Towards physiological complexity with in vitro single-molecule biophysics

Philos Trans R Soc Lond B Biol Sci. 2012 Dec 24;368(1611):20120271. doi: 10.1098/rstb.2012.0271. Print 2013 Feb 5.

Abstract

Single-molecule biology has matured in recent years, driven to greater sophistication by the development of increasingly advanced experimental techniques. A progressive appreciation for its unique strengths is attracting research that spans an exceptionally broad swath of physiological phenomena--from the function of nucleosomes to protein diffusion in the cell membrane. Newfound enthusiasm notwithstanding, the single-molecule approach is limited to an intrinsically defined set of biological questions; such limitation applies to all experimental approaches, and an explicit statement of the boundaries delineating each set offers a guide to most fruitfully orienting in vitro single-molecule research in the future. Here, we briefly describe a simple conceptual framework to categorize how submolecular, molecular and intracellular processes are studied. We highlight the domain of single-molecule biology in this scheme, with an emphasis on its ability to probe various forms of heterogeneity inherent to populations of discrete biological macromolecules. We then give a general overview of our high-throughput DNA curtain methodology for studying protein-nucleic acid interactions, and by contextualizing it within this framework, we explore what might be the most enticing avenues of future research. We anticipate that a focus on single-molecule biology's unique strengths will suggest a new generation of experiments with greater complexity and more immediately translatable physiological relevance.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Review

MeSH terms

  • Animals
  • Biological Transport
  • Biophysical Phenomena*
  • Cell Membrane / chemistry
  • Cell Tracking / methods
  • Chromatin Assembly and Disassembly
  • DNA / chemistry*
  • DNA-Binding Proteins / chemistry*
  • Eukaryota / chemistry
  • Eukaryota / cytology*
  • Fluorescent Dyes / chemistry
  • High-Throughput Nucleotide Sequencing
  • Image Processing, Computer-Assisted / methods
  • Lipid Bilayers / chemistry
  • Microscopy, Fluorescence
  • Nucleosomes / chemistry*
  • Protein Interaction Mapping

Substances

  • DNA-Binding Proteins
  • Fluorescent Dyes
  • Lipid Bilayers
  • Nucleosomes
  • DNA