Seeing genetic and epigenetic information without DNA denaturation using sequence-enabled reassembly (SEER)

Jason R. Porter, Sarah H. Lockwood, David J. Segal, Indraneel Ghosh

Research output: Chapter in Book/Report/Conference proceedingChapter

1 Citation (Scopus)

Abstract

Virtually all methods for reading the sequence of bases in DNA rely on the ability to denature double-stranded DNA into single strands and then use Watson-Crick base-pairing rules to hybridize the strands with high specificity to another DNA primer or probe. However, nature frequently uses an alternative method, reading the sequence information directly from double-stranded DNA using sequence-specific DNA-binding proteins. Here we describe methods for the construction and testing of sequence probes based on engineered zinc finger DNA-binding proteins. Background is reduced using split-reporter molecules, and signal is amplified using enzymatic reporters. The resulting sequence-enabled reassembly (SEER) probes can be configured to detect DNA sequence (genetic) or DNA methylation (epigenetic) information.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
Pages365-382
Number of pages18
Volume649
DOIs
StatePublished - 2010

Publication series

NameMethods in Molecular Biology
Volume649
ISSN (Print)10643745

Fingerprint

Nucleic Acid Denaturation
Epigenomics
DNA-Binding Proteins
Reading
DNA
DNA Primers
Zinc Fingers
DNA Probes
DNA Methylation
Base Pairing

Keywords

  • beta-lactamase
  • diagnostics
  • DNA sequence
  • Double-stranded DNA
  • engineered zinc finger proteins
  • fluorescent detection
  • green florescent protein
  • luciferase
  • methylation

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics
  • Medicine(all)

Cite this

Porter, J. R., Lockwood, S. H., Segal, D. J., & Ghosh, I. (2010). Seeing genetic and epigenetic information without DNA denaturation using sequence-enabled reassembly (SEER). In Methods in Molecular Biology (Vol. 649, pp. 365-382). (Methods in Molecular Biology; Vol. 649). https://doi.org/10.1007/978-1-60761-753-2_23

Seeing genetic and epigenetic information without DNA denaturation using sequence-enabled reassembly (SEER). / Porter, Jason R.; Lockwood, Sarah H.; Segal, David J.; Ghosh, Indraneel.

Methods in Molecular Biology. Vol. 649 2010. p. 365-382 (Methods in Molecular Biology; Vol. 649).

Research output: Chapter in Book/Report/Conference proceedingChapter

Porter, JR, Lockwood, SH, Segal, DJ & Ghosh, I 2010, Seeing genetic and epigenetic information without DNA denaturation using sequence-enabled reassembly (SEER). in Methods in Molecular Biology. vol. 649, Methods in Molecular Biology, vol. 649, pp. 365-382. https://doi.org/10.1007/978-1-60761-753-2_23
Porter JR, Lockwood SH, Segal DJ, Ghosh I. Seeing genetic and epigenetic information without DNA denaturation using sequence-enabled reassembly (SEER). In Methods in Molecular Biology. Vol. 649. 2010. p. 365-382. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-60761-753-2_23
Porter, Jason R. ; Lockwood, Sarah H. ; Segal, David J. ; Ghosh, Indraneel. / Seeing genetic and epigenetic information without DNA denaturation using sequence-enabled reassembly (SEER). Methods in Molecular Biology. Vol. 649 2010. pp. 365-382 (Methods in Molecular Biology).
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