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Douglas E. Smith

Bio: Douglas E. Smith is an academic researcher from University of California, Berkeley. The author has contributed to research in topics: Processivity & Molecular motor. The author has an hindex of 1, co-authored 1 publications receiving 966 citations.

Papers
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Journal ArticleDOI
18 Oct 2001-Nature
TL;DR: The force–velocity relationship of the motor is established and it is found that the rate-limiting step of the machine's cycle is force dependent even at low loads, suggesting that this force may be available for initiating the ejection of the DNA from the capsid during infection.
Abstract: As part of the viral infection cycle, viruses must package their newly replicated genomes for delivery to other host cells. Bacteriophage straight phi29 packages its 6.6-microm long, double-stranded DNA into a 42 x 54 nm capsid by means of a portal complex that hydrolyses ATP. This process is remarkable because entropic, electrostatic and bending energies of the DNA must be overcome to package the DNA to near-crystalline density. Here we use optical tweezers to pull on single DNA molecules as they are packaged, thus demonstrating that the portal complex is a force-generating motor. This motor can work against loads of up to 57 pN on average, making it one of the strongest molecular motors reported to date. Movements of over 5 microm are observed, indicating high processivity. Pauses and slips also occur, particularly at higher forces. We establish the force-velocity relationship of the motor and find that the rate-limiting step of the motor's cycle is force dependent even at low loads. Notably, the packaging rate decreases as the prohead is filled, indicating that an internal force builds up to approximately 50 pN owing to DNA confinement. Our data suggest that this force may be available for initiating the ejection of the DNA from the capsid during infection.

1,022 citations


Cited by
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Journal ArticleDOI
23 Jan 2003-Nature
TL;DR: The specific bonding of DNA base pairs provides the chemical foundation for genetics and this powerful molecular recognition system can be used in nanotechnology to direct the assembly of highly structured materials with specific nanoscale features, as well as in DNA computation to process complex information.
Abstract: The specific bonding of DNA base pairs provides the chemical foundation for genetics. This powerful molecular recognition system can be used in nanotechnology to direct the assembly of highly structured materials with specific nanoscale features, as well as in DNA computation to process complex information. The exploitation of DNA for material purposes presents a new chapter in the history of the molecule.

2,528 citations

Journal ArticleDOI
TL;DR: These techniques are described and illustrated with examples highlighting current capabilities and limitations of single-molecule force spectroscopy.
Abstract: Single-molecule force spectroscopy has emerged as a powerful tool to investigate the forces and motions associated with biological molecules and enzymatic activity. The most common force spectroscopy techniques are optical tweezers, magnetic tweezers and atomic force microscopy. Here we describe these techniques and illustrate them with examples highlighting current capabilities and limitations.

2,155 citations

Journal ArticleDOI
23 Jan 2003-Nature
TL;DR: The basic features of DNA were elucidated during the half-century following the discovery of the double helix, but it is only during the past decade that researchers have been able to manipulate single molecules of DNA to make direct measurements of its mechanical properties.
Abstract: The basic features of DNA were elucidated during the half-century following the discovery of the double helix. But it is only during the past decade that researchers have been able to manipulate single molecules of DNA to make direct measurements of its mechanical properties. These studies have illuminated the nature of interactions between DNA and proteins, the constraints within which the cellular machinery operates, and the forces created by DNA-dependent motors.

1,254 citations

Journal ArticleDOI
TL;DR: Although technical in nature, these developments have important implications for the expanded use of optical tweezers in biochemical research and thus should be of general interest.
Abstract: It has been over 20 years since the pioneering work of Arthur Ashkin, and in the intervening years, the field of optical tweezers has grown tremendously. Optical tweezers are now being used in the investigation of an increasing number of biochemical and biophysical processes, from the basic mechanical properties of biological polymers to the multitude of molecular machines that drive the internal dynamics of the cell. Innovation, however, continues in all areas of instrumentation and technique, with much of this work focusing on the refinement of established methods and on the integration of this tool with other forms of single-molecule manipulation or detection. Although technical in nature, these developments have important implications for the expanded use of optical tweezers in biochemical research and thus should be of general interest. In this review, we address these recent advances and speculate on possible future developments.

1,062 citations

Journal ArticleDOI
TL;DR: In nanopore analytics, individual molecules pass through a single nanopore giving rise to detectable temporary blockades in ionic pore current, which ranges from nucleic acids, peptides, proteins, and biomolecular complexes to organic polymers and small molecules.
Abstract: In nanopore analytics, individual molecules pass through a single nanopore giving rise to detectable temporary blockades in ionic pore current. Reflecting its simplicity, nanopore analytics has gained popularity and can be conducted with natural protein as well as man-made polymeric and inorganic pores. The spectrum of detectable analytes ranges from nucleic acids, peptides, proteins, and biomolecular complexes to organic polymers and small molecules. Apart from being an analytical tool, nanopores have developed into a general platform technology to investigate the biophysics, physicochemistry, and chemistry of individual molecules (critical review, 310 references).

1,022 citations