Previous fluorescence correlation spectroscopy (FCS) measurements of DNA hairpin folding dynamics revealed at least three conformational states of the DNA are present, distinguished by the brightness of fluorescent dye-quencher labels. Rapid fluctuations between two of the states occurred on time scales observable by FCS. A third state that was static on the FCS time scale was also observed. In this study, we investigate these conformational states using newly developed higher-order FCS techniques. It is shown that conventional FCS alone cannot uniquely distinguish the conformational states or assign their roles in the observed mechanism. The additional information offered by higher-order FCS makes it possible (i) to uniquely identify the static and rapidly fluctuating states and (ii) to directly measure the brightnesses and populations of all three observed states. The rapid fluctuations occurring on the FCS time scale are due to a reversible reaction between the two lowest brightness levels, attributed to the folded and random-coil conformations of the DNA. Evidence is presented that the third state, which is the brightest, may be associated with spatially extended unfolded conformations that are isolated from the more compact conformations by a substantial barrier. These conformations attain a maximum equilibrium population of nearly 10% near physiological temperatures and salt concentrations.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1021/acs.jpcb.8b10703 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Structural basis for the conformational protection of nitrogenase from O.
Nature
January 2025
Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA.
The low reduction potentials required for the reduction of dinitrogen (N) render metal-based nitrogen-fixation catalysts vulnerable to irreversible damage by dioxygen (O). Such O sensitivity represents a major conundrum for the enzyme nitrogenase, as a large fraction of nitrogen-fixing organisms are either obligate aerobes or closely associated with O-respiring organisms to support the high energy demand of catalytic N reduction. To counter O damage to nitrogenase, diazotrophs use O scavengers, exploit compartmentalization or maintain high respiration rates to minimize intracellular O concentrations.
View Article and Find Full Text PDFStructural basis for the transport and regulation mechanism of the multidrug resistance-associated protein 2.
Nat Commun
January 2025
Laboratory of Membrane Biology and Biophysics, The Rockefeller University, New York, NY, USA.
Multidrug resistance-associated protein 2 (MRP2) is an ATP-powered exporter important for maintaining liver homeostasis and a potential contributor to chemotherapeutic resistance. Using cryogenic electron microscopy (cryo-EM), we determine the structures of human MRP2 in three conformational states: an autoinhibited state, a substrate-bound pre-translocation state, and an ATP-bound post-translocation state. In the autoinhibited state, the cytosolic regulatory (R) domain plugs into the transmembrane substrate-binding site and extends into the cytosol to form a composite ATP-binding site at the surface of nucleotide-binding domain 2.
View Article and Find Full Text PDFImpact of cold plasma-assisted Non-thermal deamidation and glycosylation on the construction of sugar derivative-zein conjugates for enhancing pickering foam stability: Technical principles and molecular interactions.
Food Res Int
January 2025
State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Nutrition and Safety, Ministry of Education, College of Food Science and Engineering, Tianjin University of Science & Technology, No. 9, No. 13 Ave., TEDA, Tianjin 300457, China. Electronic address:
There is an urgent need for stable, plant-based Pickering foams to address the growing consumer demand for sustainable, low-calorie, aerated sweet foods. This study employed a cold plasma-assisted deamidation and glycosylation (CPDG) approach to promote hydrophilic reassembly of zein, resulting in the formation of sugar derivative-zein conjugates. This was accomplished by coupling deamidated zein with polyhydroxy sugars including sucralose (Suc), maltitol (Mal), mannitol (Man), and stevioside (Ste).
View Article and Find Full Text PDFOne-pot ligation of multiple mRNA fragments on dsDNA splint advancing regional modification and translation.
Nucleic Acids Res
January 2025
Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, The College of Life Sciences, Sichuan University, 24 South Section 1, 1st Ring Road, Chengdu, Sichuan 610064, P.R. China.
Region-specific RNA modifications are crucial for advancing RNA research and therapeutics, including messenger RNA (mRNA)-based vaccines and immunotherapy. However, the predominant method, synthesizing regionally modified mRNAs with short single-stranded DNA (ssDNA) splints, encounters challenges in ligating long mRNA fragments due to the formation of RNA self-folded complex structures. To address this issue, we developed an efficient strategy using an easily obtained long double-stranded DNA (dsDNA) as a ligation splint after in situ denaturing, while parts of this dsDNA are the templates for transcribing mRNA fragments.
View Article and Find Full Text PDFStructural and bioinformatics analyses identify deoxydinucleotide-specific nucleases and their association with genomic islands in gram-positive bacteria.
Nucleic Acids Res
January 2025
CSSB Centre for Structural Systems Biology, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany.
Dinucleases of the DEDD superfamily, such as oligoribonuclease, Rexo2 and nanoRNase C, catalyze the essential final step of RNA degradation, the conversion of di- to mononucleotides. The active sites of these enzymes are optimized for substrates that are two nucleotides long, and do not discriminate between RNA and DNA. Here, we identified a novel DEDD subfamily, members of which function as dedicated deoxydinucleases (diDNases) that specifically hydrolyze single-stranded DNA dinucleotides in a sequence-independent manner.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!