Energy transfer double resonance

Okamura, Y. and Watanabe, Y. (2006). Detecting RNA/DNA hybridization using double-labeled donor probes with enhanced fluorescence resonance energy transfer signals. Methods Mol. Biol. 335, 43-56. 

Double-resonance spectroscopy involves the use of two different sources of radiation. In the context of EPR, these usually are a microwave and a radiowave or (less common) a microwave and another microwave. The two combinations were originally called ENDOR (electron nuclear double resonance) and ELDOR (electron electron double resonance), but the development of many variations on this theme has led to a wide spectrum of derived techniques and associated acronyms, such as ESEEM (electron spin echo envelope modulation), which is a pulsed variant of ENDOR, or DEER (double electron electron spin resonance), which is a pulsed variant of ELDOR. The basic principle involves the saturation (partially or wholly) of an EPR absorption and the subsequent transfer of spin energy to a different absorption by means of the second radiation, leading to the detection of the difference signal. The requirement of saturability implies operation at close to liquid helium, or even lower, temperatures, which, combined with long experimentation times, produces a... 

The free energy of activation for the proton shift process in the interconversion between tautomeric forms 8 and 9 was measured by the Fors6n-Hoffman double resonance saturation transfer method and determined to be 16.2 kcal mof1 (Figure 7) <20040BC1227>. This value was an average over three different structures (R = Me, Et, Pr1). 

Norman, D. G., Grainger, R. J., Uhrin, D., and Lilley, D. M. J. (2000). The location of Cyanine-3 on double-stranded DNA importance for fluorescence resonance energy transfer studies. Biochemistry 39, 6317-6324. 

More recently double stranded DNA-binding dyes, (e.g., SYBR Green), have been introduced (Giulietti et al. 2001) which removed the need for an expensive, specific probe to be designed. Other sophisticated tools have been developed to work in conjunction with the Taqman method, for example molecular beacons, scorpions and hybridisation probes. These techniques rely on the FRET (Fluorescence Resonance Energy Transfer) principle but do not require the nuclease activity of the Taq polymerase. The different real-time... 

The 1,3-diazepine 83 (R = CF3, Alk = CH3) has been shown to have the NH structure in the solid state <20040BC1227>. The average free energy of activation for interconversion of the tautomers 83 and 84 (R = H, Aik = Me, Et, Pr1) has been determined to be 16.2 kcal mol1 by the ForsenHoffman double resonance saturation transfer method <20040BC1227>. The most stable tautomeric forms of a variety of diazepine derivatives have been documented in CHEC-III(13) and earlier editions. 

Figure 37-24 Common probes and dyes for real-time PCR. f/J Double-stranded DNA dyes show a significant increase in fluorescence when bound to DNA (hv = excitation light). (2) Adjacent hybridization probes. Fluorescence resonance energy transfer (FRET) is illustrated between a donor and acceptor fluorophore.The x indicates phosphorylation of the 3 terminus of the probe to prevent polymerase extension. (3) FRET between a labeled primer and a single hybridization probe. (4) Hydrolysis probes are cleaved between the reporter and quencher, resulting in increased fluorescence. (5) Hairpin probes are quenched in the native conformation, but increase in fluorescence when hybridized. (6) Hairpin primers retain their native, quenched conformation until they are incorporated into a double-stranded product (Modified with permission of the publisher from Pritham GH, Wittwer CT Continuous f/uorescent monitoring of PCR.J Clin Ug Assay 1998, 21 404-412. 1998 Clinical Ligand Assay Society, Inc.)...

A combination of N CPMAS NMR, N quadrupole double resonance, and x-ray studies of solid 3,5-dimethylpyrazole (19) between 270 K and 350 K has been necessary to discuss the intermolecular proton transfer in a structure like (55) <89JA7304> the experimental evidence (species HHH and DDD) is consistent with a correlated triple hydrogen jump with an activation energy of 11 kcal mol". The cases of 3,5-diphenyl-4-bromopyrazole (a dimer like (54)) and 3,5-diphenyl-pyrazole (a tetramer like (56)) were subsequently studied <92JA9657> here also proton jumps were found with activation energies similar to those found for (19). The dynamic behavior of pyrazole... 

Radford (1961, 1962) and Radford and Broida (1962) presented a complete theory of the Zeeman effect for diatomic molecules that included perturbation effects. This led to a series of detailed investigations of the CN B2E+ (v — 0) A2II (v = 10) perturbation in which many of the techniques of modern high-resolution molecular spectroscopy and analysis were first demonstrated anticrossing spectroscopy (Radford and Broida, 1962, 1963), microwave optical double resonance (Evenson, et at, 1964), excited-state hyperfine structure with perturbations (Radford, 1964), effect of perturbations on radiative lifetimes and on inter-electronic-state collisional energy transfer (Radford and Broida, 1963). A similarly complete treatment of the effect of a magnetic field on the CO a,3E+ A1 perturbation complex is reported by Sykora and Vidal (1998). The AS = 0 selection rule for the Zeeman Hamiltonian leads to important differences between the CN B2E+ A2II and CO a/3E+ A1 perturbation plus Zeeman examples, primarily in the absence in the latter case of interference effects between the Zeeman and intramolecular perturbation terms. 

The nearest-neighbour excited-state exchange matrix elements in dimers of 1,2,4,5-tetrachlorobenzene (TCB) have been independently obtained using high-resolution phosphorescent - microwave double resonance (p.m.d.r.) and o.d.m.r. techniques. The authors conclude that the matrix element for energy transfer in the triplet state of TCB is not the same for dimer and exciton states. 

To illustrate reactive vibrational dynamics in a very different type of unimolecular reaction, we consider the trans-cis isomerization of diimide (HNNH). The central N—N bond is a double bond, so the barrier to isomerization from trans to cis is quite high, 192 kJ/mol. Spears (63,64) developed a model to describe the high-energy vibrations of diimide in all six degrees of freedom. We demonstrated that nonlinear resonance interactions are critical to the dynamics of mode-mode energy transfer into and out of the torsional vibration (63). We also found, however, that these resonant interactions were detuned before the excitation of the torsional mode was sufficient to achieve isomerization. 

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