AptaDB: Result

Interaction ID: 1

Aptamer sequence: ACGAAGCUUGAUCCCGUUUGCCGGUCGAUCGCUUCGA

Target unique ID: A6MI22

Aptamer ID	Aptamer descriptor	Target chemistry	Target name	Affinity	Binding Conditions/Buffer	PubMed ID
Apta_1	RNA Tat	Protein	A6MI22_9HIV1	120 pM	50 mM Tris-HCl (pH 7.8) and 50 mM KCl	10886365

Aptamer Sequence:	ACGAAGCUUGAUCCCGUUUGCCGGUCGAUCGCUUCGA
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_1	Description	RNA Tat
Aptamer chemistry	RNA	Length	37 nt
GC content	56.8%	Molecular weight	11,783.98 Da
Molarity of 1 μg/μl solution	84.86 μM	Number of G-quadruplexes	No QGRS found
G-Score	N/A	Function	Targeted binding
Sequence	ACGAAGCUUGAUCCCGUUUGCCGGUCGAUCGCUUCGA
Applications	Binding to target proteins

Type	Detail	Type	Detail
Uniprot ID	A6MI22	Protein name	Protein Tat (Transactivating regulatory protein)
Gene name(s)	tat	Organism	Protein Tat (Transactivating regulatory protein)
Status	unreviewed in uniprot database	Length	106
Mass	12,122	Activity regulation	N/A
Involvement in disease	N/A	Catalytic activity	N/A
PDB ID(s)	N/A
Function	Extracellular circulating Tat can be endocytosed by surrounding uninfected cells via the binding to several surface receptors such as CD26, CXCR4, heparan sulfate proteoglycans (HSPG) or LDLR.

	Interaction ID	1
	Target type	Protein
	Target unique ID	A6MI22
	Activity	120 pM
	Binding Conditions/Buffer	50 mM Tris-HCl (pH 7.8) and 50 mM KCl
	Assay	Determination of equilibrium dissociation constants (Kd) for binding of TAR-1 and of RNATat to CQ. Representative autoradiograms obtained from gel-shift assays for analysis of binding of TAR-1 and RNATat to CQ (A and B, respectively)
	PubMed ID	10886365

Aptamer ID	Aptamer chemistry	Sequence	Similarity
Apta_133	RNA	GGGAGGACGAUGCGGUGAGUCGUUCCCUUCGUCCCCAGACGACUCGCCCGA	54.90%
Apta_89	RNA	AAUAACCUUAAUGCGACGUUGGUUCGUCAACAUGG	54.05%
Apta_90	RNA	ACAACCUAAAUGCGACGUUGGGUCAAAAACGUGAA	54.05%
Apta_313	RNA	UGCCCUGCCCUCACCCGUUAGCCUGAGCGCCCCGCA	54.05%
Apta_1122	RNA	ACAACCCGGAACAACGUCUAACAGUGUACCAUAACCCGGCAUUCA	53.33%
Apta_131	RNA	GGGAGGACGAUGCGGUCCUGUCGUCUGUUCGUCCCCAGACGACUCGCCCGA	52.94%
Apta_132	RNA	GGGAGGACGAUGCGGCGUUUCCUCUGGUUCGUCCCCAGACGACUCGCCCGA	52.94%
Apta_135	RNA	GGGAGGACGAUGCGGAUUCUGGUUACUGGCCGCCCCAGACGACUCGCCCGA	52.94%
Apta_315	RNA	GGGAGGACGAUGCGGUCGUAUUAUCCGCUGCACGCCAGACGACUCGCCCGA	52.94%
Apta_1144	RNA	ACGAGUCUGGUCCUUCCUCCCUAAUUGCUGUUGAGGUAUCGGCUACAACAA	52.94%
Apta_1211	RNA	ACUAGCCUCAUCAGCUCAUGUGCCCCUCCGCCUGGAUCAC	52.50%
Apta_632	RNA	GACGAGAAGGAGUGCUGGUUAUACUAGCGGUUAGGUCACUCGUC	52.27%
Apta_1141	RNA	ACGAGUCUGGUCCUUCCUUUGACGACUAUUGUUUGGUAUCGAUCAACAACAA	51.92%
Apta_431	RNA	CAGGCAUGCCUAGCUAAGCAGCCCAUGGCUUAUGCGCGGAAUAUUGGCUUCCGUUC	51.79%
Apta_87	RNA	UACCGACUAGCAAAACCUGCUGGCGACGUUUAGAU	51.35%
Apta_88	RNA	AAUAACCUUAAUGCGACGUUGGUUUGUCAACAACG	51.35%
Apta_716	RNA	GGCGCUUCAUGCCGAAAGGCCCGUUGUAACGUC	51.35%
Apta_855	RNA	UCACUGUUAUCCGAUAGCAGCGCGGGAUGA	51.35%
Apta_955	RNA	ACGUAUCCCUUUUCGCGUA	51.35%
Apta_956	RNA	ACGUUUCCCUUUUCGCGUA	51.35%

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