Single molecule transcription profiling with AFM

Jason Reed, Bhubaneswar 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

Fingerprint

Transcription
atomic force microscopy
Molecules
constrictions
molecules
plasmids
gene expression
Microarrays
nanotechnology
Nanotechnology
Gene expression
genes
enzymes
coding
Plasmids
Enzymes
Complementary DNA
Genes
Tissue
sensitivity

ASJC Scopus subject areas

  • Engineering (miscellaneous)
  • Materials Science(all)
  • Physics and Astronomy (miscellaneous)

Cite this

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

Single molecule transcription profiling with AFM. / Reed, Jason; Mishra, Bhubaneswar; Pittenger, Bede; Magonov, Sergei; Troke, Joshua; Teitell, Michael A.; Gimzewski, James K.

In: Nanotechnology, Vol. 18, No. 4, 044032, 31.01.2007.

Research output: Contribution to journalArticle

Reed, J, Mishra, B, Pittenger, B, Magonov, S, Troke, J, Teitell, MA & Gimzewski, JK 2007, 'Single molecule transcription profiling with AFM', Nanotechnology, vol. 18, no. 4, 044032. https://doi.org/10.1088/0957-4484/18/4/044032
Reed J, Mishra B, Pittenger B, Magonov S, Troke J, Teitell MA et al. Single molecule transcription profiling with AFM. Nanotechnology. 2007 Jan 31;18(4). 044032. https://doi.org/10.1088/0957-4484/18/4/044032
Reed, Jason ; Mishra, Bhubaneswar ; Pittenger, Bede ; Magonov, Sergei ; Troke, Joshua ; Teitell, Michael A. ; Gimzewski, James K. / Single molecule transcription profiling with AFM. In: Nanotechnology. 2007 ; Vol. 18, No. 4.
@article{3d87c448b9da4527a60a65f16792a990,
title = "Single molecule transcription profiling with AFM",
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.",
author = "Jason Reed and Bhubaneswar Mishra and Bede Pittenger and Sergei Magonov and Joshua Troke and Teitell, {Michael A.} and Gimzewski, {James K.}",
year = "2007",
month = "1",
day = "31",
doi = "10.1088/0957-4484/18/4/044032",
language = "English (US)",
volume = "18",
journal = "Nanotechnology",
issn = "0957-4484",
publisher = "IOP Publishing Ltd.",
number = "4",

}

TY - JOUR

T1 - Single molecule transcription profiling with AFM

AU - Reed, Jason

AU - Mishra, Bhubaneswar

AU - Pittenger, Bede

AU - Magonov, Sergei

AU - Troke, Joshua

AU - Teitell, Michael A.

AU - Gimzewski, James K.

PY - 2007/1/31

Y1 - 2007/1/31

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=33846809306&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=33846809306&partnerID=8YFLogxK

U2 - 10.1088/0957-4484/18/4/044032

DO - 10.1088/0957-4484/18/4/044032

M3 - Article

VL - 18

JO - Nanotechnology

JF - Nanotechnology

SN - 0957-4484

IS - 4

M1 - 044032

ER -