Vanderbilt University School of
868A RRB 37232
Macromolecular X-ray Crystallography
Structural Biology of Circadian Clocks, native and
chemically modified nucleic acids, and trans-lesion DNA polymerase-DNA
On-going efforts in my laboratory focus on the following areas. (i) Structure/function analyses of native and chemically modified nucleic acids and etiology of nucleic acid structure. Using chemical synthesis and structure determination at high resolution, the effects of chemical modifications on the structures of DNA and RNA are examined and the results correlated with stability and in vitro and in vivo activity data to direct the design of nucleic acid analogs with improved efficacies for antisense and RNAi applications. We are collaborating with researchers from Alnylam Pharmaceuticals Inc. (Cambridge, MA) and Isis Pharmaceuticals Inc. (Carlsbad, CA) to exploit insights from structural studies for the design of next generation antisense and siRNA therapeutics. (ii) Chemistry and biology of carcinogen-DNA adducts. This program examines relationships between the structure and biological processing of damaged bases by Y-class trans-lesion DNA polymerases (i.e. Dpo4 from Sulfolobus solfataricus and human Pol-iota, Pol-kappa and Pol-eta). Using in vitro primer extension assays in combination with steady state and pre-steady state kinetics as well as mass spectrometry, we are probing the effects on the accuracy of replication of a range of adducts inside the template strand (8-oxo-dG, O6-methyl-dG, N2-methyl-dG, 1,N2-etheno-dG, acrolein, cyclic pyrimidine dimers and others). Crystal structures of binary Pol-DNA and ternary Pol-DNA-dNTP complexes are determined to shed light on the consequences of individual lesions for the accuracy of bypass. (iii) The cyanobacterial KaiABC circadian clock. The circadian clock of Synechococcus elongatus can be reconstituted in vitro with the three proteins KaiA, KaiB and KaiC in the presence of ATP and Mg2+. KaiC is the central cog and exhibits kinase, phosphatase and ATPase activities, KaiA enhances KaiC phosphorylation and KaiB antagonizes KaiA. Remarkably, this post-translational timer exhibits all the hallmarks of circadian clocks - a period of ca. 24 hours, entrainment and temperature compensation - thus permitting its dissection by biochemical and biophysical means. Using a hybrid structural approach including single crystal X-ray crystallography, electron microscopy and small angle X-ray and neutron scattering in combination with functional studies in vitro and in vivo, we are analyzing the protein-protein interactions and mechanistic aspects of this molecular clock.
Pallan, PS, Ittig, D, H??roux, A, Wawrzak, Z, Leumann, CJ, Egli, M. Crystal structure of tricyclo-DNA: an unusual compensatory change of two adjacent backbone torsion angles. Chem Commun (Camb), (7), 883-5, 2008.
Pattanayek, R, Williams, DR, Pattanayek, S, Mori, T, Johnson, CH, Stewart, PL, Egli, M. Structural model of the circadian clock KaiB-KaiC complex and mechanism for modulation of KaiC phosphorylation. EMBO J, 27(12), 1767-78, 2008. PMCID:2435126
Wang, F, Li, F, Ganguly, M, Marky, LA, Gold, B, Egli, M, Stone, MP. A bridging water anchors the tethered 5-(3-aminopropyl)-2''-deoxyuridine amine in the DNA major groove proximate to the N+2 C.G base pair: implications for formation of interstrand 5''-GNC-3'' cross-links by nitrogen mustards. Biochemistry, 47(27), 7147-57, 2008. PMCID:2730145
Wang, Y, Musser, SK, Saleh, S, Marnett, LJ, Egli, M, Stone, MP. Insertion of dNTPs opposite the 1,N2-propanodeoxyguanosine adduct by Sulfolobus solfataricus P2 DNA polymerase IV. Biochemistry, 47(28), 7322-34, 2008. PMCID:2753402
Egli, M, Lubini, P, Pallan, PS. The long and winding road to the structure of homo-DNA. Chem Soc Rev, 36(1), 31-45, 2007.
Egli, M, Pallan, PS. Insights from Crystallographic Studies into the Structural and Pairing Properties
of Nucleic Acid Analogs and Chemically Modified DNA and RNA Oligonucleotides. Annu Rev Biophys Biomol Struct, , , 2007.
Egli, M, Sarkhel, S. Lone pair-aromatic interactions: to stabilize or not to stabilize. Acc Chem Res, 40(3), 197-205, 2007.
Eoff, RL, Angel, KC, Egli, M, Guengerich, FP. Molecular basis of selectivity of nucleoside triphosphate incorporation opposite
O6-benzylguanine by sulfolobus solfataricus DNA polymerase DPO4 steady-state and pre-steady-state kinetics
and X-ray crystallography of correct and incorrect pairing. J Biol Chem, , , 2007.
Eoff, RL, Irimia, A, Angel, KC, Egli, M, Guengerich, FP. Hydrogen bonding of 7,8-dihydro-8-oxodeoxyguanosine with a charged residue in the little finger domain determines miscoding events in Sulfolobus solfataricus DNA polymerase Dpo4. J Biol Chem, 282(27), 19831-43, 2007.
Eoff, RL, Irimia, A, Egli, M, Guengerich, FP. Sulfolobus solfataricus DNA polymerase Dpo4 is partially inhibited by "wobble"
pairing between O6-methylguanine and cytosine, but accurate bypass is preferred. J Biol Chem, 282(2), 1456-67, 2007.
Irimia, A, Eoff, RL, Pallan, PS, Guengerich, FP, Egli, M. Structure and activity of Y-class DNA polymerase DPO4 from Sulfolobus solfataricus with templates containing the hydrophobic thymine analog 2,4-difluorotoluene. J Biol Chem, 282(50), 36421-33, 2007.
Li, F, Pallan, PS, Maier, MA, Rajeev, KG, Mathieu, SL, Kreutz, C, Fan, Y, Sanghvi, J, Micura, R, Rozners, E, Manoharan, M, Egli, M. Crystal structure, stability and in vitro RNAi activity of oligoribonucleotides containing the ribo-difluorotoluyl nucleotide: insights into substrate requirements by the human RISC Ago2 enzyme. Nucleic Acids Res, 35(19), 6424-38, 2007. PMCID:2095806
Loukachevitch, LV, Egli, M. Crystallization and preliminary X-ray analysis of Escherichia coli RNase HI-dsRNA
complexes. Acta Crystallograph Sect F Struct Biol Cryst Commun, 63(Pt 2), 84-8, 2007. PMCID:2330121
Luka, Z, Pakhomova, S, Loukachevitch, LV, Egli, M, Newcomer, ME, Wagner, C. 5-methyltetrahydrofolate is bound in intersubunit areas of rat liver folate-binding
protein glycine N-methyltransferase. J Biol Chem, 282(6), 4069-75, 2007.
Mori, T, Williams, DR, Byrne, MO, Qin, X, Egli, M, McHaourab, HS, Stewart, PL, Johnson, CH. Elucidating the Ticking of an In Vitro Circadian Clockwork. PLoS Biol, 5(4), e93, 2007. PMCID:1831719
Pallan, PS, Egli, M. Selenium modification of nucleic acids: preparation of phosphoroselenoate derivatives
for crystallographic phasing of nucleic acid structures. Nat Protoc, 2(3), 640-6, 2007.
Pallan, PS, Egli, M. Selenium modification of nucleic acids: preparation of oligonucleotides with
incorporated 2''-SeMe-uridine for crystallographic phasing of nucleic acid structures. Nat Protoc, 2(3), 647-51, 2007.
Pallan, PS, Lubini, P, Bolli, M, Egli, M. Backbone-base inclination as a fundamental determinant of nucleic acid self- and cross-pairing. Nucleic Acids Res, 35(19), 6611-24, 2007. PMCID:2095819
Pallan, PS, Lubini, P, Egli, M. A left-handed supramolecular assembly around a right-handed screw axis in the
crystal structure of homo-DNA. Chem Commun (Camb), (14), 1447-9, 2007.
Egli, M, Pallan, PS, Pattanayek, R, Wilds, CJ, Lubini, P, Minasov, G, Dobler, M, Leumann, CJ, Eschenmoser, A. Crystal structure of homo-DNA and nature''s choice of pentose over hexose in
the genetic system. J Am Chem Soc, 128(33), 10847-56, 2006.
Irimia, A, Zang, H, Loukachevitch, LV, Eoff, RL, Guengerich, FP, Egli, M. Calcium is a cofactor of polymerization but inhibits pyrophosphorolysis by
the Sulfolobus solfataricus DNA polymerase Dpo4. Biochemistry, 45(19), 5949-56, 2006.
Li, F, Sarkhel, S, Wilds, CJ, Wawrzak, Z, Prakash, TP, Manoharan, M, Egli, M. 2''-Fluoroarabino- and arabinonucleic acid show different conformations, resulting
in deviating RNA affinities and processing of their heteroduplexes with RNA by RNase H. Biochemistry, 45(13), 4141-52, 2006. PMCID:2553321
Pallan, PS, von Matt, P, Wilds, CJ, Altmann, KH, Egli, M. RNA-Binding affinities and crystal structure of oligonucleotides containing
five-atom amide-based backbone structures. Biochemistry, 45(26), 8048-57, 2006.
Pattanayek, R, Williams, DR, Pattanayek, S, Xu, Y, Mori, T, Johnson, CH, Stewart, PL, Egli, M. Analysis of KaiA-KaiC protein interactions in the cyano-bacterial circadian
clock using hybrid structural methods. EMBO J, 25(9), 2017-28, 2006. PMCID:1456936
Xia, J, Noronha, A, Toudjarska, I, Li, F, Akinc, A, Braich, R, Frank-Kamenetsky, M, Rajeev, KG, Egli, M, Manoharan, M. Gene silencing activity of siRNAs with a ribo-difluorotoluyl nucleotide. ACS Chem Biol, 1(3), 176-83, 2006.
Zang, H, Irimia, A, Choi, JY, Angel, KC, Loukachevitch, LV, Egli, M, Guengerich, FP. Efficient and high fidelity incorporation of dCTP opposite 7,8-dihydro-8-oxodeoxyguanosine
by Sulfolobus solfataricus DNA polymerase Dpo4. J Biol Chem, 281(4), 2358-72, 2006.
Diop-Frimpong, B, Prakash, TP, Rajeev, KG, Manoharan, M, Egli, M. Stabilizing contributions of sulfur-modified nucleotides: crystal structure
of a DNA duplex with 2''-O-[2-(methoxy)ethyl]-2-thiothymidines. Nucleic Acids Res, 33(16), 5297-307, 2005. PMCID:1216336
Egli, M, Minasov, G, Tereshko, V, Pallan, PS, Teplova, M, Inamati, GB, Lesnik, EA, Owens, SR, Ross, BS, Prakash, TP, Manoharan, M. Probing the influence of stereoelectronic effects on the biophysical properties
of oligonucleotides: comprehensive analysis of the RNA affinity, nuclease resistance, and crystal structure
of ten 2''-O-ribonucleic acid modifications. Biochemistry, 44(25), 9045-57, 2005.
Haeberli, P, Berger, I, Pallan, PS, Egli, M. Syntheses of 4''-thioribonucleosides and thermodynamic stability and crystal
structure of RNA oligomers with incorporated 4''-thiocytosine. Nucleic Acids Res, 33(13), 3965-75, 2005. PMCID:1178003
Pallan, PS, Marshall, WS, Harp, J, Jewett, FC, Wawrzak, Z, Brown, BA, Rich, A, Egli, M. Crystal structure of a luteoviral RNA pseudoknot and model for a minimal ribosomal
frameshifting motif. Biochemistry, 44(34), 11315-22, 2005. PMCID:2556298
Zang, H, Goodenough, AK, Choi, JY, Irimia, A, Loukachevitch, LV, Kozekov, ID, Angel, KC, Rizzo, CJ, Egli, M, Guengerich, FP. DNA adduct bypass polymerization by Sulfolobus solfataricus DNA polymerase
Dpo4: analysis and crystal structures of multiple base pair substitution and frameshift products with
the adduct 1,N2-ethenoguanine. J Biol Chem, 280(33), 29750-64, 2005.
Cook, S, Hugli, O, Egli, M, Menard, B, Thalmann, S, Sartori, C, Perrin, C, Nicod, P, Thorens, B, Vollenweider, P, Scherrer, U, Burcelin, R. Partial gene deletion of endothelial nitric oxide synthase predisposes to exaggerated
high-fat diet-induced insulin resistance and arterial hypertension. Diabetes, 53(8), 2067-72, 2004.
Egli, M. Nucleic acid crystallography: current progress. Curr Opin Chem Biol, 8(6), 580-91, 2004.
Egli, M. "Deoxyribo nanonucleic acid"; antiparallel, parallel, and unparalleled. Chem Biol, 11(8), 1027-9, 2004.
Johnson, CH, Egli, M. Visualizing a biological clockwork''s cogs. Nat Struct Mol Biol, 11(7), 584-5, 2004.
Pattanayek, R, Sethaphong, L, Pan, C, Prhavc, M, Prakash, TP, Manoharan, M, Egli, M. Structural rationalization of a large difference in RNA affinity despite a
small difference in chemistry between two 2''-O-modified nucleic acid analogues. J Am Chem Soc, 126(46), 15006-7, 2004.
Pattanayek, R, Wang, J, Mori, T, Xu, Y, Johnson, CH, Egli, M. Visualizing a circadian clock protein: crystal structure of KaiC and functional
insights. Mol Cell, 15(3), 375-88, 2004.
Prakash, TP, P??schl, A, Lesnik, E, Mohan, V, Tereshko, V, Egli, M, Manoharan, M. 2''-O-[2-(guanidinium)ethyl]-modified oligonucleotides: stabilizing effect on
duplex and triplex structures. Org Lett, 6(12), 1971-4, 2004.
Xu, Y, Mori, T, Pattanayek, R, Pattanayek, S, Egli, M, Johnson, CH. Identification of key phosphorylation sites in the circadian clock protein
KaiC by crystallographic and mutagenetic analyses. Proc Natl Acad Sci U S A, 101(38), 13933-8, 2004. PMCID:518856
Egli, M, Tereshko, V, Mushudov, GN, Sanishvili, R, Liu, X, Lewis, FD. Face-to-face and edge-to-face pi-pi interactions in a synthetic DNA hairpin
with a stilbenediether linker. J Am Chem Soc, 125(36), 10842-9, 2003.
Pallan, PS, Wilds, CJ, Wawrzak, Z, Krishnamurthy, R, Eschenmoser, A, Egli, M. Why does TNA cross-pair more strongly with RNA than with DNA? an answer from
X-ray analysis. Angew Chem Int Ed Engl, 42(47), 5893-5, 2003.
Sarkhel, S, Rich, A, Egli, M. Water-nucleobase "stacking": H-pi and lone pair-pi interactions in the atomic
resolution crystal structure of an RNA pseudoknot. J Am Chem Soc, 125(30), 8998-9, 2003.
Egli, M. DNA-cation interactions: quo vadis. Chem Biol, 9(3), 277-86, 2002.
Egli, M, Minasov, G, Su, L, Rich, A. Metal ions and flexibility in a viral RNA pseudoknot at atomic resolution. Proc Natl Acad Sci U S A, 99(7), 4302-7, 2002. PMCID:123643
Joseph, B, Egli, M, Koppekin, A, Thompson, T. Food choice in people with Prader-Willi syndrome: quantity and relative preference. Am J Ment Retard, 107(2), 128-35, 2002.
Teplova, M, Wilds, CJ, Wawrzak, Z, Tereshko, V, Du, Q, Carrasco, N, Huang, Z, Egli, M. Covalent incorporation of selenium into oligonucleotides for X-ray crystal
structure determination via MAD: proof of principle. Multiwavelength anomalous dispersion. Biochimie, 84(9), 849-58, 2002.
Wilds, CJ, Maier, MA, Tereshko, V, Manoharan, M, Egli, M. Direct observation of a cytosine analogue that forms five hydrogen bonds to
guanosine: guanidino G-clamp. Angew Chem Int Ed Engl, 41(1), 115-7, 2002.
Wilds, CJ, Pattanayek, R, Pan, C, Wawrzak, Z, Egli, M. Selenium-assisted nucleic acid crystallography: use of phosphoroselenoates
for MAD phasing of a DNA structure. J Am Chem Soc, 124(50), 14910-6, 2002.
Wilds, CJ, Wawrzak, Z, Krishnamurthy, R, Eschenmoser, A, Egli, M. Crystal structure of a B-form DNA duplex containing (L)-alpha-threofuranosyl
(3''-->2'') nucleosides: a four-carbon sugar is easily accommodated into the backbone of DNA. J Am Chem Soc, 124(46), 13716-21, 2002.
Joseph, B, Egli, M, Sutcliffe, JS, Thompson, T. Possible dosage effect of maternally expressed genes on visual recognition memory in Prader-Willi syndrome. Am J Med Genet, 105(1), 71-5, 2001.
Tereshko, V, Teplova, M, Brunzelle, J, Watterson, DM, Egli, M. Crystal structures of the catalytic domain of human protein kinase associated
with apoptosis and tumor suppression. Nat Struct Biol, 8(10), 899-907, 2001.
Tereshko, V, Wallace, ST, Usman, N, Wincott, FE, Egli, M. X-ray crystallographic observation of "in-line" and "adjacent" conformations
in a bulged self-cleaving RNA/DNA hybrid. RNA, 7(3), 405-20, 2001. PMCID:1370097
Tereshko, V, Wilds, CJ, Minasov, G, Prakash, TP, Maier, MA, Howard, A, Wawrzak, Z, Manoharan, M, Egli, M. Detection of alkali metal ions in DNA crystals using state-of-the-art X-ray
diffraction experiments. Nucleic Acids Res, 29(5), 1208-15, 2001. PMCID:29719
Wilds, CJ, Minasov, G, Natt, F, von Matt, P, Altmann, KH, Egli, M. Studies of a chemically modified oligodeoxynucleotide containing a 5-atom amide
backbone which exhibits improved binding to RNA. Nucleosides Nucleotides Nucleic Acids, 20(4-7), 991-4, 2001.
Sachdev, RN, Egli, M, Stonecypher, M, Wiley, RG, Ebner, FF. Enhancement of cortical plasticity by behavioral training in acetylcholine-depleted adult rats. J Neurophysiol, 84(4), 1971-81, 2000.
Teplova, M, Tereshko, V, Sanishvili, R, Joachimiak, A, Bushueva, T, Anderson, WF, Egli, M. The structure of the yrdC gene product from Escherichia coli reveals a new
fold and suggests a role in RNA binding. Protein Sci, 9(12), 2557-66, 2000. PMCID:2144518
Egli, M, Roper, T, Feurer, I, Thompson, T. Architectural acoustics in residences for adults with mental retardation and its relation to perceived homelikeness. Am J Ment Retard, 104(1), 53-66, 1999.
Egli, M, Joseph, B, Thompson, T. Transfer of social attributions in stimulus equivalence classes by preschool children. Psychol Rep, 80(1), 3-21, 1997.
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