We Solve medical tasks using working aptamers

Aptamer Selection, Characterization, 3D Structure Simulation And Target Identification

MATHEMATICAL ANALYSIS OF APTAMERS

We will make mathematical analysis of your aptamers, just click the button

MATHEMATICAL ANALYSIS IS NEEDED

TO CHOOSE APTAMERS CONTAINING A G-QUARTET OR DETERMINE THE MOST PROBABLE ACTIVE site OF THE APTAMER

If you are interested in the presence of a G-quartet or the nucleotide sequence of the most likely active site of the aptamer, we can also determine this using mathematical analysis. Such an analysis of the aptamer allows you to choose the functional part, so that in the synthesis you "cut off" everything unnecessary.

TO FOLLOW THE ENRICHMENT OF THE SEQUENCES OF OLIGONUCLEOTIDES FROM ROUND TO ROUND

If you are interested in how the enrichment of aptamer sequences occurred from the first to the final round, then you can do sequencing and mathematical analysis of all rounds of selection. This will provide more complete information about the potential specificity of the selected aptamers to the target.

TO CHOOSE APTAMERS FROM A LARGE DATA ARRAY

After applying the technology of high throughput sequencing, a large array of oligonucleotide sequences is obtained from which it is difficult to select the leading aptamers. Mathematical analysis or HT-SELEX allows us to identify aptamer families and evaluate the “fitness landscape”. This allows you to select the most promising sequences for their further optimization and validation.

STAGES OF MATHEMATICAL ANALYSIS

1

stage

Quality control of sequencing results: deletion of readings that do not meet some quality criterion (Q20 or Q30).

2

STAGE

Selecting chains corresponding to each specific index (when using multiplexing) and filtering aptamers by the length of the chain (selecting words whose sizes are close to the word size of the source library).

3

STAGE

Removing aptamer constant regions (primers) in order to isolate the variable part and count the number of copies of each aptamer in the pool.

4

STAGE

Clustering aptamers in a pool and highlighting the most representative clusters using the Hamming distance, the local Hamming distance, or the weight of the optimal local alignment as a proximity measure.

5

STAGE

Analysis of cluster enrichment during the transition from the previous round of selection to the next (in the case of sequencing pools of several rounds) and the selection of candidate aptamers.

6

STAGE

Search for DNA subwords of each candidate aptamer that are most likely to participate in the formation of the aptamer-target complex.

7

STAGE

Calculation of the probability that G-quadruplexes are present in the 3d structure of the candidate aptamers.

WE USE INNOVATIve TECHNOLOGIES

APTABID

AptaBiD allows us to isolate proteins that bind to specific aptamers. With the help of this method it becomes possible to determine the direct target of the aptamer.

TISSUE SELEX

The method for generating aptamers which are capable to bind with tissue targets.

CELL SELEX

This technology involves the selection of aptamers for the whole cells. This allows us to obtain aptamers that are able to bind to the target in its native conformation.

LIGS

The method identifies highly selective aptamers against a predetermined epitope expressed on the cell surface. Monoclonal antibody interacts with its cognate epitope to outcompete and replace specific aptamers from an enriched SELEX pool.

SAXS

This method is used for determination of the nanoscale density differences in the sample. This makes it possible to determine the size and shape of the macromolecule.

HT SELEX

HT SELEX is the method that increases the sensitivity over traditional cloning and sequencing applications and reduces the number of rounds required to achieve detectable enrichment.

THE RESULTS YOU'LL GET

Lists of aptamers

Lists of aptamers of each pool with the number of copies of each aptamer.

Aptamer families

Aptamer families obtained by clustering pools.

representatives of families

The most typical representatives of families - a set of the candidate aptamers for synthesis and validation.

Candidate aptamers

Enrichment statistics of the candidate aptamers.

The DNA subword

The DNA subword of the each candidate aptamer that is most likely to participate in the formation of the aptamer-target complex.

G-quadruplexes

Probabilities that G-quadruplexes are present in the 3d structure of the candidate aptamers.

SCIENTISTS INVOLVED IN THE STUDY

Changing your mind and changing world
CHIEF RESEARCHER

DMITRIJ VEPRINCEV

Ph.D. in Physical-Mathematical Sciences
Changing your mind and changing world
LEADING RESEARCHER

ANNA BLAGODATOVA

Ph.D. in Biological Sciences
Changing your mind and changing world
LEADING RESEARCHER

OLGA KOLOVSKAYA

Ph.D. in Biological Sciences
Changing your mind and changing world
LEADING RESEARCHER

GALINA ZAMAY

Ph.D. in Biological Sciences

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