Details

Autor(en) / Beteiligte

• Singh, Mani Prabha
• Jennings, Travis L
• Strouse, Geoffrey F

Titel

Tracking Spatial Disorder in an Optical Ruler by Time-Resolved NSET

Ist Teil von

• The journal of physical chemistry. B, 2009-01, Vol.113 (2), p.552-558

Ort / Verlag

United States: American Chemical Society

Erscheinungsjahr

2009

Quelle

MEDLINE

Beschreibungen/Notizen

• For biomolecular applications, potential interactions between newly developed dye molecules and the biomolecule of interest can dramatically influence the accuracy of optical ruler techniques. By utilizing nanometal surface energy transfer (NSET), an optical technique is developed that allows the nature of interactions between dyes and a biomolecule, namely DNA, to be directly assessed. To demonstrate the method, interactions between well-known molecular dyes based on carboxyfluorescein (FAM, noninteracting) and Cy5 (known intercalator) with DNA is probed. The results demonstrate that FAM exhibits no interactions with the DNA backbone and is adequately represented as a solvent exposed dye, while the commonly used near-IR dye Cy5 exhibits two discrete interactions that depend on the site of appendage and the length of the linker arm. The exact population and nature of Cy5 interaction with the DNA indicates a 37% ratio of intercalation for the internal C6, a 42% ratio for an internal C3 spacer length, and no evidence of interaction for terminal labeling. The results allow quantitative assignment of the site occupation of donors to be analyzed providing a powerful set of information for use of dyes in FRET based optical ruler technologies without the need of single molecule methods or the assumption of an averaged site occupation for the donor.