DNA sequence-dependent variation in nucleosome structure, stability, and dynamics detected by a FRET-based analysisThis paper is one of a selection of papers published in this Special Issue, entitled 29th Annual International Asilomar Chromatin and Chromosomes Conference, and has undergone the Journal’s usual peer review process.

2009 ◽  
Vol 87 (1) ◽  
pp. 323-335 ◽  
Author(s):  
L. Kelbauskas ◽  
N. Woodbury ◽  
D. Lohr
Keyword(s):  
Dna Sequence ◽  
Peer Review Process ◽  
Regulatory Element ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
5S Rdna ◽  
Structure Stability ◽  
Dna Dynamics ◽  
Nucleosome Structure ◽  
Sequence Dependent

Förster resonance energy transfer (FRET) techniques provide powerful and sensitive methods for the study of conformational features in biomolecules. Here, we review FRET-based studies of nucleosomes, focusing particularly on our work comparing the widely used nucleosome standard, 5S rDNA, and 2 promoter-derived regulatory element-containing nucleosomes, mouse mammary tumor virus (MMTV)-B and GAL10. Using several FRET approaches, we detected significant DNA sequence-dependent structure, stability, and dynamics differences among the three. In particular, 5S nucleosomes and 5S H2A/H2B-depleted nucleosomal particles have enhanced stability and diminished DNA dynamics, compared with MMTV-B and GAL10 nucleosomes and particles. H2A/H2B-depleted nucleosomes are of interest because they are produced by the activities of many transcription-associated complexes. Significant location-dependent (intranucleosomal) stability and dynamics variations were also observed. These also vary among nucleosome types. Nucleosomes restrict regulatory factor access to DNA, thereby impeding genetic processes. Eukaryotic cells possess mechanisms to alter nucleosome structure, to generate DNA access, but alterations often must be targeted to specific nucleosomes on critical regulatory DNA elements. By endowing specific nucleosomes with intrinsically higher DNA accessibility and (or) enhanced facility for conformational transitions, DNA sequence-dependent nucleosome dynamics and stability variations have the potential to facilitate nucleosome recognition and, thus, aid in the crucial targeting process. This and other nucleosome structure and function conclusions from FRET analyses are discussed.

Na+ and K+ Ions Differently Affect Nucleosome Structure, Stability, and Interactions with Proteins

2021 ◽  
pp. 1-11
Author(s):  
Tatyana V. Andreeva ◽  
Natalya V. Maluchenko ◽  
Anastasiia L. Sivkina ◽  
Oleg V. Chertkov ◽  
Maria E. Valieva ◽  
...  
Keyword(s):  
Energy Transfer ◽  
Rna Polymerase Ii ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Inorganic Ions ◽  
Structure Stability ◽  
Ion Concentrations ◽  
Nucleosome Structure ◽  
Nucleosomal Dna ◽  
Stabilizing Effect

Inorganic ions are essential factors stabilizing nucleosome structure; however, many aspects of their effects on DNA transactions in chromatin remain unknown. Here, differential effects of K+ and Na+ on the nucleosome structure, stability, and interactions with protein complex FACT (FAcilitates Chromatin Transcription), poly(ADP-ribose) polymerase 1, and RNA polymerase II were studied using primarily single-particle Förster resonance energy transfer microscopy. The maximal stabilizing effect of K+ on a nucleosome structure was observed at ca. 80–150 mM, and it decreased slightly at 40 mM and considerably at >300 mM. The stabilizing effect of Na+ is noticeably lower than that of K+ and progressively decreases at ion concentrations higher than 40 mM. At 150 mM, Na+ ions support more efficient reorganization of nucleosome structure by poly(ADP-ribose) polymerase 1 and ATP-independent uncoiling of nucleosomal DNA by FACT as compared with K+ ions. In contrast, transcription through a nucleosome is nearly insensitive to K+ or Na+ environment. Taken together, the data indicate that K+ environment is more preserving for chromatin structure during various nucleosome transactions than Na+ environment.

scholarly journals Spatial Distribution and Function of Sterol Regulatory Element-Binding Protein 1a and 2 Homo- and Heterodimers by In Vivo Two-Photon Imaging and Spectroscopy Fluorescence Resonance Energy Transfer

2005 ◽  
Vol 25 (8) ◽  
pp. 2946-2956 ◽  
Author(s):  
Aikaterini Zoumi ◽  
Shrimati Datta ◽  
Lih-Huei L. Liaw ◽  
Cristen J. Wu ◽  
Gopi Manthripragada ◽  
...  
Keyword(s):  
Energy Transfer ◽  
Fluorescence Resonance Energy Transfer ◽  
Regulatory Element ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Two Photon ◽  
Sterol Regulatory Element ◽  
Photon Imaging ◽  
Imaging And Spectroscopy

ABSTRACT Sterol regulatory element-binding proteins (SREBPs) are a subfamily of basic helix-loop-helix-leucine zipper proteins that regulate lipid metabolism. We show novel evidence of the in vivo occurrence and subnuclear spatial localization of both exogenously expressed SREBP-1a and -2 homodimers and heterodimers obtained by two-photon imaging and spectroscopy fluorescence resonance energy transfer. SREBP-1a homodimers localize diffusely in the nucleus, whereas SREBP-2 homodimers and the SREBP-1a/SREBP-2 heterodimer localize predominantly to nuclear speckles or foci, with some cells showing a diffuse pattern. We also used tethered SREBP dimers to demonstrate that both homo- and heterodimeric SREBPs activate transcription in vivo. Ultrastructural analysis revealed that the punctate foci containing SREBP-2 are electron-dense nuclear bodies, similar or identical to structures containing the promyelocyte (PML) protein. Immunofluorescence studies suggest that a dynamic interplay exists between PML, as well as another component of the PML-containing nuclear body, SUMO-1, and SREBP-2 within these nuclear structures. These findings provide new insight into the overall process of transcriptional activation mediated by the SREBP family.

scholarly journals A New FRET-Based Sensitive DNA Sensor for Medical Diagnostics using PNA Probe and Water-Soluble Blue Light Emitting Polymer

2008 ◽  
Vol 2008 ◽  
pp. 1-6 ◽  
Author(s):  
Nidhi Mathur ◽  
Anamika Aneja ◽  
P. K. Bhatnagar ◽  
P. C. Mathur
Keyword(s):  
Dna Sequence ◽  
Low Cost ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Medical Diagnostics ◽  
Water Soluble ◽  
Complementary Sequence ◽  
Sequence Detection ◽  
Light Emitting ◽  
Dna Sequence Detection

A reliable, fast, and low-cost biosensor for medical diagnostics using DNA sequence detection has been developed and tested for the detection of the bacterium “Bacillus anthracis.” In this sensor, Poly [9,9-di (6,6′- N,N′trimethylammonium) hexylfluorenyl-2, 7-diyl)-alt-co- (1,4-phenylene)] dibromide salt (PFP) has been taken as cationic conjugated polymer (CCP) and PNA attached with fluorescein dye (PNAC∗) as a probe. The basic principle of this sensor is that when aPNAC∗probe is hybridized with a single strand DNA (ssDNA) having complementary sequence, Forster resonance energy transfer (FRET) may take place from PFP to thePNAC∗/DNA complex. If the FRET is efficient, the photoluminescence from the PFP will be highly quenched and that fromPNAC∗will be enhanced. On the other hand, if the DNA sequence is noncomplementary to PNA, FRET will not occur.

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