Maximum-entropy decomposition of fluorescence correlation spectroscopy data: application to liposome?human serum albumin association

Módos, Károly; Galántai, Rita; Bárdos-Nagy, Irén; Wachsmuth, Malte; Tóth, Katalin; Fidy, Judit; Langowski, Jörg

doi:10.1007/s00249-003-0343-6

Cited by 30 publications

(17 citation statements)

References 9 publications

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“…8 Upon increasing albumin concentration, the diffusion time decreases, indicating formation of slower-diffusing species consistent with the expected TSPP association with the protein (85% at [TSPP]/[BSA] = 100). However, a dependence of D with the solution pH is detected: At pH = 7.4, D = (0.65 ± 0.05) × 10 −10 m 2 s −1 , in agreement with literature data obtained with mesoporphyrin IX dihydrochloride by FCS, 38 whereas at pH = 2.5, D = (0.90 ± 0.08) × 10 −10 m 2 s −1 (FIG. 4).…”

Section: Fcssupporting

confidence: 90%

Ordered Self‐assembly of Protonated Porphyrin Induced by the Aqueous Environment of Biomimetic Systems

Andrade¹,

Costa²

2008

Annals of the New York Academy of Sciences

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Water-soluble ionic porphyrins show an interesting self-association pattern in acidic conditions under which highly ordered aggregates are stabilized. Herein we give an overview of the template effect of biological interfaces in tetrakis(4-sulfonatophenyl)porphyrin TSPP self-aggregation, in which we point out the possibility of tuning this process by screening the charge repulsion through ionic strength and pH. We give special emphasis to the use of fluorescence lifetime imaging microscopy and of fluorescence correlation spectroscopy to visualize and characterize these molecular aggregates.

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Section: Fcssupporting

confidence: 90%

Ordered Self‐assembly of Protonated Porphyrin Induced by the Aqueous Environment of Biomimetic Systems

Andrade¹,

Costa²

2008

Annals of the New York Academy of Sciences

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“…An additional approach for analyzing complex translational diffusion data is the maximum entropy method (3,20,23,32). Periasamy and Verkman (32) adopted this approach to analyze both modeled and experimental fluorescence recovery after photobleaching data.…”

Section: Discussionmentioning

confidence: 99%

“…This problem is solved by defining a quantity Q, such that, Q ¼ lS ÿ C, where l is a Lagrange multiplier. Q is extremized in such a way that l is dynamically adjusted guiding the program toward subsequent lower values of x 2 along the path of maximum entropy (K. Garai and S. Maiti, Tata Institute of Fundamental Research, personal communication, 2006) as opposed to the algorithm described by Modos et al (20). For a more detailed explanation on the algorithm per se, see Skilling and Bryan (17).…”

Section: Memfcs and Fickian Diffusionmentioning

confidence: 99%

Multiple Diffusion Mechanisms Due to Nanostructuring in Crowded Environments

Sanabria

Kubota

Waxham

2007

Biophysical Journal

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One of the key questions regarding intracellular diffusion is how the environment affects molecular mobility. Mostly, intracellular diffusion has been described as hindered, and the physical reasons for this behavior are: immobile barriers, molecular crowding, and binding interactions with immobile or mobile molecules. Using results from multi-photon fluorescence correlation spectroscopy, we describe how immobile barriers and crowding agents affect translational mobility. To study the hindrance produced by immobile barriers, we used sol-gels (silica nanostructures) that consist of a continuous solid phase and aqueous phase in which fluorescently tagged molecules diffuse. In the case of molecular crowding, translational mobility was assessed in increasing concentrations of 500 kDa dextran solutions. Diffusion of fluorescent tracers in both sol-gels and dextran solutions shows clear evidence of anomalous subdiffusion. In addition, data from the autocorrelation function were analyzed using the maximum entropy method as adapted to fluorescence correlation spectroscopy data and compared with the standard model that incorporates anomalous diffusion. The maximum entropy method revealed evidence of different diffusion mechanisms that had not been revealed using the anomalous diffusion model. These mechanisms likely correspond to nanostructuring in crowded environments and to the relative dimensions of the crowding agent with respect to the tracer molecule. Analysis with the maximum entropy method also revealed information about the degree of heterogeneity in the environment as reported by the behavior of diffusive molecules.

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“…Ten readings were taken at each site and averaged; readings that showed bleaching were discarded. Best fits for the autocorrelation curves were chosen and recorded using Quickfit (Press et al, 1992), and in some cases, the MaxEnt fitting program (Modos et al, 2004) was also used to help determine which fit was optimal. …”

mentioning

confidence: 99%

Rapid, Diffusional Shuttling of Poly(A) RNA between Nuclear Speckles and the Nucleoplasm

Politz

Tuft

Prasanth

et al. 2006

MBoC

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Speckles are nuclear bodies that contain pre-mRNA splicing factors and polyadenylated RNA. Because nuclear poly(A) RNA consists of both mRNA transcripts and nucleus-restricted RNAs, we tested whether poly(A) RNA in speckles is dynamic or rather an immobile, perhaps structural, component. Fluorescein-labeled oligo(dT) was introduced into HeLa cells stably expressing a red fluorescent protein chimera of the splicing factor SC35 and allowed to hybridize. Fluorescence correlation spectroscopy (FCS) showed that the mobility of the tagged poly(A) RNA was virtually identical in both speckles and at random nucleoplasmic sites. This same result was observed in photoactivation-tracking studies in which caged fluorescein-labeled oligo(dT) was used as hybridization probe, and the rate of movement away from either a speckle or nucleoplasmic site was monitored using digital imaging microscopy after photoactivation. Furthermore, the tagged poly(A) RNA was observed to rapidly distribute throughout the entire nucleoplasm and other speckles, regardless of whether the tracking observations were initiated in a speckle or the nucleoplasm. Finally, in both FCS and photoactivation-tracking studies, a temperature reduction from 37 to 22°C had no discernible effect on the behavior of poly(A) RNA in either speckles or the nucleoplasm, strongly suggesting that its movement in and out of speckles does not require metabolic energy. INTRODUCTIONNuclear speckles are morphologically distinct regions of the nucleoplasm that contain pre-mRNA splicing components as well as poly(A) RNA (Carter et al., 1993;Zhang et al., 1994;Lamond and Spector, 2003). They are operationally defined by their immunostaining with a variety of pre-mRNA splicing factor antibodies, and they also show in situ hybridization signal using probes for poly(A). When these sites are viewed in the electron microscope, most of them are found to represent interchromatin granule clusters (Fakan et al., 1984. However, RNA polymerase II transcription sites are distributed throughout the nucleus, indicating that although some of the RNA present in interchromatin granules/speckles is nascent, transcription is not restricted to this compartment, and much of the poly(A) RNA there has likely been transcribed previously and/or at distant sites (Fakan and Nobis, 1978;Wansink et al., 1993, Zeng et al., 1997, Neugebauer and Roth, 1997, Cmarko et al., 1999Guillot et al., 2004). Indeed, although transcripts that are being rapidly produced or that contain many introns are sometimes observed in speckles at the light microscopy level (Johnson et al., 2000;Shopland et al., 2003), the majority of studies over the years has indicated that most speckles are not primary sites of pre-mRNA splicing (for reviews, see Mattaj, 1994;Huang and Spector, 1996a;Neugebauer and Roth, 1997;Lamond and Spector, 2003). In two cases, a single species of pre-mRNA has been followed from its transcription site to the nuclear pore, and in neither case did the RNA seem to accumulate in nuclear subcompartments (Singh et al.,...

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Maximum-entropy decomposition of fluorescence correlation spectroscopy data: application to liposome?human serum albumin association

Cited by 30 publications

References 9 publications

Ordered Self‐assembly of Protonated Porphyrin Induced by the Aqueous Environment of Biomimetic Systems

Ordered Self‐assembly of Protonated Porphyrin Induced by the Aqueous Environment of Biomimetic Systems

Multiple Diffusion Mechanisms Due to Nanostructuring in Crowded Environments

Rapid, Diffusional Shuttling of Poly(A) RNA between Nuclear Speckles and the Nucleoplasm

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