Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 340
Aptamer sequence: ACCGGGCGTACACCGTCGCGGCACATGTCTGAATGCGTTTAGTCTCTGTG
Target unique ID: P16070
| Aptamer ID | Aptamer descriptor | Target chemistry | Target name | Affinity | Binding Conditions/Buffer | PubMed ID |
|---|---|---|---|---|---|---|
| Apta_335 | S5 | Protein | CD44_HUMAN | 779 nM | 50 mM NaH2PO4/ Na2HPO4 buffer pH 7.5 containing 300 mM NaCl and 0.01% (v/v) Tween 20 | 32379519 |
Structure information of aptamer
| Aptamer Sequence: | ACCGGGCGTACACCGTCGCGGCACATGTCTGAATGCGTTTAGTCTCTGTG |
| The optimal secondary structure in dot-bracket notation: | .(((((((.....)))).)))((((...(((((....)))))....)))) |
| The centroid secondary structure in dot-bracket notation: | .(((((((.....)))).)))((((...(((((....)))))....)))) |
The MFE structure
The Centroid structure
The mountain plot representation
Aptamer information
| Type | Detail | Type | Detail |
|---|---|---|---|
| Aptamer ID | Apta_335 | Description | S5 |
| Aptamer chemistry | DNA | Length | 50 nt |
| GC content | 58.0% | Molecular weight | 15,624.78 Da |
| Molarity of 1 μg/μl solution | 64.00 μM | Number of G-quadruplexes | No QGRS found |
| G-Score | N/A | Function | Targeted therapy |
| Sequence | ACCGGGCGTACACCGTCGCGGCACATGTCTGAATGCGTTTAGTCTCTGTG | ||
| Applications | Bind to CD44 with nanomolar affinities and efficiently inhibit the growth of leukemic cancer cells characterized by high expression of CD44 | ||
Target information
| Type | Detail | Type | Detail |
|---|---|---|---|
| Uniprot ID | P16070 | Protein name | CD44 antigen (CDw44) (Epican) (Extracellular matrix receptor III) (ECMR-III) (GP90 lymphocyte homing/adhesion receptor) (HUTCH-I) (Heparan sulfate proteoglycan) (Hermes antigen) (Hyaluronate receptor) (Phagocytic glycoprotein 1) (PGP-1) (Phagocytic glycoprotein I) (PGP-I) (CD antigen CD44) |
| Gene name(s) | CD44 LHR MDU2 MDU3 MIC4 | Organism | CD44 antigen (CDw44) (Epican) (Extracellular matrix receptor III) (ECMR-III) (GP90 lymphocyte homing/adhesion receptor) (HUTCH-I) (Heparan sulfate proteoglycan) (Hermes antigen) (Hyaluronate receptor) (Phagocytic glycoprotein 1) (PGP-1) (Phagocytic glycoprotein I) (PGP-I) (CD antigen CD44) |
| Status | reviewed in uniprot database | Length | 742 |
| Mass | 81,538 | Activity regulation | N/A |
| Involvement in disease | N/A | Catalytic activity | N/A |
| PDB ID(s) | 1POZ;1UUH;2I83;4PZ3;4PZ4;6TXS; |
 |
Function | Cell-surface receptor that plays a role in cell-cell interactions, cell adhesion and migration, helping them to sense and respond to changes in the tissue microenvironment. |
Activity data
 |
Interaction ID | 340 |
| Target type | Protein | |
| Target unique ID | P16070 | |
| Activity | 779 nM | |
| Binding Conditions/Buffer | 50 mM NaH2PO4/ Na2HPO4 buffer pH 7.5 containing 300 mM NaCl and 0.01% (v/v) Tween 20 |
|
| Assay | Affinities of s5 and s5rev toward CD44 HABD. Dissociation constants (Kd) were determined by microscale thermophoresis |
|
| PubMed ID | 32379519 |
Similar aptamers
| Aptamer ID | Aptamer chemistry | Sequence | Similarity |
|---|---|---|---|
| Apta_336 | DNA | CATGCTTCCCCAGGGAGATGACCGGGGCGTACACCGTCGCGGCACATGTCTGAATGCGTTTAGTCTCTGTGG | |
| Apta_484 | DNA | CAGGGAGGGACAGGGCGGGAATTTGTATGATGGTTCGTTTGCTCG | |
| Apta_487 | DNA | CGGGGAGTTGGGAGGGGGGGCAAAGCCTGTGTATTTATCTTCTGT | |
| Apta_357 | DNA | ACAATGTCGCTCTCCGCCGCAGGAGCATTGTCTGTCTTTATGCTTCTCTTTTTTGTTGC | |
| Apta_1127 | DNA | TCGGGCGAGTCGTCTGCGAGGCAACAAGCTCGTAATCCGCATCGTCCTCCC | |
| Apta_946 | DNA | TACCGGGTAATATGCACACATGCTGATAGCAAGCAATGCA | |
| Apta_1026 | DNA | GGGGGGTGTATCGTTGACGAGTTGCGCGTGCGTCTCGTG | |
| Apta_1287 | DNA | GCCCGCATGCCGTCAAGCAATGTTAATCTTGTTTTGATTTCG | |
| Apta_1228 | DNA | GGCCACCAAACCACACCGTCGCAACCGCGAGAACCGAAGTAGTGATCATGTCCCTGCGTG | |
| Apta_220 | DNA | ATCAACTCACCGTAGGTCTAGTGAGAACTTCAAGTCTACT | |
| Apta_480 | DNA | CGGCACACCTCGGTCGGTTTGTATGGCGAGCTGGTTTTTT | |
| Apta_602 | DNA | GGGCGAGAACAGTGTCCCAGTCGCTAGTTTTCTCTGCCC | |
| Apta_649 | DNA | GCACACCGATGGCGGTCCTGTTTAGGGGGTGTGCGTG | |
| Apta_692 | DNA | ACGTTGACGCTGGTGCCCGCTTGTGGTGCGAGTGTTGTGT | |
| Apta_1067 | DNA | GCGCGGTACCGCGCTAACGGAGGTTGCGTCCGT | |
| Apta_1215 | DNA | GTCGAATCAGCACCTCTGCATAGGTTACGTTTATACTGCG | |
| Apta_1257 | DNA | CGACGCACAGTCGCTGGTGCGTACCTGGTTGCCGTTGTGT | |
| Apta_1261 | DNA | GGGCGGACGCTAGGTGGTGATGCTGTGCTACACGTGTTGT | |
| Apta_1262 | DNA | ACAAGGGGTGCAGGGGTCCGCGATTGTGACTGTGTGTGCG | |
| Apta_1212 | DNA | CTGTTCTCGGTCGCGACCTATCTGGTCGTCGCCGCGCTCGTGTTCGGAACGCTCATCGCGTTCGGGCTCGGCG |
DEV TOOL
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