Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 341
Aptamer sequence: CATGCTTCCCCAGGGAGATGACCGGGGCGTACACCGTCGCGGCACATGTCTGAATGCGTTTAGTCTCTGTGG
Target unique ID: P16070
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_336 S5rev Protein CD44_HUMAN 238 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: CATGCTTCCCCAGGGAGATGACCGGGGCGTACACCGTCGCGGCACATGTCTGAATGCGTTTAGTCTCTGTGG
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_336 Description S5rev
Aptamer chemistry DNA Length 72 nt
GC content 59.7% Molecular weight 22,463.12 Da
Molarity of 1 μg/μl solution 44.52 μM Number of G-quadruplexes No QGRS found
G-Score N/A Function Targeted therapy
Sequence CATGCTTCCCCAGGGAGATGACCGGGGCGTACACCGTCGCGGCACATGTCTGAATGCGTTTAGTCTCTGTGG
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 341
Target type Protein
Target unique ID P16070
Activity 238 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_335 DNA ACCGGGCGTACACCGTCGCGGCACATGTCTGAATGCGTTTAGTCTCTGTG 69.44%
Apta_1035 DNA ATGCGGATCCCGCGCGGGTCTGAGGAGTGCGCGGTGCCAGTGAGTGCGCGAAGCTTGCGC 54.17%
Apta_1070 DNA CCGTATCGCCCAGGCAACTGGGCTAAACTTCCCAGAGGGAACGAAACCTGGG 54.17%
Apta_1104 DNA TACGACTCACTATAGGGATCCCCCCGAGTGAAGAGCAGGACAGCGGGACAGCGTCGAATTCCCTTTAGTGAGGGTT 53.95%
Apta_99 DNA AGCAGCACAGAGGTCAGATGTCGGGCGGTTCGGGACCTTGCTGCGACATATGCGTATTATCCTATGCGTGCTACCGTGAA 53.75%
Apta_99 DNA AGCAGCACAGAGGTCAGATGTCGGGCGGTTCGGGACCTTGCTGCGACATATGCGTATTATCCTATGCGTGCTACCGTGAA 53.75%
Apta_742 DNA ATCGTCTGCTCCGTCCAATAGGACCGATAGGAACCACGGACTGCATGTTTCTGCATTTGACGTGGTTTGGTGTGAGGTCGTGC 53.01%
Apta_651 DNA CCTGCACCTCGTCCAGCATGCACACCGATGGCGGTCCTGTTTAGGGGGTGTGCGTG 52.78%
Apta_686 DNA GGTCACCAACAACAGGGAGCGCTACGCGAAGGGTCAATGTGACGTCATGCGGATGTGTGG 52.78%
Apta_688 DNA GCCATGACAACCAGAGGTACCCCCGCCCACCAGCCCCGAAGTCTGTCAGCCTAGTTGTTG 52.78%
Apta_910 DNA TCACGTGCATGATAGACGGCGAAGCCGTCGAGTTGCTGTGTGCCGATGCACGTGA 52.78%
Apta_993 DNA AATCCGACCACGAGAGCAGACCGACCACAGCATTATCTAAACCCATTAGTCTAGTCCTGG 52.78%
Apta_1034 DNA ATGCGGATCCCGCGCGCGACCGTGTCAGCGGGGACTAGCGGTGTAGCGCGAAGCTTGCGC 52.78%
Apta_1230 DNA GGCGATAGGCAGTGTTGCGGGGTCGGAGAGCGAGGTAATAGCGTGTATGGGTGCTGTGTG 52.78%
Apta_107 DNA AGCAGCACAGAGGTCAGATGTTCATTTCAGTTGACCGATAGCATTGAGCAATGATCTATTCCTATGCGTGCTACCGTGAA 52.50%
Apta_107 DNA AGCAGCACAGAGGTCAGATGTTCATTTCAGTTGACCGATAGCATTGAGCAATGATCTATTCCTATGCGTGCTACCGTGAA 52.50%
Apta_178 DNA AGCAGCACAGAGGTCAGATGCGGTATGCTGGGTCATCTAACTGGGGATATTCTGATATTGCCTATGCGTGCTACCGTGAA 52.50%
Apta_838 DNA TGAGCCCAAGCCCTGGTATGTAGTAATGGTGCGTACAGGCGACGGGGTCCAGGCTGGAGGGGCAGGTCTACTTTGGGATC 52.50%
Apta_412 DNA CACGACTCTCACCTCATAGCtGGTGGGGTTCCCGGGAGGGCGGCTACGGGTTCCGTAATCAGATTTGTGTCTGGTTCTGTAGACGGCTTG 52.22%
Apta_933 DNA GACGCTTACTCAGGTGTGACTCGGGGTGTAGCTCGTTATGATTCGGACAAGACTTACCTTGCGCCTCTGGGATCGAAGGACGCAGATGAAGTCTC 51.58%

ABOUT

AptaDB is an online database we developed to integrate comprehensive information about aptamer.
The detail of this database is described here:

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