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Proceedings Paper

Changes in the end-to-end distance distribution in an oligonucleotide following hybridization
Author(s): Lawrence J. Parkhurst; Kay M. Parkhurst
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Paper Abstract

A 16-mer deoxy oligonucleotide was labeled at the 5' end with x- rhodamine and at the 3' end with fluorescein. The fluorescence lifetime of the donor, fluorescein, under conditions for resonance energy transfer, was studied using the SLM 4850 multiharmonic frequency phase fluorometer in order to obtain information on the end-to-end distance distribution P(R) in the oligomer. When this doubly labeled oligonucleotide was hybridized to its 16-mer complement, the fluorescein fluorescence decay could be very well described by a P(R) that was a symmetric shifted Gaussian with center at 68.4 angstrom and (sigma) equals6.4 angstrom. Simulations suggested that part of the width might be attributable to a distribution in (kappa) 2. In the single- stranded labeled oligomer, there was enhanced energy transfer from the fluorescein to the rhodamine and the best fitting symmetrical shifted Gaussian representation of P(R) was centered at 53.8 angstrom with (kappa) equals6.9 angstrom. There was significant lack of fit with this model, however. A model independent procedure was developed for extracting P(R) as a sum of weighted Hermite polynomials. This procedure gave a P(R) with a large negative region at R<20 angstrom, suggesting that rotational averaging for (kappa) 2 was not quite complete prior to significant decay of the donor excited state.

Paper Details

Date Published: 17 August 1994
PDF: 9 pages
Proc. SPIE 2137, Time-Resolved Laser Spectroscopy in Biochemistry IV, (17 August 1994); doi: 10.1117/12.182758
Show Author Affiliations
Lawrence J. Parkhurst, Univ. of Nebraska (United States)
Kay M. Parkhurst, Univ. of Nebraska (United States)

Published in SPIE Proceedings Vol. 2137:
Time-Resolved Laser Spectroscopy in Biochemistry IV
Joseph R. Lakowicz, Editor(s)

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