Base stacking in A fluorescent dinucleoside monophosphate: εApεA

B. M. Baker; J. Vanderkool; N. R. Kallenbach

doi:10.1002/bip.1978.360170519

Base stacking in A fluorescent dinucleoside monophosphate: εApεA

B. M. Baker, J. Vanderkool, N. R. Kallenbach

Chemistry

Research output: Contribution to journal › Article › peer-review

Abstract

The optical properties of the 1,N⁶ ‐ etheno derivative of ApA (εApεA) have been studied. Absorbance and CD measurements suggest that (1) neutral salts tend to unstack this molecule and (2) the stacking interaction is weaker than in ApA. εApεA is found to be quenched strongly with respect to the monomer. (εAMP); this quenching is solvent dependent (1M NaCl > 5M NaClo₄>40%glycerol) and increases with the ratio of temperature to viscosity (T/η) in each case. Fluorescence lifetime measurements also reveal a temperature‐ and solvent‐dependent decay which is nonlinear on a semilog plot. In the presence of 95% glycerol, this decay return to linearity. These data have been considered from two points of view: (1) two‐state pictures which are based on thermodynamic least‐squares fit to quatum yield and CD curves, together with two exponential fits to the decay curves and (2) a dynamical model in which relatives fluorophore motion leads to deexcitation via intramolecular collision. A simple model of type (2) gives qualitative agreement with the observed behavior.

Original language	English (US)
Pages (from-to)	1361-1372
Number of pages	12
Journal	Biopolymers
Volume	17
Issue number	5
DOIs	https://doi.org/10.1002/bip.1978.360170519
State	Published - May 1978

ASJC Scopus subject areas

Biophysics
Biochemistry
Biomaterials
Organic Chemistry

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title = "Base stacking in A fluorescent dinucleoside monophosphate: εApεA",

abstract = "The optical properties of the 1,N6 ‐ etheno derivative of ApA (εApεA) have been studied. Absorbance and CD measurements suggest that (1) neutral salts tend to unstack this molecule and (2) the stacking interaction is weaker than in ApA. εApεA is found to be quenched strongly with respect to the monomer. (εAMP); this quenching is solvent dependent (1M NaCl > 5M NaClo4>40%glycerol) and increases with the ratio of temperature to viscosity (T/η) in each case. Fluorescence lifetime measurements also reveal a temperature‐ and solvent‐dependent decay which is nonlinear on a semilog plot. In the presence of 95% glycerol, this decay return to linearity. These data have been considered from two points of view: (1) two‐state pictures which are based on thermodynamic least‐squares fit to quatum yield and CD curves, together with two exponential fits to the decay curves and (2) a dynamical model in which relatives fluorophore motion leads to deexcitation via intramolecular collision. A simple model of type (2) gives qualitative agreement with the observed behavior.",

author = "Baker, {B. M.} and J. Vanderkool and Kallenbach, {N. R.}",

year = "1978",

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doi = "10.1002/bip.1978.360170519",

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AU - Baker, B. M.

AU - Vanderkool, J.

AU - Kallenbach, N. R.

PY - 1978/5

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N2 - The optical properties of the 1,N6 ‐ etheno derivative of ApA (εApεA) have been studied. Absorbance and CD measurements suggest that (1) neutral salts tend to unstack this molecule and (2) the stacking interaction is weaker than in ApA. εApεA is found to be quenched strongly with respect to the monomer. (εAMP); this quenching is solvent dependent (1M NaCl > 5M NaClo4>40%glycerol) and increases with the ratio of temperature to viscosity (T/η) in each case. Fluorescence lifetime measurements also reveal a temperature‐ and solvent‐dependent decay which is nonlinear on a semilog plot. In the presence of 95% glycerol, this decay return to linearity. These data have been considered from two points of view: (1) two‐state pictures which are based on thermodynamic least‐squares fit to quatum yield and CD curves, together with two exponential fits to the decay curves and (2) a dynamical model in which relatives fluorophore motion leads to deexcitation via intramolecular collision. A simple model of type (2) gives qualitative agreement with the observed behavior.

AB - The optical properties of the 1,N6 ‐ etheno derivative of ApA (εApεA) have been studied. Absorbance and CD measurements suggest that (1) neutral salts tend to unstack this molecule and (2) the stacking interaction is weaker than in ApA. εApεA is found to be quenched strongly with respect to the monomer. (εAMP); this quenching is solvent dependent (1M NaCl > 5M NaClo4>40%glycerol) and increases with the ratio of temperature to viscosity (T/η) in each case. Fluorescence lifetime measurements also reveal a temperature‐ and solvent‐dependent decay which is nonlinear on a semilog plot. In the presence of 95% glycerol, this decay return to linearity. These data have been considered from two points of view: (1) two‐state pictures which are based on thermodynamic least‐squares fit to quatum yield and CD curves, together with two exponential fits to the decay curves and (2) a dynamical model in which relatives fluorophore motion leads to deexcitation via intramolecular collision. A simple model of type (2) gives qualitative agreement with the observed behavior.

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Base stacking in A fluorescent dinucleoside monophosphate: εApεA

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