AptaDB: Result

Interaction ID: 322

Aptamer sequence: UGCCCUGCCCUCACCCGUUAGCCUGAGCGCCCCGCA

Target unique ID: P14780

Aptamer ID	Aptamer descriptor	Target chemistry	Target name	Affinity	Binding Conditions/Buffer	PubMed ID
Apta_313	F3Bomf	Protein	MMP9_HUMAN	20 nM	50 mM Tris HCl, pH 7.4, 50 mM NaCl, 100 mM KCl, 5 mM CaCl2, 1 mM Magnesium Acetate	23043415

Aptamer Sequence:	UGCCCUGCCCUCACCCGUUAGCCUGAGCGCCCCGCA
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

Type	Detail	Type	Detail
Aptamer ID	Apta_313	Description	F3Bomf
Aptamer chemistry	RNA	Length	36 nt
GC content	72.2%	Molecular weight	11,586.70 Da
Molarity of 1 μg/μl solution	86.31 μM	Number of G-quadruplexes	No QGRS found
G-Score	N/A	Function	Targeted binding
Sequence	UGCCCUGCCCUCACCCGUUAGCCUGAGCGCCCCGCA
Applications	Used for ex vivo imaging slices of human brain tumors

Type	Detail	Type	Detail
Uniprot ID	P14780	Protein name	Matrix metalloproteinase-9 (MMP-9) (EC 3.4.24.35) (92 kDa gelatinase) (92 kDa type IV collagenase) (Gelatinase B) (GELB) [Cleaved into: 67 kDa matrix metalloproteinase-9; 82 kDa matrix metalloproteinase-9]
Gene name(s)	MMP9 CLG4B	Organism	Matrix metalloproteinase-9 (MMP-9) (EC 3.4.24.35) (92 kDa gelatinase) (92 kDa type IV collagenase) (Gelatinase B) (GELB) [Cleaved into: 67 kDa matrix metalloproteinase-9; 82 kDa matrix metalloproteinase-9]
Status	reviewed in uniprot database	Length	707
Mass	78,458	Activity regulation	Inhibited by histatin-3 1/24 (histatin-5)
Involvement in disease	Intervertebral disc disease (IDD)	Catalytic activity	Reaction=Cleavage of gelatin types I and V and collagen types IV and V
PDB ID(s)	1GKC;1GKD;1ITV;1L6J;2OVX;2OVZ;2OW0;2OW1;2OW2;4H1Q;4H2E;4H3X;4H82;4HMA;4JIJ;4JQG;4WZV;4XCT;5CUH;5I12;5TH6;5TH9;5UE3;5UE4;6ESM;
Function	Matrix metalloproteinase that plays an essential role in local proteolysis of the extracellular matrix and in leukocyte migration.

No relevant experimental diagram	Interaction ID	322
	Target type	Protein
	Target unique ID	P14780
	Activity	20 nM
	Binding Conditions/Buffer	50 mM Tris HCl, pH 7.4, 50 mM NaCl, 100 mM KCl, 5 mM CaCl2, 1 mM Magnesium Acetate
	Assay	N/A
	PubMed ID	23043415

Aptamer ID	Aptamer chemistry	Sequence	Similarity
Apta_365	RNA	GGACCUAUGCAGUAGCCAGUGUGGACUGGGCUGCCCCCCC	60.00%
Apta_855	RNA	UCACUGUUAUCCGAUAGCAGCGCGGGAUGA	55.56%
Apta_1288	RNA	GGCGCACUGGCGCUGCGCCUUCGGGCGCCAAUCGUAGCGUGUCGGCGCC	55.10%
Apta_1	RNA	ACGAAGCUUGAUCCCGUUUGCCGGUCGAUCGCUUCGA	54.05%
Apta_1292	RNA	GGCACGUGUAUUACCCUAGUGGUCGACGUGCC	52.78%
Apta_849	RNA	UCCCGAUUACUGUACAUACCUUAGCCCAUAGCUGGCUGC	51.28%
Apta_425	RNA	UGCCGCCAUAUCACACGGAUUUAAUCGCCGUAGAAAAGCAUGUCAAAGCCG	50.98%
Apta_152	RNA	UUACCACGCGCUCUUAACUGCUAGCGCCAUGGC	50.00%
Apta_374	RNA	GUCCCGUGCGCAAAAGUUCUUAGCGCUAGCAGUCCUAGUUGC	50.00%
Apta_588	RNA	CCGGUGCGCAUAACCACCUCAGUGCGAGCAAGGAA	50.00%
Apta_714	RNA	GGCGGUUCCUGCCGAAAGGCUCGUGGCAACGUC	50.00%
Apta_717	RNA	GGCGCAGCCCGCCGAAAGGCACGUGGAACCGUC	50.00%
Apta_856	RNA	UGGGCCGGAGGUUAGCUUGCCCAUGGCAAGCAGGGCGCCACGGACCCA	50.00%
Apta_447	RNA	ACGCUCAACGAGCCAGGAACAUCGACGUCAGCAAACGCGAGCGCAACCAGUAACACC	49.12%
Apta_131	RNA	GGGAGGACGAUGCGGUCCUGUCGUCUGUUCGUCCCCAGACGACUCGCCCGA	49.02%
Apta_132	RNA	GGGAGGACGAUGCGGCGUUUCCUCUGGUUCGUCCCCAGACGACUCGCCCGA	49.02%
Apta_315	RNA	GGGAGGACGAUGCGGUCGUAUUAUCCGCUGCACGCCAGACGACUCGCCCGA	49.02%
Apta_426	RNA	UGCCGCUAUAAUGCACGGAUUUAAUCGCCGUAGAAAAGCAUGUCAAAGCCG	49.02%
Apta_1122	RNA	ACAACCCGGAACAACGUCUAACAGUGUACCAUAACCCGGCAUUCA	48.89%
Apta_431	RNA	CAGGCAUGCCUAGCUAAGCAGCCCAUGGCUUAUGCGCGGAAUAUUGGCUUCCGUUC	48.21%

ABOUT