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Title: Site-specific cleavage of genomic DNA mediated by triple helix formation

Abstract

Physical isolation of large segments of chromosomal DNA is a major goal of human genetics. This would be greatly assisted by a generalizable technique for the cleavage of chromosomal DNA at a single site. Pyrimidine oligonucleotide directed triple helix formation is a generalizable motif for the site specific recognition of duplex DNA. This thesis describes the application of oligonucleotide directed triple helix formation to bind unique target sites in bacteriophage [lambda], yeast, and human genomic DNA. Cleavage at the binding sites are achieved by affinity cleaving with EDTA[center dot]Fe(II) derivatized oligonucleotides, alkylation with bromoacetyl derivatized oligonucleotides, and by site specific triple helix mediated methylase inhibition followed by digestion with the cognate endonuclease. Cleavage of genomic substrates with progressively greater complexity is described. Bacteriophage [lambda] genomic DNA (48.5 kilobase pairs) was targeted at a single endogenous homopurine site within the origin of replication. This substrate was also used to demonstrate cooperative binding of heterologous oligonucleotides to duplex DNA at contiguous binding sites. An engineered target site on yeast chromosome III (340 kilobase pairs) was cut quantitatively at a single site within total yeast genomic DNA (14 megabase pairs) by both chemical and enzymatic techniques. Techniques for the identification of endogenous triplemore » helix target sites within unsequenced genetic markers were developed and successfully used to characterize a target site on human chromosome 4, proximal to the Huntington disease gene. As a test for the site specific cleavage of gigabase DNA, this site near the end of human chromosome 4 was cleaved by triple helix mediated enzymatic cleavage. This generated a specific 3.6 Mb fragment in greater than 80% yield that contained the entire candidate region for the Huntington mutation.« less

Authors:
Publication Date:
Research Org.:
California Inst. of Tech., Pasadena, CA (United States)
OSTI Identifier:
5981084
Resource Type:
Miscellaneous
Resource Relation:
Other Information: Thesis (Ph.D.)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; CHROMOSOMES; GENETIC MAPPING; DNA; CLEAVAGE; HUMAN POPULATIONS; GENETICS; GENES; HELICAL CONFIGURATION; MOLECULAR STRUCTURE; BIOLOGY; CONFIGURATION; MAPPING; MICROSTRUCTURE; NUCLEIC ACIDS; ORGANIC COMPOUNDS; POPULATIONS; 550400* - Genetics

Citation Formats

Strobel, S A. Site-specific cleavage of genomic DNA mediated by triple helix formation. United States: N. p., 1992. Web.
Strobel, S A. Site-specific cleavage of genomic DNA mediated by triple helix formation. United States.
Strobel, S A. 1992. "Site-specific cleavage of genomic DNA mediated by triple helix formation". United States.
@article{osti_5981084,
title = {Site-specific cleavage of genomic DNA mediated by triple helix formation},
author = {Strobel, S A},
abstractNote = {Physical isolation of large segments of chromosomal DNA is a major goal of human genetics. This would be greatly assisted by a generalizable technique for the cleavage of chromosomal DNA at a single site. Pyrimidine oligonucleotide directed triple helix formation is a generalizable motif for the site specific recognition of duplex DNA. This thesis describes the application of oligonucleotide directed triple helix formation to bind unique target sites in bacteriophage [lambda], yeast, and human genomic DNA. Cleavage at the binding sites are achieved by affinity cleaving with EDTA[center dot]Fe(II) derivatized oligonucleotides, alkylation with bromoacetyl derivatized oligonucleotides, and by site specific triple helix mediated methylase inhibition followed by digestion with the cognate endonuclease. Cleavage of genomic substrates with progressively greater complexity is described. Bacteriophage [lambda] genomic DNA (48.5 kilobase pairs) was targeted at a single endogenous homopurine site within the origin of replication. This substrate was also used to demonstrate cooperative binding of heterologous oligonucleotides to duplex DNA at contiguous binding sites. An engineered target site on yeast chromosome III (340 kilobase pairs) was cut quantitatively at a single site within total yeast genomic DNA (14 megabase pairs) by both chemical and enzymatic techniques. Techniques for the identification of endogenous triple helix target sites within unsequenced genetic markers were developed and successfully used to characterize a target site on human chromosome 4, proximal to the Huntington disease gene. As a test for the site specific cleavage of gigabase DNA, this site near the end of human chromosome 4 was cleaved by triple helix mediated enzymatic cleavage. This generated a specific 3.6 Mb fragment in greater than 80% yield that contained the entire candidate region for the Huntington mutation.},
doi = {},
url = {https://www.osti.gov/biblio/5981084}, journal = {},
number = ,
volume = ,
place = {United States},
year = {Wed Jan 01 00:00:00 EST 1992},
month = {Wed Jan 01 00:00:00 EST 1992}
}

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