- SASDCB5: Light encoded DNA biosensor: e14C DNA (e14C) -
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Open data
ID or keywords:
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Basic information
Entry
Database: SASBDB / ID: SASDCB5
Sample
Light encoded DNA biosensor: e14C DNA
e14C (DNA)
Citation
Journal: ACS Chem Biol / Year: 2018 Title: Optical and Structural Characterization of a Chronic Myeloid Leukemia DNA Biosensor. Authors: Mílton Cordeiro / Ana Rita Otrelo-Cardoso / Dmitri I Svergun / Petr V Konarev / João Carlos Lima / Teresa Santos-Silva / Pedro Viana Baptista / Abstract: Selective base pairing is the foundation of DNA recognition. Here, we elucidate the molecular and structural details of a FRET-based two-component molecular beacon relying on steady-state ...Selective base pairing is the foundation of DNA recognition. Here, we elucidate the molecular and structural details of a FRET-based two-component molecular beacon relying on steady-state fluorescence spectroscopy, small-angle X-ray scattering (SAXS), microscale thermophoresis (MST), and differential electrophoretic mobility. This molecular beacon was designed to detect the most common fusion sequences causing chronic myeloid leukemia, e14a2 and e13a2. The emission spectra indicate that the self-assembly of the different components of the biosensor occurs sequentially, triggered by the fully complementary target. We further assessed the structural alterations leading to the specific fluorescence FRET signature by SAXS, MST, and the differential electrophoretic mobility, where the size range observed is consistent with hybridization and formation of a 1:1:1 complex for the probe in the presence of the complementary target and revelator. These results highlight the importance of different techniques to explore conformational DNA changes in solution and its potential to design and characterize molecular biosensors for genetic disease diagnosis.
Contact author
Petr Konarev (EMBL-Hamburg, European Molecular Biology Laboratory (EMBL) - Hamburg outstation, Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany)
Name: Light encoded DNA biosensor: e14C DNA / Specimen concentration: 1 mg/ml
Buffer
Name: 154 mM NaCl / pH: 8.3
Entity #711
Type: DNA / Description: e14C / Formula weight: 5.496 / Num. of mol.: 1 Sequence:
ccacgccaaa ccacgaaa
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Experimental information
Beam
Instrument name: ESRF BM29 / City: Grenoble / 国: France / Type of source: X-ray synchrotron / Wavelength: 0.1 Å / Dist. spec. to detc.: 3 mm
Detector
Name: Pilatus 1M
Scan
Title: Light encoded DNA biosensor: e14C DNA / Measurement date: Jun 16, 2016 / Storage temperature: 10 °C / Cell temperature: 10 °C / Exposure time: 0.05 sec. / Number of frames: 20 / Unit: 1/nm /
Min
Max
Q
0.0771
4.9518
Distance distribution function P(R)
Sofotware P(R): GNOM 4.6 / Number of points: 512 /
Min
Max
Q
0.1266
4.949
P(R) point
20
531
R
0
5
Result
Experimental MW: 6 kDa / Type of curve: merged
P(R)
Guinier
Guinier error
Forward scattering, I0
10.71
10.65
0.016
Radius of gyration, Rg
1.29 nm
1.25 nm
0.05
Min
Max
D
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5
Guinier point
16
203
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