Physical mapping of chromosomes would be facilitated by methods of breaking large DNA into manageable fragments or cutting uniquely at genetic markers of interest. Our long-term objective is to provide chemical methods for efficient cleavage at single sites in megabase and gigabase DNA (human chromosomes). Oligonucleotide-directed triple helix formation is a versatile method for the sequence specific recognition of 15 base pairs of DNA. Due to the length of the recognition site, in a formal sense, this is one million times more sequence specific than that available with most restriction enzymes. It is important to determine whether the full potential of this cleavage specificity can be realized. Our program combines synthetic organic chemistry, biophysical methods, and molecular biology to learn about the relationship of structure to function in the area of creating reagents for recognition and modification of DNA biopolymers.
Specific aims are (1) test the high yield double strand cleavage reactions at 5'-(pur)/m.(pyr)/n-3' target sequences in megabase DNA utilizing a new class of pyrimidine oligonucleotides equipped with the N-bromoacetamide at the 3' end, (2) test purine N-bromoacetamide- oligonucleotides for high yield double strand cleavage of single sites in megabase DNA and examine cleavage of DNA at an internal GC base pair utilizing a novel designed base (nebularine-N-bromoacetamide), (3) study sequence composition effects, modified bases, and mismatches at a single site in DNA by cooperatively binding oligonucleotides, (4) study the thermodynamics of oligonucleotides containing the novel base D/3 and test their use for targeting trinucleotide repeats such as (CAG)n, (5) characterize the intermediates in the joint molecule formed in a RecA- mediated strand exchange using affinity cleavage methods on a RecA nucleoprotein filament.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
2R01GM051747-06A1
Application #
2190447
Study Section
Bio-Organic and Natural Products Chemistry Study Section (BNP)
Project Start
1989-07-01
Project End
1999-03-31
Budget Start
1995-04-01
Budget End
1996-03-31
Support Year
6
Fiscal Year
1995
Total Cost
Indirect Cost
Name
California Institute of Technology
Department
Chemistry
Type
Schools of Engineering
DUNS #
078731668
City
Pasadena
State
CA
Country
United States
Zip Code
91125
Mysore, Veena S; Szablowski, Jerzy; Dervan, Peter B et al. (2016) A DNA-binding Molecule Targeting the Adaptive Hypoxic Response in Multiple Myeloma Has Potent Antitumor Activity. Mol Cancer Res 14:253-66
Szablowski, Jerzy O; Raskatov, Jevgenij A; Dervan, Peter B (2016) An HRE-Binding Py-Im Polyamide Impairs Hypoxic Signaling in Tumors. Mol Cancer Ther 15:608-17
Kang, JeenJoo S; Dervan, Peter B (2015) A sequence-specific DNA binding small molecule triggers the release of immunogenic signals and phagocytosis in a model of B-cell lymphoma. Q Rev Biophys 48:453-64
Kang, JeenJoo S; Meier, Jordan L; Dervan, Peter B (2014) Design of sequence-specific DNA binding molecules for DNA methyltransferase inhibition. J Am Chem Soc 136:3687-94
Raskatov, Jevgenij A; Szablowski, Jerzy O; Dervan, Peter B (2014) Tumor xenograft uptake of a pyrrole-imidazole (Py-Im) polyamide varies as a function of cell line grafted. J Med Chem 57:8471-6
Martínez, Thomas F; Phillips, John W; Karanja, Kenneth K et al. (2014) Replication stress by Py-Im polyamides induces a non-canonical ATR-dependent checkpoint response. Nucleic Acids Res 42:11546-59
Raskatov, Jevgenij A; Puckett, James W; Dervan, Peter B (2014) A C-14 labeled Py-Im polyamide localizes to a subcutaneous prostate cancer tumor. Bioorg Med Chem 22:4371-5
Nickols, Nicholas G; Szablowski, Jerzy O; Hargrove, Amanda E et al. (2013) Activity of a Py-Im polyamide targeted to the estrogen response element. Mol Cancer Ther 12:675-84
Edwards, Jonathan S; Betts, Laurie; Frazier, Monica L et al. (2013) Molecular basis of antibiotic multiresistance transfer in Staphylococcus aureus. Proc Natl Acad Sci U S A 110:2804-9
Hargrove, Amanda E; Raskatov, Jevgenij A; Meier, Jordan L et al. (2012) Characterization and solubilization of pyrrole-imidazole polyamide aggregates. J Med Chem 55:5425-32

Showing the most recent 10 out of 20 publications