co-PI, National Science Foundation Nanotechnology in Undergraduate Education, "Integration of Nanotechnology into the Core Chemistry Curriculum at Mount Holyoke College" (2004-2006)

PI, Camille and Henry Dreyfus Faculty Start-up Grant for Undergraduate Institutions "Needle in a Haystack: Removing Base Lesions from DNA" (2003-2008)

Co-PI, National Science Foundation Major Research Instrumentation Grant, "Acquisition of an Atomic Force Microscope at Mount Holyoke College" (2003-2005)

Howard Hughes Predoctoral Fellowship in Biochemistry (1996)

Phi Beta Kappa induction (1996)

Barry M. Goldwater Scholar (1994)

Seminars, Presentations, and Posters

"Effect of Base Lesions on the DNA Duplex" (seminar), Northeastern University, May 17, 2012.

"Effect of Base Lesions on the DNA Duplex" (seminar), Birthday Symposium for Jacqueline Barton, California Institute of Technology, March 30, 2012.

"Effect of Base Lesions on the DNA Duplex" (seminar), Occidental College, March 29, 2012.

"Effect of Base Lesions on the DNA Duplex" (seminar), Brown University, March 6, 2012.

"Biophysical and Biochemical Characterization of Bdellovibrio Predators" (poster), Biophysical Society National Meeting, March 2011.

“Peer Led Undergraduate Mentoring System (PLUMS)" (presentation and workshop), Oberlin College, September 2010.

Co-chair, “Nanoscale Characterization of Microbes” and “Nanoscale Characterization of Cells” sessions, American Chemical Society National Meeting, Boston MA, August 2010.

"Peer-Led Undergraduate Mentoring System (PLUMS)" (presentation and panel discussion), Union College, Consortium on High Achievement and Success, May 22, 2009.

"Exploring Biochemical and Biophysical Complexity of Native Bacterial Biofilms with Atomic Force Microscopy" (seminar), Department of Chemical and Biochemical Engineering, Washington State University, April 22, 2009.

"Physical Properties of Native Biofilm Cells Explored Using Atomic Force Microscopy" (poster), Biophysical Society National Meeting, February 2009.

"Effect of Base Lesions on Duplex DNA" (seminar), Barnard College, April 4, 2008.

"Effect of Base Lesions on the DNA Duplex" (seminar) California Institute of Technology, January 13, 2008.

"Effect of Base Lesions on the DNA Duplex" (seminar) College of the Holy Cross, September 21, 2007.

"Effect of Base Lesions on Duplex DNA" (poster), American Chemical Society National Meeting, August 2007.

"Effect of Base Lesions on Duplex DNA," (poster), 15th Annual Conversation on Biomolecular Structure and Dynamics, SUNY Albany, NY, June 2007.

"Needle in a Haystack: Removing Base Lesions from DNA," (seminar) Radcliffe Institute for Advanced Study, Harvard University, March 2007.

"Life at the Nanoscale: Applications of Atomic Force Microscopy to Biological Systems" (seminar) Wellesley College, June 22, 2005.

"Interaction of Octahedral Ruthenium Complexes with DNA by Atomic Force Microscopy" (poster) American Chemical Society National Meeting, August 2004.

"Integration of Peer-Led Workshops into the Organic Chemistry Curriculum" (seminar) American Chemical Society National Meeting, August 2004.

"Life at the Nanoscale: Applications of Atomic Force Microscopy to Biological Systems" (seminar) Smith College, November 13, 2003.

"Long-Range Damage to DNA" (poster) Gordon Research Seminar: Eukaryotic DNA Repair, January 2003

"Long-Range Damage to DNA in Nucleosomes" (poster) Gordon Research Seminar: Nucleic Acids, June 2002

" Long-Range Oxidation of Guanine Bases in DNA by Metallointercalators" (seminar) Gordon Graduate Research Seminar: Bioinorganic Chemistry, January 2001

"Long-Range Charge Transport to Oxidize Guanine Bases in DNA" (seminar)HHMI Meeting of Predoctoral and Physician Postdoctoral Fellows, September 2000.

"Charge transport through DNA in biological systems" (seminar) American Chemical Society National Meeting, March 2000.

"Oxidation of Guanine Bases by Photoexcited Rh(III) Intercalators in Cultured Human Cells" (poster) Gordon Graduate Research Seminar: Bioinorganic Chemistry, January 2000.

"Long-Range Oxidation of Guanine Bases in DNA by Metallointercalators" (poster) Gordon Graduate Resarch Seminar: Bioinorganic Chemistry, January 1999

"Long-Range Oxidation of Guanine Doublets by Tethered Rhodium and Ruthenium Intercalators" (poster) Gordon Graduate Research Seminar: Bioinorganic Chemistry, January 1998.

Presentations by Undergraduate Students and Collaborators at National Meetings

Emma Garst:"Using Microfluidics to Explore Chemotaxis by the Predatory Bacterium Bdellovibrio bacteriovorus," poster at the Gordon Research Conference, Applied and Environmental Microbiology, July 2011.

Emma Garst: "Using Microfluidics to Explore Chemotaxis by the Predatory Bacterium Bdellovibrio bacteriovorus," Belinda Wenke: "Kinetic and Thermodynamic Effects of the Thymine Dimer on Duplex DNA," Catherine Dietrich: "Construction and Single-Molecule Characterization of a DNA Hairpin Construct Based on the TAR RNA Sequence" poster prize winner!,posters at the ACS Connecticut Valley Local Section Meeting, April 2011.

Emma Garst: "Using Microfluidics to Explore Chemotaxis by the Predatory Bacterium Bdellovibrio bacteriovorus," Elisa Frankel and Belinda Wenke: "Kinetic and Thermodynamic Effects of the Thymine Dimer on Duplex DNA," Catherine Dietrich "Construction and Single-Molecule Characterization of a DNA Hairpin Construct Based on the TAR RNA Sequence," Anne Murdaugh: "Probing the Interactive Forces between Bacterial Biofilm Cells and Surfaces with AFM, Sara Barnes: "Interaction and Positioning of Nucleosome Core Particles on DNA Containing the Guanine-Derived Oxidative Lesion Spiroiminodihydantoin," posters at the Biophysical Society National Meeting, Baltimore MD, March 2011.

Anne Murdaugh: "Probing the Interaction Forces between Bacterial Biofilms and Surfaces with Atomic Force Microscopy" seminar at the American Chemical Society National Meeting, Boston MA, August 2010.

Anne Murdaugh: "Probing the Mechanical Properties of Bacterial Biofilms and Predators with Atomic Force Microscopy" seminar at the Asylum Research Course, Harvard University, Fall 2011.

Catherine Volle: "Characterization of Lipopolysaccharide Monolayers fromBdellovibrio Predator and E. coli Prey," American Society for Microbiology National Meeting, June 2008.

Catherine Volle: "Characterization of Lipopolysaccharide Monolayers fromBdellovibrio Predator and E. coli Prey by Langmuir-Blodgettry and Atomic Force Microscopy," Biophysical Society National Meeting, February 2008.

Catherine Volle: “How Bdellovibrio Recognizes its Prey: Characterization of Prey and Predator Cell Surface Lipopolysaccharides.” Megan Ferguson: “Structure and Function of a Pigment Produced by Host-IndependentBdellovibrio bacteriovorus," American Chemical Society National Meeting, August 2007.

Megan Ferguson: “Probing Living Escherichia coli Biofilms in Fluid using Quantitative Atomic Force Microscopy Measurements.”  Catherine Volle: “How Bdellovibrio Recognizes its Prey: Characterization of Prey and Predator Cell Surface Lipopolysaccharides.” Megan Ferguson: “Structure and Function of a Pigment Produced by Host-Independent Bdellovibrio bacteriovorus,"American Society for Microbiology National Meeting, May 2007.

Amy Rumora: "Thymine Dimer-Induced Structural Changes to the DNA Base Pair Stack." Jacqueline Wade: "Measuring the Rate of Base Lesion Excision from Supercoiled DNA Substrates by Formamido-pyrimidine Glycosylase."Stephanie Azan: "Characterization of Lipopolysaccharide Monolayers fromBdellovibrio Predator and E.coli Prey by Langmuir-Blodgettry and Atomic Force Microscopy." Catherine Volle: "Characterization of Lipopolysaccharides from Bdellovibrio Predator and E. coli Prey by Chromatographic, Electrophoretic, and Spectroscopic Techniques,"Biophysical Society National Meeting, March 2007.

Dana Vladescu: "Mapping the phase diagram of DNA force-induced melting in the presence of DNA intercalators," Biophysical Society National Meeting, February 2006.

Elaine Ly: "Examination of Groove-Binding and Intercalation into DNA by Atomic Force Microscopy," National Conference on Undergraduate Research, Spring 2005

Elaine Ly: "Examination of Groove-Binding and Intercalation into DNA by Atomic Force Microscopy" "Visualizing Bacterial Predation by Atomic Force Microscopy," Biophysical Society National Meeting, February 2004.

Professional Society Memberships

American Chemical Society

Biophysical Society

Sigma Xi

College Service

Mt. Holyoke

Academic Priorities Committee (2008-2010)

Founder and Coordinator, PLUMS Program, Mount Holyoke College (2004-Present) Created and organized a peer-led workshop and mentoring program for General and Organic Chemistry. Presented our pedagogical developments at the Chemical Education section of the August 2004 ACS National Meeting and the May 2009 meeting of CHAS.

Biochemistry Program Committee member (2003-present)

HHMI Summer Research Program selection committee (Spring 2005, 2006, 2010)

HHMI Science Curriculum Working Group (2004-2006; 2009-2010)

Prehealth Professions Committee member (2007-2012)

Frances Harriet Williams Award selection committee member (2004-2006)

Professional Service and Outreach

Panelist, HHMI Gilliam Graduate Fellows Workshop, Chevy Chase MD (May 2009)

Panelist, National Symposium on the Advancement of Women in Science, Harvard University (Spring 2007)

Invited speaker, Harvard Women in Chemistry (Fall 2006)

Invited speaker, Harvard Women in Physics (Fall 2006)

Panelist, Lyon's Network "Conference on Leadership and Careers,"Mount Holyoke College (Spring 2006)

Panelist, ALANA Science student symposium, Smith College (Spring 2005)

Reviewer Grant reveiwer and panelist for the National Science Foundation. Manuscript reveiwer for the Journal of the American Chemical Society,LangmuirBiochemistryUltramicroscopyMicronMicroscopy and Analysis, and Microbiology.

Chair, Gordon Research Conference: Graduate Seminar in Bioinorganic Chemistry (2000). Also vice-chair (1999) and representative to the GRC (2000).