PubMed:22114185
Annnotations
{"target":"https://pubannotation.org/docs/sourcedb/PubMed/sourceid/22114185","sourcedb":"PubMed","sourceid":"22114185","source_url":"http://www.ncbi.nlm.nih.gov/pubmed/22114185","text":"Binding and cleavage of DNA with the restriction enzyme EcoR1 using time-resolved second harmonic generation.\nThe binding of EcoR1 to a 90-bp DNA duplex attached to colloidal microparticles and the subsequent cleavage by the enzyme was observed in real time and label-free with time-resolved second harmonic (SH) spectroscopy. This method provides a unique way to investigate biomolecular interactions based on its sensitivity to changes in structure and electrical charge on formation of a complex and subsequent dynamics. The binding of EcoR1 to the recognition sequence in DNA appears as a rapid increase in the SH signal, which is attributed to the enzyme-induced change in the DNA conformation, going from a rod-like to a bent shape. In the presence of the cofactor Mg(2+), the subsequent decay in the SH signal was monitored in real time as the following processes occurred: cleavage of DNA, dissociation of the enzyme from the DNA, and diffusion of the 74-bp fragment into the bulk solution leaving the 16-bp fragment attached to the microparticle. The observed decay was dependent on the concentration of Mg(2+), which functions as a cofactor and as an electrolyte. With SH spectroscopy the rehybridization dynamics between the rehybridized microparticle bound and free cleaved DNA fragments was observed in real time and label-free following the cleavage of DNA. Collectively, the experiments reported here establish SH spectroscopy as a powerful method to investigate equilibrium and time-dependent biological processes in a noninvasive and label-free way.","tracks":[{"project":"LitCoin-PubTator-for-Tuning","denotations":[{"id":"1","span":{"begin":1113,"end":1119},"obj":"ChemicalEntity"}],"attributes":[{"subj":"1","pred":"source","obj":"LitCoin-PubTator-for-Tuning"}]},{"project":"LitCoin-Disease-Tuning-1","denotations":[{"id":"T1","span":{"begin":898,"end":910},"obj":"DiseaseOrPhenotypicFeature"}],"attributes":[{"id":"A1","pred":"ID:","subj":"T1","obj":"D004213"},{"subj":"T1","pred":"source","obj":"LitCoin-Disease-Tuning-1"}]},{"project":"LitEisuke","denotations":[{"id":"T1","span":{"begin":898,"end":910},"obj":"DiseaseOrPhenotypicFeature"}],"attributes":[{"id":"A1","pred":"#label","subj":"T1","obj":"D004213"},{"subj":"T1","pred":"source","obj":"LitEisuke"}]},{"project":"Allie","denotations":[{"id":"SS1_22114185_1_0","span":{"begin":292,"end":307},"obj":"expanded"},{"id":"SS2_22114185_1_0","span":{"begin":309,"end":311},"obj":"abbr"}],"relations":[{"id":"AE1_22114185_1_0","pred":"abbreviatedTo","subj":"SS1_22114185_1_0","obj":"SS2_22114185_1_0"}],"attributes":[{"subj":"SS1_22114185_1_0","pred":"source","obj":"Allie"},{"subj":"SS2_22114185_1_0","pred":"source","obj":"Allie"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"LitCoin-PubTator-for-Tuning","color":"#c293ec","default":true},{"id":"LitCoin-Disease-Tuning-1","color":"#93eca8"},{"id":"LitEisuke","color":"#ec9397"},{"id":"Allie","color":"#93b1ec"}]}]}}