Changes in the end-to-end distance distribution in an oligonucleotide following hybridization

Lawrence J. Parkhurst; Kay M. Parkhurst

doi:10.1117/12.182758

17 August 1994 Changes in the end-to-end distance distribution in an oligonucleotide following hybridization

Lawrence J. Parkhurst, Kay M. Parkhurst

Proceedings Volume 2137, Time-Resolved Laser Spectroscopy in Biochemistry IV; (1994) https://doi.org/10.1117/12.182758
Event: OE/LASE '94, 1994, Los Angeles, CA, United States

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.

Citation Download Citation

Lawrence J. Parkhurst and Kay M. Parkhurst "Changes in the end-to-end distance distribution in an oligonucleotide following hybridization", Proc. SPIE 2137, Time-Resolved Laser Spectroscopy in Biochemistry IV, (17 August 1994); https://doi.org/10.1117/12.182758

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