Measuring a slight difference in stretch between GC and at rich regions within the human genome

Jeffrey G. Reifenberger, Hui Min Chuang, Kevin D. Dorfman, Han Cao

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

We present a method for measuring the difference in stretch between GC and AT rich regions within genomic DNA from a human cell line NA 12878. Individual molecules of long DNA contain fluorescent labels at a 7 base recognition site from Nt.BspQI and are confined in an array of nanochannels allowing for the molecules to be aligned to the human reference. Data was collected on over 450,000 DNA molecules and once aligned, the fluorescent nick sites within individual molecules provided a precise ruler for measuring stretch based on the known GC content within a pair of nick sites.

Original languageEnglish (US)
Title of host publication21st International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2017
PublisherChemical and Biological Microsystems Society
Pages289-290
Number of pages2
ISBN (Electronic)9780692941836
StatePublished - Jan 1 2020
Event21st International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2017 - Savannah, United States
Duration: Oct 22 2017Oct 26 2017

Publication series

Name21st International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2017

Conference

Conference21st International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2017
CountryUnited States
CitySavannah
Period10/22/1710/26/17

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Keywords

  • DNA
  • GC content
  • Nanochannel
  • Stretch

Cite this

Reifenberger, J. G., Chuang, H. M., Dorfman, K. D., & Cao, H. (2020). Measuring a slight difference in stretch between GC and at rich regions within the human genome. In 21st International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2017 (pp. 289-290). (21st International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2017). Chemical and Biological Microsystems Society.