NSET Molecular Beacon Analysis of Hammerhead RNA Substrate Binding and Catalysis

Jennings, Travis L.; Schlatterer, Jörg C.; Singh, Mukesh Kumar; Greenbaum, Nancy L.; Strouse, Geoffrey F.

doi:10.1021/nl052458a

Cited by 94 publications

(167 citation statements)

References 33 publications

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“…NSET has mainly been found to be in good agreement with experimental data (using organic dyes and quantum dots as donors) if the nanoparticles are of small size (below about 3 nm diameter) and thus do not have any plasmon bands [79,80,82,84,87,88]. Nevertheless, also larger Au nanoparticles of up to 18 nm diameters showed experimental NSET behavior [77,78,90,91].…”

Section: Bret and Cretsupporting

confidence: 74%

“…Copyright 2012, American Chemical Society.) distance dependence, which has been investigated in theory [71][72][73][74][75][76] and in practice for different energy donors such as organic dyes [77][78][79][80][81][82][83][84], semiconductor quantum dots [85][86][87][88][89][90], or fluorescent proteins [91]. Among all these different systems, different mechanisms have been proposed to be responsible for the energy transfer and a general model for energy transfer to metal nanoparticles does not exist.…”

Section: Bret and Cretmentioning

confidence: 99%

“…The NSET model proposed by Strouse and coworkers [79,80,[82][83][84] uses a d À4 distance dependence (n ¼ 4), which significantly increases (about twofold) the distance range of FRET. They proposed the following NSET transfer rate:…”

Section: Bret and Cretmentioning

confidence: 99%

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How to Apply FRET: From Experimental Design to Data Analysis

Hildebrandt

2013

FRET – Förster Resonance Energy Transfer

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Introduction: FRET -More Than a Four-Letter Word! F€ orster resonance energy transfer (FRET) is a very special scientific topic because it inspires and challenges many theoretical and experimental scientists from different research disciplines ranging from the fundamental life sciences over theoretical physics and chemistry up to applied technology in physics, electronics, chemistry, medicine, and biology. Almost as versatile as the topic itself is the discussion about the acronym FRET or rather about the first letter "F." Should it be "F" like fluorescence, which is most often involved in FRET experiments (although FRET is a nonradiative energy transfer)? Or "F" like F€ orster, who was the first person to develop a theory relating spectroscopic data such as absorption and emission spectra to the energy transfer efficiency, donor-acceptor molecule distances and orientations (although many other scientists were involved in the discovery of FRET)? Or should the "F" be completely erased in order to circumvent the discussion (or to avoid four-letter words)? Personally, I prefer to use "F€ orster" in acknowledgment of his achievements and in order to avoid the term fluorescence, but probably the most important aspect of this discussion is the fact that it is not an important discussion. FRET is a very useful and interesting technology and its experimental application and theoretical treatment for the many possible FRET systems should be investigated, discussed, and developed. Although the main theory was contributed by F€ orster in the 1940s, FRET is a very modern technology because the r À6 distance dependence over approximately 1-20 nm fits extremely well into the recent discoveries and investigations in nanoscience and nanobiotechnology [1]. The everincreasing number of donor-acceptor pairs (cf. Chapter 14) is another evidence for the contemporary relevance of FRET.This chapter will cover the main aspects of what FRET is, what FRET can be used for (and for what it should better not be used), how a FRET experiment should be designed and performed, what mathematics is absolutely necessary, and how the experimental results can be processed and interpreted. It must also be mentioned that there is no one recipe for all FRET experiments. The main part of this chapter should rather be understood as a guide to FRET, providing useful information that FRET -Förster Resonance Energy Transfer: From Theory to Applications, First Edition. Edited by Igor Medintz and Niko Hildebrandt.

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Section: Bret and Cretsupporting

confidence: 74%

Section: Bret and Cretmentioning

confidence: 99%

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How to Apply FRET: From Experimental Design to Data Analysis

Hildebrandt

2013

FRET – Förster Resonance Energy Transfer

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“…Molecular beacon-based assays for DNA sensing measurements, for example, produce 100-fold sensitivity enhancements using Au NMs compared to previous dye-dye combinations [466][467][468][469]. Au NP-fluorophore complexes show promise for in vitro diagnostic applications as "noses," with the ability to discern between various bacteria species and strains, proteins in complex solutions, and between cancerous and healthy cell lines [470].…”

Section: 53mentioning

confidence: 99%

Materials for FRET Analysis: Beyond Traditional Dye–Dye Combinations

Sapsford

Wildt

Mariani

et al. 2013

FRET – Förster Resonance Energy Transfer

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The intrinsic sensitivity (r 6 dependence) of F€ orster (or fluorescence) resonance energy transfer (FRET) to nanoscale changes in the donor/acceptor separation distance has made FRET an invaluable biophysical tool in a variety of applications, ranging from studying the structure and conformation of proteins and nucleic acids to examining biomolecular interactions, including its use in in vitro and in vivo bioassays [1][2][3][4][5][6][7]. While the myriad of FRET configurations and techniques currently in use are covered throughout this book, here we focus primarily on the materials utilized as donor or acceptor probes in FRET rather than the process itself [3,5,8,9]. Our 2006 review paper on this topic serves as the foundation for this updated chapter [3]. The materials were divided into three main categories: organic materials that include "traditional" dye fluorophores, dark quenchers, polymers, and carbon nanomaterials (NMs); inorganic materials such as metal chelates, metal, and semiconductor nanocrystals; and fluorophores of biological origin such as fluorescent proteins (FPs), amino acids, and fluorescence generated from enzymatic bioluminescence (BL) and chemiluminescence (CL). These materials may function as FRET donors and/or acceptors, depending upon experimental design. Many of the new materials developed and/or new donor-acceptor probe combinations used address some of the inherent complications of more traditional FRET materials, including photobleaching, spectral cross talk, and direct excitation of the acceptor species, and examples of these will be highlighted and discussed throughout the chapter. Since the vast majority of FRET applications are biological in nature, they routinely involve some type of biomolecule labeling strategy, which ultimately plays a significant and fundamental role in the success and interpretation of the resulting FRET. Therefore, we begin the chapter with a brief discussion of the bioconjugation techniques commonly utilized for FRET and points to consider, followed by sections highlighting the current and emerging materials that are used, or have the potential to be used, in FRET applications.

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“…As such, the use of AuNPs as energy acceptors enables the energy transfer to be valid even in the excess distance of the traditional FRET. One of the feasible mechanisms might be associated with the property of metal surface; it was reported that the metal surface extended the effective energy transfer distance up to 22 nm, resulting in a high energy transfer efficiency (Dulkeith et al, 2002;Jennings et al, 2006a;Jennings et al, 2006b;Pons et al, 2007;Yun et al, 2005). The initial report of protease detection with a QD-AuNP system was made by Chang et al (Chang et al, 2005).…”

Section: Qdmentioning

confidence: 99%

Energy Transfer-Based Multiplex Analysis Using Quantum Dots

Kim¹

2012

Quantum Dots - A Variety of New Applications

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NSET Molecular Beacon Analysis of Hammerhead RNA Substrate Binding and Catalysis

Cited by 94 publications

References 33 publications

How to Apply FRET: From Experimental Design to Data Analysis

How to Apply FRET: From Experimental Design to Data Analysis

Materials for FRET Analysis: Beyond Traditional Dye–Dye Combinations

Energy Transfer-Based Multiplex Analysis Using Quantum Dots

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