BioVectis

DNAPointer System beta version

The DNAPointer (R) System is an open, vertical, slab gel electrophoretic platform which offers worldwide the most precise gel (not the cooling medium) temperature control down to 0,2st.C. at the 4-65 st.C range during up to 40W electrophoresis. Those technical features makes it possible to separate, for example, two 3D structural isoforms of a one RNA molecule, differ by 0,6 kcal/mol of a free energy only. And because it's native electrophoretic conditions, material from separated bands, might be extracted and used for further advance structural or compound identification analysis, using eg. NMR or cryo-EM, or NGS and MS respectively.

Applications example:

minor genetic variants discovery and detection at heterogeneous clinical and biological material
protein-protein and protein-nucleic acids and protein-ligands complexes discovery and analysis
3D RNA stricture analysis and sample optimization

R&D collaboration offer

We are looking for R&D Partners interested in the development with us specific protocols based on the unique DNAPointer System technical and analytical features related to the study of 3D structure, composition, and sample optimization of different complexes types and 3D RNA struture:

protein-protein and protein-ligand
protein-nucleic acids
protein-membrane
oligonucleotides 3D structure determination

For more information please contact directly : dr Krzysztof Kucharczyk at : k.kucharczyk@biovectis.com

Application

Protein-Protein and Protein-nucleic acids complexes analysis in vitro

The DNAPointer System offers exceptional level (0,1 C) of samples/gel temperature control during the native electrophoresis in the range of 4-65 C. That makes possible separation of minor conformers/variants of protein complexes with over 98% reproducibility and cutting down the separation time to 20% (in comparison to classical slab gel equipment).
This high separation reproducibility and sensitivity, combined with a tolls for simultaneous self polymerization of several polyacrylamide gels in parallel (Multipol DNAPointer, cat no 105-161) makes possible fast optimization of gels ionic strengths, pH and polyacrylamide concentration.

The most often used applications are Blue Native and EMSA at 1D and 2D format. The native separation of protein complexes makes possible their further analysis by e.g. mass spectrometry, NGS, NMR, cryo-EM or biological assays.

Some example of DNAPointer System use for protein complexes analysis:

1. RNA-ligand interaction kinetics and stoichiometry by 25 min.EMSA (Nilsson, P et al., 2007 )

2. RNA spatial conformers separation with 0.5 kcal/mol resolution (Pachulska-Wieczorek, K, at al., 2006)

3. Protein-protein interaction kinetics (Wrobel et al, 2015)

4. Transient/labile protein interaction (Hellman, L. at al., 2007)

5. protein-n.acids binding proteins discovery by 2D EMSA (Stead, J at al., 2007)

Application

Minor genetic Variants Discovery and Detection at heterogeneous clinical and biological material.

DNAPointer System and Multitemperature single strand conformation polymorphism (MSSCP) genotyping method offers fast and cost effective approach to discover minor genetic variants present at the heterogeneous biological and clinical material down to 0,1% level of minor variants presence. Due to its high sensitivity and reproducibility, this method could be applied for a large-scale screening of minor genetic variants present at oncological and virological samples.

Application

Oncology

Drug resistant genetic markers discovery and detection

Gene FLT3 ex.14 is a one of oncology drug targets. The FLT3 kinase inactivation has been established as a therapeutic intervention across many different indications and tumours types.
The detection in the tumour material the drug resistant genetic variants leads is vital imporation to deliver optimal treatment to individual patient.
Using the MSSCP genotyping method we detected wt and drug resistant mutant in one clinical material from patient A2. (left panel, line A2) The DNA sequence of each variants is shown on the right panel.

Figure. The presence of drug sensitive and drug resistant genetic variant was disclosed in the
clinical material form patient A2 by the MSSCP method.

Virology

HBV - drug resistant genetic minor variants detection

The MALDI-TOF MS and the MSSCP genotyping method have shown that same sensitivity level of detection of the minor drug resistant HBV variants present in patients samples down to 0,5% of total genomic material.

J. Clin. Microbiol. 2014, 52(1):9.

High-Throughput Matrix-Assisted Laser Desorption Ionization–Time
of Flight Mass Spectrometry as an Alternative Approach to Monitoring Drug Resistance of Hepatitis B Virus

Magda Rybicka,a Piotr Stalke,b Marcin Dreczewski,b Tomasz Smiatacz,b Krzysztof Piotr Bielawskia
Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Polanda; Department of Infectious Diseases, Medical University
of Gdansk, Gdansk, Poland

Long-term antiviral therapy of chronic hepatitis B virus (HBV) infection can lead to the selection of drug-resistant HBV variants and treatment failure. Moreover, these HBV strains are possibly present in treatment-naive patients. Currently available assays for the detection of HBV drug resistance can identify mutants that constitute>5% of the viral population. Furthermore, drug resistant HBV variants can be detected when a viral load is>104 copies/ml (1,718 IU/ml). The aim of this study was to compare matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) and multitemperature singlestrand conformation polymorphism (MSSCP) with commercially available assays for the detection of drug-resistant HBV strains. HBV DNA was extracted from 87 serum samples acquired from 45 chronic hepatitis B (CHB) patients. The 37 selected HBV variants were analyzed in 4 separate primer extension reactions on the MALDI-TOF MS. Moreover, MSSCP for identifying drug-resistant HBV YMDD variants was developed and turned out to be more sensitive than INNOLiPA HBV DR and direct
sequencing. MALDI-TOF MS had the capability to detect mutant strains within a mixed viral population occurring with an allelic frequency of approximately 1% (with a specific value of>102 copies/ml, also expressed as>17.18 IU/ml). In our study, MSSCP detected 98% of the HBV YMDD variants among strains detected by the MALDI-TOF MS assay. The routine tests revealed
results of 40% and 11%, respectively, for INNOLiPA and direct sequencing. The commonly available HBV tests are less sensitive than MALDI-TOF MS in the detection of HBV-resistant variants, including quasispecies.

Ordering



105-151	Glass Plates for DNA Pointer System	2 pairs
105-121	Comb 1.0 mm thick (33 or 44 samples)	2
105-112	Spacers 1.0 mm thick	1 pair
105-161	Multipol (for simultanous polimerization of 8 gels)	1
105-181	Glass container with lid (for silver staining of the gel)	1
105-191	DRYOUT set for gel drying (with 35 foil pices)	1

Accessories

Cat. no.	Description
105-161	MULTIPOL for simultanous polimerization of 8 gels
105-151	Glass plates for DNA Pointer
105-171	Glass plates drying rack
105-181	Glass container with lid (for silver staining of the gel)
105-111	Spacers 0.5 mm thick
105-112	Spacers 1.0 mm thick
105-121	Comb 0.5 mm thick/24 samples
105-122	Comb 0.5 mm thick/33 samples
105-123	Comb 0.5 mm thick/44 samples
105-124	Comb 1.0 mm thick/24 samples
105-125	Comb 1.0 mm thick/33 samples
105-126	Comb 1.0 mm thick/44 samples
152-102	Wiring cable
105-191	DRYOUT Set for gel drying (with 35 foil pieces)

Parameters	Value
Temperature	2 -65 C
Temperature stabilization	0.2 C
Max. sample number	36
Max. Voltage	3000 V
Max. Current	300 mA
Power	600 W
Dimensions (wxdxh)	347 x 424 x 388 mm
Weight	14 kg
Power supply	230 V/50