Single molecule transcription profiling with AFM**Based on invited talk at the International Conference on Nanoscience and Technology2006.

Abstract

Established techniques for global gene expression profiling, such as microarrays, facefundamental sensitivity constraints. Due to greatly increasing interest in examining minutesamples from micro-dissected tissues, including single cells, unorthodox approaches,including molecular nanotechnologies, are being explored in this application. Here, weexamine the use of single molecule, ordered restriction mapping, combined with AFM, tomeasure gene transcription levels from very low abundance samples. We frame the problemmathematically, using coding theory, and present an analysis of the critical error sourcesthat may serve as a guide to designing future studies. We follow with experiments detailingthe construction of high density, single molecule, ordered restriction maps fromplasmids and from cDNA molecules, using two different enzymes, a result notpreviously reported. We discuss these results in the context of our calculations.