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15 Nov 2004

Volume 85, Issue 20, pp. 4561-4807

Issue Cover Spotlight Figure

Appl. Phys. Lett. 85, 4768 (2004); http://dx.doi.org/10.1063/1.1818331 (3 pages)

G. Walter, N. Holonyak, M. Feng, and R. Chan
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Kinetic measurement of ribosome motor stalling force

Deepak Kumar Sinha, U. S. Bhalla, and G. V. Shivashankar

Appl. Phys. Lett. 85, 4789 (2004); http://dx.doi.org/10.1063/1.1821647 (3 pages) | Cited 7 times

Online Publication Date: 16 November 2004

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We measure the ribosome motor stalling forces to unzip mRNA polymers during gene expression. An approach of using the changes in the reaction rate constants to determine the molecular motor forces is presented. Specific antisense DNA oligomers complementary to mRNA templates are used as kinetic barriers for estimating the ribosome forces using real time bioluminescence detection of luciferase gene expression. The rate constants are determined by comparing the experimental data with numerical simulation of gene expression to deduce the ribosome force (26.5±1 pN) required to unzip mRNA polymers. Understanding the forces generated by the ribosome may also enable the construction of information-based artificial nanoscale machines.
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87.14.G- Nucleic acids
87.15.M- Spectra of biomolecules
87.16.Nn Motor proteins (myosin, kinesin dynein)
82.20.Pm Rate constants, reaction cross sections, and activation energies

Direct determination of the equilibrium unbinding potential profile for a short DNA duplex from force spectroscopy data

Aleksandr Noy

Appl. Phys. Lett. 85, 4792 (2004); http://dx.doi.org/10.1063/1.1819982 (3 pages) | Cited 3 times

Online Publication Date: 16 November 2004

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Modern force microscopy techniques allow researchers to use mechanical forces to probe interactions between biomolecules. However, such measurements often happen in nonequilibrium regime, which precludes straightforward extraction of the equilibrium energy information. Here we use the work-averaging method based on Jarzynski equality to reconstruct the equilibrium interaction potential from the unbinding of a complementary 14-mer DNA duplex from the results of nonequilibrium single-molecule measurements. The reconstructed potential reproduces most of the features of the DNA stretching transition, previously observed only in equilibrium stretching of long DNA sequences. We also compare the reconstructed potential with the thermodynamic parameters of DNA duplex unbinding and show that the reconstruction accurately predicts duplex melting enthalpy.
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87.14.G- Nucleic acids
68.37.Ps Atomic force microscopy (AFM)
65.40.G- Other thermodynamical quantities
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