SASDCH5: Light encoded DNA biosensor: e13AB DNA (e13AB)

Basic information

• Entry: Database: SASBDB / ID: SASDCH5

Sample

Light encoded DNA biosensor: e13AB DNA

• e13AB (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 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)

Models

• Model #1337: ; Type: dummy / Radius of dummy atoms: 4.25 A / Chi-square value: 12.569; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: Light encoded DNA biosensor: e13AB DNA / Specimen concentration: 0.25-2.00
• Buffer: Name: 154 mM NaCl / pH: 8.3

Entity #717

Type: DNA / Description: e13AB / Formula weight: 79.448 / Num. of mol.: 1
Sequence:

ccacgccaaa cgctgaaggg cttcttcctt atttttggcg tggccacgcc aaacgctgaa gggcttcttc cttatttttg gcgtggccac gccaaacgct gaagggcttc ttccttattt ttggcgtggc cacgccaaac gctgaagggc ttcttcctta tttttggcgt ggccacgcca aacgctgaag ggcttcttcc ttatttttgg cgtggccacg ccaaacgctg aagggcttct tccttatttt tggcgtgg

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: e13AB DNA / Measurement date: Nov 22, 2013 / Storage temperature: 5 °C / Cell temperature: 5 °C / Exposure time: 0.05 sec. / Number of frames: 20 / Unit: 1/nm /

	Min	Max
Q	0.2435	4.4936

Distance distribution function P(R)

Sofotware P(R): GNOM 4.6 / Number of points: 494 /

	Min	Max
Q	0.2457	4.494
P(R) point	50	543
R	0	20

Result

Type of curve: merged

	Experimental	Standard	Standard error	Porod
MW	79 kDa	78 kDa	5	75 kDa
Volume	-	-	-	103 nm3

	P(R)	P(R) error	Guinier	Guinier error
Forward scattering, I0	167	10	156.117	1.48
Radius of gyration, Rg	5.4 nm	0.4	4.73 nm	0.04

	Min	Max	Error
D	-	20	1
Guinier point	1	8	-