Time-resolved fluorescence resonance energy transfer: A versatile tool for the analysis of nucleic acids

Klostermeier, Dagmar; Millar, David P.

doi:10.1002/bip.10146

Cited by 102 publications

(72 citation statements)

References 50 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…The phenomenon of FRET describes the transfer of energy from a fluorophore (donor) in an excited state to a neighboring fluorophore (acceptor) through dipole-dipole interaction occurring in the range of 1-10 nm (14). It can be used for quantitative determination of molecular proximity and intermolecular interactions (36) including protein-protein (22,39), protein-DNA (25), protein-membrane, and three-dimensional structure of molecules (6,23).…”

Section: Resultsmentioning

confidence: 99%

High mobility group box 1 protein interacts with multiple Toll-like receptors

Park¹,

Gamboni‐Robertson²,

He³

et al. 2006

American Journal of Physiology-Cell Physiology

818

605

View full text Add to dashboard Cite

High mobility group box 1 (HMGB1), originally described as a DNA-binding protein, can also be released extracellularly and functions as a late mediator of inflammatory responses. Although recent reports have indicated that the receptor for advanced glycation end products (RAGE) as well as Toll-like receptor (TLR)2 and TLR4 are involved in cellular activation by HMGB1, there has been little evidence of direct association between HMGB1 and these receptors. To examine this issue, we used fluorescence resonance energy transfer (FRET) and immunoprecipitation to directly investigate cell surface interactions of HMGB1 with TLR2, TLR4, and RAGE. FRET images in RAW264.7 macrophages demonstrated association of HMGB1 with TLR2 and TLR4 but not RAGE. Transient transfections into human embryonic kidney-293 cells showed that HMGB1 induced cellular activation and NF-Bdependent transcription through TLR2 or TLR4 but not RAGE. Coimmunoprecipitation also found interaction between HMGB1 and TLR2 as well as TLR4, but not with RAGE. These studies provide the first direct evidence that HMGB1 can interact with both TLR2 and TLR4 and also supply an explanation for the ability of HMGB1 to induce cellular activation and generate inflammatory responses that are similar to those initiated by LPS. fluorescence resonance energy transfer; receptor of advanced glycation end products HIGH MOBILITY GROUP BOX 1 (HMGB1) protein, originally described as a DNA-binding protein that stabilizes nucleosomes and facilitates transcription, can also be released extracellularly by monocytes and macrophages stimulated by LPS, TNF-␣, or IL-1 (2, 44). Extracellular HMGB1 has been demonstrated to participate in inflammatory processes, including delayed endotoxin lethality and acute lung injury (1,44,46), and also appears to be involved in pathophysiological processes associated with cellular necrosis, such as acetaminophen-induced liver injury (34).Although HMGB1 and LPS appear to initiate similar intracellular events, including activation of kinases such as p38, ERK1/2, and Akt and transcriptional factors including NF-B, that lead to production of proinflammatory cytokines, gene arrays demonstrated differences in expression profiles with each of these stimuli (12, 30). Unlike LPS, which primarily increased the activity of IKK-␤, HMGB1 exposure resulted in activation of both IKK-␣ and IKK-␤ (31). In addition, culture of neutrophils lacking Toll-like receptor (TLR)4 with HMGB1, but not with LPS, still resulted in enhanced nuclear translocation of NF-B (31). Such results suggest that the receptors interacting with HMGB1 and leading to cellular activation and gene transcription are likely to be distinct from TLR4, which is responsible for LPS-induced responses (40). Recent data indicate that HMGB1 interacts not only with TLR4 but also with TLR2 and the receptor for advanced glycation end products (RAGE) (31, 46). In particular, a decrease in NF-B-dependent reporter gene expression after transfection with dominantnegative constructs to TLR2, TLR4, or both, demonstr...

show abstract

Section: Resultsmentioning

confidence: 99%

High mobility group box 1 protein interacts with multiple Toll-like receptors

Park¹,

Gamboni‐Robertson²,

He³

et al. 2006

American Journal of Physiology-Cell Physiology

818

605

View full text Add to dashboard Cite

show abstract

“…For example, fluorophore labeling of RNA at predefined sites is essential for structural and functional investigation (Walter and Burke 2000;Klostermeier and Millar 2001b;Sastry 2001;Walter 2001;Walter et al 2001). Specific 5Ј-end modifications of RNA may be achieved through transcription initiation with 5Ј-modified guanosine derivatives (Burgin and Pace 1990;Seelig and Jaschke 1999;Sastry 2001;Zhang et al 2001a,b).…”

Section: Discussionmentioning

confidence: 99%

Synthesis of adenosine derivatives as transcription initiators and preparation of 5′ fluorescein- and biotin-labeled RNA through one-step in vitro transcription

Huang¹,

Wang²,

Coleman³

et al. 2003

RNA

View full text Add to dashboard Cite

Expanding our previous finding of an adenosine-initiated transcription system, we now demonstrate that either the 5 site or the N6 site of adenosine nucleotides can be modified extensively without abolishing their ability to initiate transcription under the T7 2.5 promoter. Two series of amino derivatives of adenosine nucleotides were synthesized. Fluorescein and biotin groups were coupled to AMP derivatives through linkers of different sizes and hydrophobicities. Both fluorescein-and biotin-conjugated (at either the 5 or N6 site) adenosine nucleotides can act as efficient transcription initiators, producing fluorescein-and biotin-labeled RNA at the specific 5 end by a one-step transcription procedure, eliminating posttranscriptional modification. Furthermore, N6-modified adenosine derivative-initiated transcription synthesizes 5 end modified RNA with a free phosphate group, providing the possibility for further derivatization. The current finding makes easily available a variety of site-specifically functionalized RNA, which may be used in nucleic acid detection, RNA structural and functional investigation, and generation and isolation of novel functional RNA.

show abstract

“…This has been demonstrated clearly by FRET studies on nucleic acid constructs. [26] Systems such as DNA four-way junctions (Holliday junctions) [27] and the RNA K-turn [28] have revealed dynamic behavior in solution. This can result in erroneous, or misleading, results being obtained from steady-state FRET.…”

Section: Introductionmentioning

confidence: 99%

Distance Determination in Heterogeneous DNA Model Systems by Pulsed EPR

et al. 2007

View full text Add to dashboard Cite

Many biological systems, especially those based on nucleic acids, are structurally heterogeneous in solution. We demonstrate here the ability to measure multiple distances, of between 2 and 7 nm, from a heterogeneous mixture of double-spin-labeled DNA duplexes. We have constructed a DNA distance ruler based on the attachment of nitroxide spin labels to 2'-amino-modified nucleosides. The distribution of distances between the spin labels was obtained by Tikhonov regularization analysis of the dipolar coupling evolution data measured by using the electron paramagnetic resonance method, pulsed-electron double resonance (PELDOR). Optimization of the conditions and techniques used in the preparation of the samples has allowed us to increase the sensitivity and reduce aggregation artifacts. As a result, we have been able to demonstrate deconvolution of distances from structurally heterogeneous samples and show the limits of the technique by examining data derived from up to five DNA duplexes, in a single mixture, in which the concentration of each species was as low as 5 microM.

show abstract

Time-resolved fluorescence resonance energy transfer: A versatile tool for the analysis of nucleic acids

Cited by 102 publications

References 50 publications

High mobility group box 1 protein interacts with multiple Toll-like receptors

High mobility group box 1 protein interacts with multiple Toll-like receptors

Synthesis of adenosine derivatives as transcription initiators and preparation of 5′ fluorescein- and biotin-labeled RNA through one-step in vitro transcription

Distance Determination in Heterogeneous DNA Model Systems by Pulsed EPR

Contact Info

Product

Resources

About