Single molecule transcription profiling with AFM

Jason Reed, Bud Mishra, Bede Pittenger, Sergei Magonov, Joshua Troke, Michael A. Teitell, James K. Gimzewski

Research output: Contribution to journalArticle

Abstract

Established techniques for global gene expression profiling, such as microarrays, face fundamental sensitivity constraints. Due to greatly increasing interest in examining minute samples from micro-dissected tissues, including single cells, unorthodox approaches, including molecular nanotechnologies, are being explored in this application. Here, we examine the use of single molecule, ordered restriction mapping, combined with AFM, to measure gene transcription levels from very low abundance samples. We frame the problem mathematically, using coding theory, and present an analysis of the critical error sources that may serve as a guide to designing future studies. We follow with experiments detailing the construction of high density, single molecule, ordered restriction maps from plasmids and from cDNA molecules, using two different enzymes, a result not previously reported. We discuss these results in the context of our calculations.

Original languageEnglish (US)
Article number044032
JournalNanotechnology
Volume18
Issue number4
DOIs
StatePublished - Jan 31 2007

ASJC Scopus subject areas

  • Bioengineering
  • Chemistry(all)
  • Materials Science(all)
  • Mechanics of Materials
  • Mechanical Engineering
  • Electrical and Electronic Engineering

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    Reed, J., Mishra, B., Pittenger, B., Magonov, S., Troke, J., Teitell, M. A., & Gimzewski, J. K. (2007). Single molecule transcription profiling with AFM. Nanotechnology, 18(4), [044032]. https://doi.org/10.1088/0957-4484/18/4/044032