Mary Hatcher-Skeers

Sidney J. Weinberg, Jr. Chair in Natural Sciences
Professor of Chemistry

Email: mhatcher@kecksci.claremont.edu
Office: Keck Science Center 104C
Phone: 909-607-1586
Office Hours:
Web Site: https://faculty.jsd.claremont.edu/mhatcher

Educational Background

Bachelor of Arts in Biochemistry and Cell Biology
Minor in English Literature
University of California at San Diego, San Diego CA

Master of Science in Chemistry
San Francisco State University, San Francisco CA
Thesis: “Dioxygen Diffusion in the Stratum Corneum”

Doctor of Philosophy in Physical Chemistry
University of Washington, Seattle WA
Dissertation: “A Solid-State Deuterium NMR Investigation of the Local Dynamics of Nucleotides in the EcoRI Restriction Endonuclease Binding Site”

NIH Postdoctoral Associate, Brandeis University, Waltham MA & Massachusetts Institute of Technology, Cambridge, MA

Courses Taught

• Chem 14 & 15: Basic Principles of Chemistry I & II
• Chem 29: Accelerated General Chemistry
• IBC 40: Introductory Biological Chemistry Chem 122:
• Physical Chemistry II – Quantum Mechanics
• Chem 126/127: Advanced Laboratory
• Chem 172: NMR Spectroscopy
• Chem 177: Biochemistry
• Core I: Culture, Knowledge and Representation

Research Interests

• Dynamics of protein-DNA interactions
• Solid-state and Solution NMR spectroscopy
• Effects of DNA Methylation

Thesis Topics

• NMR studies of nucleoside dynamics
• FTIR studies of dynamics in methylated DNA
• High Resolution NMR of DNA Binding Sites
• Solid-state deuterium NMR of DNA
• Effects of cobalt complexes on genetic transformations

Selected Publications

1. Khan, T.R.; Jordan, B.; Levitan, R.; Mitchell, P.S.; Wood, C.; Hatcher, M.E. (2009). An FTIR Investigation of Flanking Sequence Effects on the Structure and Flexibility of DNA Binding Sites. Biochemistry 48: 1315-1321.
2. Tian, Y., Kayatta, M., Shultis, K., Gonzalez, A., Mueller, L.J., and Hatcher, M.E. (2009). 31P NMR Investigation of Backbone Dynamics in DNA Binding Sites. The Journal of Physical Chemistry, B 113: 2596-2603.
3. Leskowitz, G.M.; Ghaderi, N.; Olsen, R.A.; Pederson, K.; Hatcher, M.E.; Mueller, L.J. (2004). The Amide Rotational Barriers in Isonicotinamide: NMR and Ab Initio Studies. Journal of Physical Chemistry 109: 1152-1158.
4. Hatcher-Skeers, M. E. invited book review. (2003). Annual Reports on NMR Spectroscopy, volume 48. J. Amer. Chem. Soc. 125: 6339.
   Abstract – Molecular dynamics (MD) simulations were carried out on the DNA oligonucleotide GGGAACAACTAG:CTAGTTGTTCCC in its native form and with guanine in the central G19:C6 base pair replaced by 8-oxoguanine (8oxoG). A box of explicit water molecules was used for solvation, and Na+ counterions were added to neutralize the system. The direction and magnitude of global bending were assessed by a technique used previously to analyze simulations of DNA containing a thymine dimer. The presence of 8oxoG did not greatly affect the magnitude of DNA bending; however, bending into the major groove was significantly more probable when 8oxoG replaced G19. Crystal structures of glycosylases bound to damaged-DNA substrates consistently show a sharp bend into the major groove at the damage site. We conclude that changes in bending dynamics that assist the formation of this kink are a part of the mechanism by which glycosylases of the base excision repair pathway recognize the presence of 8oxoG in DNA.
   Article – URL not found
5. Olsen, R.; Liu, L.; Ghaderi, N.; Johns, A.; Hatcher, M. E.; and Mueller, L. (2003). The Amide Rotational Barrier in Picolinamide and Nicotinamide: NMR and Ab Initio Studies. J. Amer. Chem. Soc. 125: 10125-10132.
   Abstract – Pyridine carboxamides are a class of medicinal agents with activity that includes the reduction of iron-induced renal damage, the regulation of nicotinamidase activity, and radio- and chemosensitization. Such pharmacological activities, and the prevalence of the carboxamide moiety and the importance of amide rotations in biology, motivate detailed investigation of energetics in these systems. In this study, we report the use of dynamic nuclear magnetic resonance to measure the amide rotational barriers in the pyridine carboxamides picolinamide and nicotinamide. The activation enthalpies and entropies of H = 12.9 ± 0.3 kcal/mol and S = -7.7 ± 0.9 cal/mol K for nicotinamide and H = 18.3 ± 0.4 kcal/mol and S = +1.3 ± 1.0 cal/mol K for picolinamide report a substantial energetic difference for these regioisomers. Ab initio calculations of the rotational barriers are in good agreement with the experimentally determined values and help partition the 5.4 kcal/mol enthalpy difference into its major contributions. Of principal importance are the variations in steric interactions in the ground states of picolinamide and nicotinamide, superior electron donation from the pyridine ring in the transition state of nicotinamide, and an intramolecular hydrogen bond in the ground state of picolinamide.
   Article – URL not found
6. Hatcher, M.E.; Hu, J.G.; Belenky, M.; Verdegem, P.; Lugtenburg, J.; Griffin, R.G.; and Herzfeld, J. (2002). Control of the Pump Cycle in Bacteriorhodopsin: Mechanisms Elucidated by Solid State NMR of the D85N Mutant. Biophysical Journal   82: 1017-1029.
   Abstract – By varying the pH, the D85N mutant of bacteriorhodopsin provides models for several photocycle intermediates of the wild-type protein in which D85 is protonated. At pH 10.8, NMR spectra of [-15N]lys-, [12-13C]retinal-, and [14,15-13C]retinal-labeled D85N samples indicate a deprotonated, 13-cis,15-anti chromophore. On the other hand, at neutral pH, the NMR spectra of D85N show a mixture of protonated Schiff base species similar to that seen in the wild-type protein at low pH, and more complex than the two-state mixture of 13-cis,15-syn, and all-trans isomers found in the dark-adapted wild-type protein. These results lead to several conclusions. First, the reversible titration of order in the D85N chromophore indicates that electrostatic interactions have a major influence on events in the active site. More specifically, whereas a straight chromophore is preferred when the Schiff base and residue 85 are oppositely charged, a bent chromophore is found when both the Schiff base and residue 85 are electrically neutral, even in the dark. Thus a “bent” binding pocket is formed without photoisomerization of the chromophore. On the other hand, when photoisomerization from the straight all-trans,15-anti configuration to the bent 13-cis,15-anti does occur, reciprocal thermodynamic linkage dictates that neutralization of the SB and D85 (by proton transfer from the former to the latter) will result. Second, the similarity between the chromophore chemical shifts in D85N at alkaline pH and those found previously in the Mn intermediate of the wild-type protein indicate that the latter has a thoroughly relaxed chromophore like the subsequent N intermediate. By comparison, indications of L-like distortion are found for the chromophore of the Mo state. Thus, chromophore strain is released in the MoMn transition, probably coincident with, and perhaps instrumental to, the change in the connectivity of the Schiff base from the extracellular side of the membrane to the cytoplasmic side. Because the nitrogen chemical shifts of the Schiff base indicate interaction with a hydrogen-bond donor in both M states, it is possible that a water molecule travels with the Schiff base as it switches connectivity. If so, the protein is acting as an inward-driven hydroxyl pump (analogous to halorhodopsin) rather than an outward-driven proton pump. Third, the presence of a significant C==N syn component in D85N at neutral pH suggests that rapid deprotonation of D85 is necessary at the end of the wild-type photocycle to avoid the generation of nonfunctional C==N syn species.
   Article – URL not found
7. Hatcher, M.E. and Aragon, E.P. (2002). Combining Active Learning with Service Learning: A Student-Driven Demonstration Project. J. Chem. Educ. 79: 462-464.
   Abstract – Chemical demonstrations are used as an active-learning tool in a general chemistry course and as a method of outreach to a local middle school. The demonstrations are planned and prepared by groups of students, who first present them to their classmates and then take them to a middle school to present them to groups of middle school children in an event known as Chemistry Day.
   Article – URL not found
8. Hatcher, M.E., Le Trong, I., Stenkamp, R., and Drobny, G.P. (2001). The Local Dynamics of the CpG Step in a DNA Crystal. J. Amer. Chem. Soc. 123: 8874-8875.
   Article – URL not found
9. Geahigan, K. B., Meints, G. M., Hatcher, M. E., Orban, J. O., and Drobny, G. P. (2000). The Dynamic Impact of CpG Methylation in DNA. Biochemistry 39: 4939-4946.
   Abstract – Solid-state deuterium NMR is used to investigate perturbations of the local, internal dynamics in the EcoRI restriction binding site, -GAATTC- induced by cytidine methylation. Methylation of the cytidine base in this sequence is known to suppress hydrolysis by the EcoRI restriction enzyme. Previous solid-state deuterium NMR studies have detected large amplitude motions of the phosphate-sugar backbone at the AT-CG junction of the unmethylated DNA sequence. This study shows that methylation of the cytidine base in a CpG dinucleotide reduces the amplitudes of motions of the phosphate-sugar backbone. These observations suggest a direct link between suppression of the amplitudes of localized, internal motions of the sugar-phosphate backbone of the DNA and inhibition of restriction enzyme cleavage.
   Article – URL not found
10. Hatcher-Skeers, M. E., (Expert Consultant). (1999). Grolier’s New Book of Popular Science.
11. Hu, J. G., Sun, B. Q., Bizounok, M., Hatcher, M. E., Lansing, J. C., Raap, J., Verdegem, P.J.E., Lugtenburg, J., Griffin, R. G., and Herzfeld, J. (1998). Early and Late Intermediates in the Bacteriorhodopsin Photocycle: A Solid-State NMR Study. Biochem. 37: 8088-8096.
    Abstract – Solid-state deuterium NMR is used to investigate perturbations of the local, internal dynamics in the EcoRI restriction binding site, -GAATTC- induced by cytidine methylation. Methylation of the cytidine base in this sequence is known to suppress hydrolysis by the EcoRI restriction enzyme. Previous solid-state deuterium NMR studies have detected large amplitude motions of the phosphate-sugar backbone at the AT-CG junction of the unmethylated DNA sequence. This study shows that methylation of the cytidine base in a CpG dinucleotide reduces the amplitudes of motions of the phosphate-sugar backbone. These observations suggest a direct link between suppression of the amplitudes of localized, internal motions of the sugar-phosphate backbone of the DNA and inhibition of restriction enzyme cleavage.
    Article – URL not found
12. Hatcher, M.E., Mattiello, D.L., Meints, G. A., Orban, J.O., and Drobny, G.P. (1998). A Solid-State Deuterium NMR Study of the Localized Dynamics at the C9pG10 Step in the DNA Dodecamer [d(CGCGAATTCGCG)]2. J. Amer. Chem. Soc. 120: 9850-9862.
    Abstract – A solid-state deuterium NMR study of localized mobility at the C9pG10 step in the DNA dodecamer [d(CGCGAATTCGCG)]2 is described. In contrast to the results of earlier deuterium NMR studies of furanose ring and backbone dynamics within the d(AATT) moiety, the furanose ring and helix backbone of dC9 display large amplitudes of motion on the 0.1 ms time scale at hydration levels characteristic of the B form structure. Solid-state deuterium NMR line shape data obtained from labeled dC9 DNA are interpreted using a composite motion model, in which the DNA oligomer is treated as rotating as a whole about the helix axis, while the base, furanose ring, and phosphodiester backbone execute localized motions. Consistent with past solid-state NMR studies, the amplitude and rate of the uniform rotation of the dC9-labeled oligomer are found to be sensitive to hydration level. Amplitudes of localized reorientational motions of C-D bonds in the furanose ring and backbone of dC9 are found to be larger than the librational amplitudes for the C-D bonds in the base of dC9, indicating that the pyrimidine base sugar does not move as a rigid entity and intersects a locally flexible region of the phosphodiester backbone. At hydration levels corresponding to 10-12 waters per nucleotide, Zeeman relaxation times for the furanose ring and backbone deuterons of dC9 in B form DNA equal 0.025 and 0.03 ms, respectively, and are the shortest relaxation times observed thus far for any deuteron in the DNA dodecamer at comparable hydration levels. The results of this solid-state NMR study suggest the existence of a significant dynamic component of sequence-specific recognition in this system.
    Article – URL not found
13.  Rienstra, C.M., Hatcher, M.E., Mueller, L.J., Sun, B.Q., Herzfeld, J., and Griffin, R.G. (1998). Efficient Multispin Homonuclear Double Quantum Recoupling for Magic-Angle Spinning NMR: ¹³C-¹³C Correlation Spectroscopy of u-¹³C-Erythromycin A. J. Amer. Chem. Soc. 120: 10602-10612.
    Abstract – We introduce a radio frequency (rf) pulse sequence for efficient homonuclear double-quantum dipolar recoupling under magic-angle spinning NMR. The sequence is optimized for two-dimensional double-quantum 13C-13C chemical shift correlation spectroscopy in multiple spin systems, such as the U-13C-labeled antibiotic erythromycin A. Spin systems such as this display a wide range of isotropic and anisotropic chemical shifts and, therefore, require a broadband dipolar recoupling sequence that minimizes the errors arising from the interaction of chemical shifts and rf inhomogeneity. The sequence should also preserve the theoretical efficiency over the powder average (~73%) provided by the C7 experiment of Levitt and co-workers (Lee, Y. K.; Kurur, N. D.; Helmle, M.; Johannessen, O. G.; Nielsen, N. C.; Levitt, M. H. Chem. Phys. Lett. 1995, 242, 304-309). We satisfy these criteria by combining the standard C7 (2-2+180) elements with -pulse permuted elements (-2+180-, in analogy to the MLEV decoupling scheme) to remove error terms over a ±10% range of rf amplitude. The new sequence, which we refer to as CMR7 (combined MLEV refocusing and C7), yields for two-spin systems broadband double-quantum filtering efficiencies greater than 70%. For multispin systems, the improved polarization transfer efficiency results in greater cross-peak intensities, facilitating assignment of U-13C-labeled molecules in the solid state.
    Article – URL not found
14. Mehta, M.A., Gregory, D.M., S. Kiihne, Mitchell, D.J., Hatcher, M.E., Shiels, J.C., and Drobny, G.P. (1996). Distance Measurements in Nucleic Acids Using Windowless Dipolar Recoupling. Solid State Nuc. Magn. Reson. 7: 221-228.
    Abstract – A windowless, homonuclear dipolar recoupling pulse sequence (DRAWS) is described and a theoretical basis for describing its recoupling performance is developed using numerical techniques. It is demonstrated that DRAWS recouples weak dipolar interactions over a broad range of experimental and molecular conditions. We discuss two spectroscopic control experiments, which help to take into account effects due to insufficient proton decoupling, relaxation, and static dipolar couplings to nearby 13C spins at natural abundance. Finally DRAWS is used in combination with selective 13C labeling to measure 13C—13C distances in five doubly labeled DNA dodecamers, [d(CGCGAAT*T*CGCG)]2, which contain the binding site for the restriction enzyme EcoRI. The longest distance reported is 4.8 Å. In most cases the distances agree well with those derived from X-ray crystallographic data, although small changes in hydration level can result in relatively large changes in internuclear distances.
    Article – URL not found
15. Hatcher, M.E. and Plachy, W.Z. (1993). Dioxygen Diffusion in the Stratum Corneum: An EPR Spin Label Study. Biochem. Biophys. Acta (Jurgen Fuchs and Lester Packer, eds.) Marcel-Dekker, New York 1149: 73-78.
16. Hatcher, M.E. and Plachy, W.Z. . (1993). Solubility – Diffusion of Oxygen in the Skin. Oxidative Stress in Dermatology.