Title:
Repair, consequence, and profile of ribonucleotides in DNA

dc.contributor.author Koh, Kyung Duk
dc.contributor.department Biology
dc.date.accessioned 2015-06-08T18:31:31Z
dc.date.available 2015-06-08T18:31:31Z
dc.date.created 2015-05
dc.date.issued 2015-03-12
dc.date.submitted May 2015
dc.date.updated 2015-06-08T18:31:31Z
dc.description.abstract Ribonucleotides, also known as ribonucleoside monophosphates (rNMPs), are the most abundant non-canonical nucleotides incorporated into genomic DNA. Despite the relevance, information about their repair pathways, consequences, and profiles is still lacking. Exploiting the use of oligonucleotides containing rNMPs in a molecular approach to generate various RNA/DNA hybrids of chosen sequence and structure at the chromosomal level in cells, we show that mispaired rNMPs embedded into genomic DNA are not only targeted by ribonucleases H (RNases H) but also by the mismatch repair (MMR) system both in E. coli and S. cerevisiae cells. In addition, we discovered that paired rNMPs in DNA are targets of both RNase H type 2 and nucleotide excision repair (NER) in yeast. Also, we report atomic force microscopy (AFM)-based single molecule elasticity measurement, molecular dynamics simulation, and nuclear magnetic resonance spectroscopy results, showing that rNMPs in short DNA duplexes can change the elastic and structural properties of DNA. Lastly, we developed ribose-seq, a method for capturing rNMPs embedded in DNA. High-throughput sequencing of rNMP-captured molecules from the yeast S. cerevisiae revealed widespread but non-random rNMP distribution with preferences in base composition of rNMPs and neighboring DNA sequence context in both nuclear and mitochondrial DNA. With ribose-seq, systematic profiling of rNMP incorporation into genomic DNA is achieved, potentially allowing determination of specific signatures of rNMPs in DNA which could help to better understand the nature of rNMP repair mechanisms, effect of rNMPs on DNA mechanical properties and structure, and eventually rNMP impact on genome integrity.
dc.description.degree Ph.D.
dc.format.mimetype application/pdf
dc.identifier.uri http://hdl.handle.net/1853/53534
dc.language.iso en_US
dc.publisher Georgia Institute of Technology
dc.subject Ribonucleotide
dc.subject DNA
dc.subject Sequencing
dc.title Repair, consequence, and profile of ribonucleotides in DNA
dc.type Text
dc.type.genre Dissertation
dspace.entity.type Publication
local.contributor.corporatename College of Sciences
local.contributor.corporatename School of Biological Sciences
relation.isOrgUnitOfPublication 85042be6-2d68-4e07-b384-e1f908fae48a
relation.isOrgUnitOfPublication c8b3bd08-9989-40d3-afe3-e0ad8d5c72b5
thesis.degree.level Doctoral
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