DNAPointer System



The DNAPointer (R) System is an open platform for ultra precise native electrophoretic separation of nucleic acids spatial conformers, protein-protein and protein - nucleic acids complexes. 

As the analytical and preparative platform in one,  DNAPointer System makes possible further samples analysis using mass spectrometry, NMR, NGS or cryo-EM. 

Main applications:
  • 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 

 
 

  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.
201706pmesprzykldaflt3ex14jpg
Figure.  The presence of drug sensitive and drug resistant genetic variant was disclosed in the
   clinical material form patient A2 by the MSSCP method.

   Application


Virology 

Influenza - mixed infections in human discovery.

The DNAPointer System and the MSSCP genotyping method was used for the first observation of the presence in one patient two different influenza viruses A1/H1N1 pdm09 and seasonal strains in that same patient.

httpfilesclickwebhomeplhomepl41353image201706msscph1n1genotypowanie1strartjpg


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.
         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

 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)