David F. Hickok Memorial Cancer Research Laboratory
800 E. 28th St., Minneapolis, MN 55407
Research Scientist: Pamela D. Popken-Harris Ph.D.
Computer Applications Coordinator: Michael R. Sullivan B.S.
Research Assistant: Lara S. Pliml B.S.
The David F. Hickok Memorial Cancer Research Laboratory is currently working with the
Mouse Mammary Tumor Virus,
an endogenous oncogenic retrovirus, as a model for breast cancer and
retroviral biochemical pathways. We have been investigating site-specific
DNA recognition by DNA regulatory proteins, the dynamics of a protein
regulated genetic switch and the origin of the genetic code.
Our work has led to a hypothesis for a protein/DNA recognition code which
has a mechanism of stereochemical complementarity between functional sites
on amino acid side chains and their cognate codon/anticodon nucleotide
base sites. In addition, our findings support a stereochemical model for
the origin of the genetic code.
Dr. Harris is also Editor-in-Chief of a peer-reviewed electronic journal called
The World Wide Web Journal of Biology.
This new journal features color graphics, movies, interactive molecules and
links to other Biological sites of interest.
Harris, L., Sullivan, M. and Hickok, D. Conservation of genetic information between regulatory protein DNA binding alpha helices and their cognate operator sites: A simple code for site-specific recognition. (1990) Computers and Mathematics with Applications 20, 1-23.
Harris, L., Sullivan, M. and Hickok, D. Genetic sequences of hormone response elements share similarity with predicted alpha helices within DNA binding domains of steroid receptor proteins: A basis for site-specific recognition. (1990) Computers and Mathematics with Applications 20, 25-48.
Harris, L., Sullivan, M. and Hickok, D. Conservation of genetic information:
A code for site-specific DNA recognition. (1993) Proc. Natl. Acad. Sci. USA 90, 5534-5538.
Link to hypertext version of this article.
Harris, L., Sullivan, M., Popken-Harris, P. and Hickok, D.
Molecular dynamics simulations in solvent of the glucocorticoid receptor
protein in complex with a glucocorticoid response element DNA sequence.
The Journal of Biomolecular Structure and Dynamics (October 1994) 12:2, 249-270.
Link to hypertext version of this article.
Harris, L., Sullivan, M., Popken-Harris, P. and Hickok, D.
Molecular dynamics simulations of the glucocorticoid receptor protein in
complex with a glucocorticoid response element in a 10 Angstrom water layer.
The World Wide Web Journal of Biology, (October 1995) an international internet journal.
Link to hypertext version of this article.
Harris, L., Sullivan, M., Popken-Harris, P. and Hickok, D.
Stereochemical complementarity between regulatory proteins' DNA recognition
helix amino acids and codon-anticodon nucleotides within their cognate DNA
binding sites: A code for DNA site-specific recognition.
Biological Structure and Dynamics, Proceedings of the Ninth Conversation,
State University of New York, Albany, NY 1995
Adenine Press 1996, pages 61-82.
Harris, L., Sullivan, M., Popken-Harris, P. and Hickok, D.
A one nanosecond molecular dynamics simulation of the glucocorticoid receptor
in complex with a glucocorticoid response element in a 10 Angstrom water layer.
The Journal of Biomolecular Structure and Dynamics (December, 1995) 13:3,
423-440.
Harris, L., Sullivan, M., Popken-Harris, P. and Hickok, D.
Molecular dynamics simulations of the estrogen receptor protein in
complex with a nonconsensus estrogen response element DNA sequence
in a 10 Angstrom water layer.
The World Wide Web Journal of Biology, (November 1996) an international internet journal.
Link to hypertext version of this article.
Harris, L., Sullivan, M., Popken-Harris, P. and Hickok, D.
Genetic information is conserved between estrogen response elements and the
c-DNA encoding the estrogen receptor DNA binding domain: A code for
site-specific DNA recognition.
The World Wide Web Journal of Biology, (February 1998) an international internet journal.
Link to hypertext version of this article.
Harris, L., Sullivan, M. and Popken-Harris, P.
Molecular dynamics simulation in solvent of the estrogen receptor protein
DNA binding domain in complex with a nonconsensus estrogen response element
DNA sequence.
Journal of Biomolecular Structure and Dynamics (December 1997) 15, 407-430.
Popken-Harris, P., Pliml, L. and Harris, L.
Genetic analyses of MMTV in the RIII strain of mouse:
evidence for a novel non-LTR retrotransposon.
22nd Congress of the International Association for Breast
Cancer Research
Athens, Greece, September 25-28, 1998
Harris, L., Sullivan, M and Hatfield
Directed Molecular Evolution.
Origins of Life and Evolution of the Biosphere.
Orig Life Evol Biosph. (August 1999) 29(4):425-35
Harris, L., Sullivan, M. and Popken-Harris, P.
Molecular Dynamics Simulation in Solvent of the Phage 434 cI Repressor Protein DNA Binding Domain Amino Acids (R1-69) in Complex with its Cognate Operator (OR1) DNA Sequence.
Journal of Biomolecular Structure and Dynamics (August 1999) 17(1):1-17.
Popken-Harris, P., Pliml, L. and Harris, L.
Sequence and genetic analyses of the 3' terminus an integration sites
of the RIII/Sa Mouse Mammary Tumor (MMTV) Exogenous provirus.*
Virus Genes (January 2001) 23(1):35-43.
*Sequence data from this paper submitted to GenBank and assigned accession numbers
AF071010, AF263910 and AF263911.
Hartmann, B., Sullivan, M. and Harris, L.
Operator recognition by the phage 434 cI repressor: MD simulations of
free and bound 50bp DNA reveal important differences between
the OR1 and OR2 sites.
Biopolymers (in press)
Harris, L., Sullivan, M. and Popken-Harris, P.
Molecular Dynamics Simulation in Solvent of the Phage 434 cI Repressor
Protein DNA Binding Domain Amino Acids (R1-69) in Complex with its
Cognate Operator (OR2) DNA Sequence.
Submitted for publication to:
Journal of Biomolecular Structure and Dynamics
Harris, L., Sullivan, M. and Popken-Harris, P.
Molecular Dynamics Simulation in Solvent of two Phage 434 cI Repressor
Protein DNA Binding Domain (R1-69) dimers in Complex with
a DNA Sequence Containing Operators OR1 and OR2.
Manuscript in preparation
The following publications are available upon request from:
Research Reports Coordinator
Minnesota Supercomputer Institute
1200 Washington Ave. So.
Minneapolis, MN 55415
Please send report number (e.g. UMSI 89/168) when requesting reprint.
UMSI 89/168 Harris, L., Sullivan, M. and Hickok, D. October 1989
Genetic sequences of hormone response elements share similarity with
predicted alpha helices within DNA binding domains of steroid receptor
proteins: A basis for site-specific recognition.
UMSI 89/169 Harris, L., Sullivan, M. and Hickok, D. October 1989
Conservation of genetic information between regulatory protein DNA binding
alpha helices and their cognate operator sites: A simple code for site-specific recognition.
UMSI 92/229 Harris, L., Sullivan, M. and Hickok, D. November 1992
Conservation of genetic information: A code for site-specific DNA recognition.
UMSI 93/74 Harris, L., Sullivan, M. and Hickok, D. May 1993
The glucocorticoid receptor DNA binding domain interacts with a glucocorticoid
response element and flanking nucleotides at sites of conserved genetic
information.
UMSI 94/170 Harris, L., Sullivan, M. Popken-Harris, P. and Hickok, D. August 1994
Molecular dynamics simulations in solvent of the glucocorticoid receptor
protein in complex with a glucocorticoid response element DNA sequence.
UMSI 95/121 Harris, L., Sullivan, M., Popken-Harris, P. and Hickok, D. May 1995
Molecular dynamics simulation of the glucocorticoid receptor
in complex with a glucocorticoid response element in a 10 Angstrom water layer.
UMSI 95/153 Harris, L., Sullivan, M., Popken-Harris, P. and Hickok, D. July 1995
Stereochemical complementarity between regulatory proteins' DNA recognition
helix amino acids and codon-anticodon nucleotides within their cognate DNA
binding sites: A code for DNA site-specific recognition.
UMSI 95/209 Harris, L., Sullivan, M., Popken-Harris, P. and Hickok, D. October 1995
A one nanosecond molecular dynamics simulation of the glucocorticoid receptor
in complex with a glucocorticoid response element in a 10 Angstrom water layer.
UMSI 96/100 Harris, L., Sullivan, M., Popken-Harris, P. and Hickok, D. May 1996
Genetic information is conserved between estrogen response elements and the
c-DNA encoding the estrogen receptor DNA binding domain: A code for
site-specific DNA recognition.
UMSI 96/194 Harris, L., Sullivan, M., Popken-Harris, P. and Hickok, D. October 1996
Molecular dynamics simulations of the estrogen receptor protein in
complex with a nonconsensus estrogen response element DNA sequence
in a 10 Angstrom water layer.
UMSI 97/66 Harris, L., Sullivan, M. and Popken-Harris, P. April 1997
Molecular dynamics simulation in solvent of the estrogen receptor protein
DNA binding domain in complex with a nonconsensus estrogen response element
DNA sequence.
UMSI 98/201 Harris, L., Sullivan, M. and Hatfield, D. November 1998
Directed Molecular Evolution.
UMSI 99/6 Harris, L., Sullivan, M. and Popken-Harris, P. January 1999
Molecular Dynamics Simulation in Solvent of the Phage 434 cI Repressor Protein DNA Binding Domain Amino Acids (R1-69) in Complex with its Cognate Operator (OR1) DNA Sequence
UMSI 2000/191 Harris, L., Sullivan, M. and Popken-Harris, P. October 2000
Molecular Dynamics Simulation in Solvent of the Phage 434 cI Repressor Protein DNA
Binding Domain Amino Acids (R1-69) in Complex with its Cognate Operator
(OR2) DNA Sequence.
UMSI 2001/120 Hartmann, B., Sullivan, M. and Harris, L.
Operator recognition by the phage 434 cI repressor: MD simulations of
free and bound 50bp DNA reveal important differences between
the OR1 and OR2 sites.
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