Selected Publications

DNA processing enzymes and DNA interacting proteins

Refereed Papers

Fridlender, B., Fry, M., Bolden, A., and Weissbach, A.  A new synthetic RNA-dependent DNA polymerase from human tissue culture cells.  Proc. Natl. Acad. Sci. USA 69: (1972) 452-455

Fry, M. and Weissbach, A.  The utilization of synthetic DNA templates by a new DNA polymerase from culture murine cells.  J. Biol. Chem. 248: (1973) 2678-2683

Fry, M. and Weisman-Shomer, P.  Altered deoxyribonucleic acid a-polymerase in senescent cultured chick embryo fibroblasts.  Biochemistry 15: (1976) 4319-4329

Kaftory, A. and Fry, M.   Highly efficient copying of single-stranded DNA by eukaryotic cell chromatin.  Nucleic Acids Res. 5: (1978) 2679-2693

Fry, M., Shearman, C.W., Martin, G.M., and Loeb, L.A.  On the accuracy of DNA synthesis directed by chromatin-associated DNA polymerase β. Biochemistry 19: (1980) 5939-5942

Fry, M., Silber, J.A., Loeb, L.A., and Martin, G.M.  Delayed and reduced cell replication and diminished levels of DNA polymerase α in regenerating livers of aging mice.  J. Cell. Physiol. 118: (1984) 225-232

Silber, J.A., Fry, M., and Loeb, L.A.  Fidelity of DNA polymerases isolated from regenerating liver chromatin of Mus musculus.  J. Biol. Chem. 260: (1985) 1304-1310

Fry, M., Lapidot, J., and Weisman-Shomer, P. A DNA template recognition protein: Partial purification from mouse liver and stimulation of DNA polymerase α. Biochemistry 24: (1985) 7549-7556

Fry, M., Weisman-Shomer, P., Lapidot, J., and Sharf, R. Template-selective stimulation of diverse DNA polymerases by the murine DNA binding protein factor D. J. Biol. Chem. 262: (1987) 8861-8867

Fry, M., Sharf, R., Weisman-Shomer, P., Evers, P. C., and Loeb, L.A.  The sequence specificity of stimulation of DNA polymerases by factor D.  J. Biol. Chem. 262: (1987) 8868-8874

Sharf, R., Weisman-Shomer, P., and Fry, M.  Rabbit liver factor D: A poly(thymidine) template stimulatory protein of DNA polymerases:  Purification and characterization.  Biochemistry 27: (1988) 2990-2997

Fry, M., Perrino, F.W., Levy, A., and Loeb, L.A.  Factor D is a selective single strand oligothymidine binding protein.  Nucleic Acids Res. 16: (1988) 199-211

Asna, N., Weisman-Shomer, P., Waldman, E., and Fry, M.  Factor C from rabbit liver: A new poly(dC) and poly[d(G-C)] template-selective stimulatory protein of DNA polymerases.  J. Biol. Chem. 264: (1989) 5245-5252

Weisman-Shomer, P., Dube, D., Perrino, F.W., Stokes, K., Loeb, L.A., and Fry, M. Sequence-specificity of the pausing of DNA polymerases.  Biochem. Biophys. Res. Commun. 164: (1989) 1149-1156

Williams, K.J., Loeb, L.A., and Fry, M.  Synthesis of DNA by human immunodeficiency virus reverse transcriptase is specifically blocked at template oligo(deoxyadenosine) tracts.  J. Biol. Chem. 265: (1990) 18682-186

Fry, M., and Loeb, L.A.  A DNA polymerase α pause site is a hot spot for nucleotide misinsertion.  Proc. Natl. Acad. Sci. USA 89: (1992) 763-767

Hoffman, J.S., Fry, M., Ji, J., Williams, K., and Loeb, L.A.  Codons 12 and 13 of H-ras proto-oncogene interrupt the progression of DNA synthesis catalyzed by DNA polymerase α.  Cancer Res. 53: (1993) 2895-2900

Shen, J.-C., Gray, M.D., Kamath-Loeb, A., Oshima, J., Fry, M., and Loeb, L.A. Werner syndrome protein: 1) DNA helicase and DNA exonuclease reside on the same polypeptide.  J. Biol. Chem. 273: (1998) 34139-34144

Kamath-Loeb, A.S., Shen, J.-C., Loeb, L.A., and Fry, M. Werner syndrome protein:  2) Characterization of the integral 3’→5’ DNA exonuclease.  J. Biol. Chem. 273: (1998) 34145-34150

Authored Book

Fry, M. and Loeb, L.A.  Animal Cell DNA Polymerases.  CRC Press, Boca Raton, Fl ISBN: 0-849-36507-4 (1986) 221 pp.

Book Chapters and Review Articles

Fry, M.  Eukaryotic DNA polymerases.  in: Enzymes of Nucleic Acids Synthesis and Modification (Jacob, S.T., ed., ISBN 08493-5517-6) CRC Press, Boca Raton, Fl. (1983) pp. 39-92

Loeb, L.A., Liu, P.K. and Fry, M.  DNA polymerase a enzymology, function, fidelity and mutagenesis. Prog. Nucleic Acids Res. Mol. Biol.  33: (1986) 57-110

Fry, M. and Loeb, L.A.  The three faces of the WS helicase. Nature Genet. 19: (1998) 308-309

Fry, M. The Werner syndrome helicase-nuclease – one protein, many mysteries. Science SAGE KE (2002);2002/13/re2  10 pp.

Fry, M. Biochemical characterization of Werner syndrome exonuclease and helicase. In: Molecular Mechanisms of Werner Syndrome Lebel, M., ed., (ISBN-0-306-4823-9) Landes Bioscience, Georgetown, TX. (2004) pp. 22-43

Kamath-Loeb, A.S., Fry, M., and Loeb, L.A. DNA helicases in human disease.  in: DNA Replication and Human Disease DePamphilis, M.L., ed., (ISBN-0-87969-766-0) Cold Spring Harbor Laboratory Press, New York (2006) pp. 435-460


Quadruplex nucleic acids interacting proteins; Fragile X syndrome

Refereed Papers

Weisman-Shomer, P. and Fry, M.  QUAD, a protein from hepatocyte chromatin that binds selectively to guanine-rich tetrahelical DNA. J. Biol. Chem. 268: (1993) 3306-3312

Weisman-Shomer, P. and Fry, M.  Stabilization of tetrahelical DNA by the quadruplex DNA binding protein QUAD.  Biochem. Biophys. Res. Commun. 205:  (1994) 305-311

Fry, M. and Loeb, L. A.  The fragile X syndrome d[CGG]n nucleotide repeats form a stable tetrahelical structure.  Proc. Natl. Acad. Sci. USA 91: (1994) 4950-4954

Nadel, Y., Weisman-Shomer, P. and Fry, M.  The Fragile X syndrome single-strand d(CGG)n nucleotide repeats readily fold-back to form unimolecular hairpin structures.  J. Biol. Chem. 270: (1995) 28970-28978

Sarig, G., Weisman-Shomer, P., Erlitzki, R. and Fry, M. Purification and characterization of qTBP42, a new single strand and quadruplex telomeric DNA binding protein from rat hepatocytes.  J. Biol. Chem. 272: (1997) 4474-4482

Erlitzki, R. and Fry, M.  Sequence-specific binding protein of single strand and unimolecular quadruplex telomeric DNA from rat hepatocytes.  J. Biol. Chem. 272: (1997) 15881-15890

Sarig, G., Weisman-Shomer, P. and Fry, M.  Telomeric and tetraplex DNA binding properties of qTBP42: a homolog of the CArG box binding protein CBF-A. Biochem. Biophys. Res. Commun. 237: (1997) 617-623

Fry, M. and Loeb, L.A.  Human Werner syndrome DNA helicase unwinds tetrahelical structures of the fragile X syndrome repeat sequence d(CGG)n. J. Biol. Chem. 274: (1999) 12797-12803

Weisman-Shomer, P., Naot, Y. and Fry, M.  Tetrahelical forms of the fragile X syndrome expanded sequence d(CGG)n are destabilized by two hnRNP-related telomeric DNA binding proteins qTBP42 and uqTBP25.  J. Biol. Chem. 275: (2000) 2231-2238

Weisman-Shomer, P., Cohen, E. and Fry, M.  Interruption of the fragile X   syndrome expanded sequence d(CGG)n by interspersed d(AGG) trinucleotides   diminishes the formation and stability of d(CGG)n tetrahelical structures. Nucleic Acids Res. 28: (2000) 1535-1541

Uliel, L., Weisman-Shomer, P., Oren-Jazan, H., Newcomb, T., Loeb, L.A., and Fry, M. Human Ku antigen tightly binds and stabilizes a tetrahelical form of the fragile X syndrome d(CGG)n expanded sequence. J. Biol. Chem. 275: (2000) 33134-33141

Kamath-Loeb, A.S., Loeb, L.A., Johansson, E., Burgers, P.M.J., and Fry, M. interactions between the Werner syndrome helicase and DNA polymerase d facilitate copying of tetraplex and hairpin structures of the d(CGG)n trinucleotide repeat sequence.  J. Biol. Chem. 276: (2001) 16439-16446

Weisman-Shomer, P., Cohen, E., and Fry, M. Distinct domains in the CArG-box binding factor-A destabilize tetraplex forms of the fragile X expanded sequence d(CGG)nNucleic Acids Res. 30: (2002) 3672-3681

Weisman-Shomer, P., Cohen, E., Hershco, I., Khateb, S., Wolfovitz-Barchad, O., Hurley, L.H., and Fry, M.  The cationic porphyrin TMPyP4 destabilizes tetraplex form of the fragile X syndrome expanded sequence d(CGG)n. Nucleic Acids Res. 31: (2003) 3963-3970

Khateb, S., Weisman-Shomer, P., Hershco, I., Loeb, L.A., and Fry, M.  Destabilization of tetraplex structures of the fragile X repeat sequence (CGG)n is mediated by homolog conserved domains in three members of the hnRNP family. Nucleic Acids Res. 32: (2004) 4145-4154

Yafe, A., Etzioni, S., Weisman-Shomer, P., and Fry, M. Formation and properties of hairpin and tetraplex structures of guanine-rich regulatory sequences of muscle-specific genes.  Nucleic Acids Res. 33: (2005) 2877-2900

Etzioni, S., Yafe, A., Khateb, S., Weisman-Shomer, P., Bengal, E., and Fry, M. Homodimeric MyoD binds preferentially tetraplex structures of regulatory sequences of muscle-specific genes.   J. Biol. Chem. 280: (2005) 26805-26812

Khateb, S., Weisman-Shomer, P., Hershco-Shani, I., Ludwig, A.L., and Fry, M. The tetraplex (CGG)n destabilizing proteins hnRNP A2 and CBF-A enhance the in vivo translation of fragile X premutation mRNA. Nucleic Acids Res. 35: (2007) 5775-5788

Shkolver, J., Etzioni, S., Weisman-Shomer, P., Yafe, A., Bengal, E., and Fry, M. MyoD uses overapping but distinct elements to bind E-box and tetraplex structures of regulatory sequences of muscle-specific genes. Nucleic Acids Res. 35: (2007) 7087-7095

Yafe, A., Shklover, J., Weisman-Shomer, P., Bengal, E., and Fry, M. Differential binding of quadruplex structures of muscle-specific genes regulatory sequences by MyoD, MRF4 and Myogenin. Nucleic Acids Res. 36: (2008) 3916-3925

Ofer, N., Weisman-Shomer, P., Shklover, J., and Fry, M. The quadruplex  r(CGG)n destabilizing cationic porphyrin TMPyP4 cooperates with hnRNPs to increase the translation efficiency of fragile X premutation mRNA. Nucleic Acids Res. 37: (2009) 2712-2722

Shklover, J., Weisman-Shomer, P., Yafe, A. and Fry, M. Quadruplex structures of muscle gene promoter sequences enhance in vivo MyoD-dependent gene expression. Nucleic Acids Res. 38: (2010) 2369-2377

Kamath-Loeb, A., Loeb, L.A., and Fry, M. The Werner syndrome protein is distinguished from the Bloom syndrome protein by its capacity to tightly bind diverse DNA structures. PLoS ONE  7: (2012) e30189. doi:10.1371/journal.pone.003018

Edited Book

Fry, M. and Usdin, K. Human Nucleotide Expansion Disorders. (Vol. 19 in a Nucleic Acids and Molecular Biology Series. Gross, H.G., ed., ISBN: 3-540-33335-5. Springer, Berlin, Heidelberg, New York (2006) 292 pp.

Book Chapters and Review Articles

Dexheimer, T.S., Fry, M. and Hurley, L.H. DNA quadruplexes and gene regulation.  In: Quadruplex Nucleic Acids S. Balasubramanian and S. Neidle, eds., ISBN-10: 0-85404-374-8. Royal Society of Chemistry Publishing (2006) pp. 180-202

Fry, M. Tetraplex DNA and its interacting proteins. Frontiers in Bioscience 12: (2007) 4336-4351

Fry, M. Regulation of gene transcription by DNA G-quadruplexes. In: Guanine Quartets: Structure and Application L. Spindler and W. Fritzsche, eds., ISBN: 978-1-84973-695-4. Royal Society of Chemistry Publishing (2012) pp. 223-236


History and philosophy of biochemistry and molecular biology

Refereed Papers

Fry, M. Dissolution of hypotheses in biochemistry: case studies. Hist. Phil. Life Sci. (2016) 38: 17., 40 pp.

Fry, M. Predictive hypotheses are ineffectual in resolving complex biochemical systems. Hist. Phil. Life Sci. (2018) 40: 25.,  46 pp.

Fry, M. Ontologically simple theories do not indicate the true nature of complex biological systems: Three test cases. Hist. Phil. Life Sci. (2020) 42: 17.

Fry, M. Crick’s adaptor hypothesis and the discovery of transfer RNA: Experiment surpassing theoretical prediction. Philos. Theor. Pract. Biol. (2022) 14: 11, 31 pp.

Fry, M. Question-driven stepwise experimental discoveries in biochemistry: two case studies.Hist. Phil. Life Sci. (2022) 44: 12, 51 pp. 


Authored Book

Fry, M. Landmark Experiments in Molecular Biology. Elsevier/Academic Press,   Amsterdam, Boston, Heidelberg, ISBN: 9780128020746 (2016) 570 pp.