AptaDB: Result

Interaction ID: 311

Aptamer sequence: ATCCTGTGAGGAATGCTCATGCATAGCAAGGGCT

Target unique ID: P11140

Aptamer ID	Aptamer descriptor	Target chemistry	Target name	Affinity	Binding Conditions/Buffer	PubMed ID
Apta_302	A6	Protein	ABRA_ABRPR	28 nM	20 mM HEPES (pH 7.35), 120 mM NaCl, 5 mM KCl, 1 mM CaCl2, 1 mM MgCl2	17055241

Aptamer Sequence:	ATCCTGTGAGGAATGCTCATGCATAGCAAGGGCT
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_302	Description	A6
Aptamer chemistry	DNA	Length	34 nt
GC content	50.0%	Molecular weight	10,746.71 Da
Molarity of 1 μg/μl solution	93.05 μM	Number of G-quadruplexes	No QGRS found
G-Score	N/A	Function	Targeted binding
Sequence	ATCCTGTGAGGAATGCTCATGCATAGCAAGGGCT
Applications	Binding to Abrin toxin

Type	Detail	Type	Detail
Uniprot ID	P11140	Protein name	Abrin-a [Cleaved into: Abrin-a A chain (EC 3.2.2.22) (rRNA N-glycosidase); Linker peptide; Abrin-a B chain]
Gene name(s)	N/A	Organism	Abrin-a [Cleaved into: Abrin-a A chain (EC 3.2.2.22) (rRNA N-glycosidase); Linker peptide; Abrin-a B chain]
Status	reviewed in uniprot database	Length	528
Mass	59,244	Activity regulation	N/A
Involvement in disease	N/A	Catalytic activity	Reaction=Endohydrolysis of the N-glycosidic bond at one specific adenosine on the 28S rRNA
PDB ID(s)	1ABR;5Z37;5Z3I;5Z3J;
Function	The A chain is responsible for inhibiting protein synthesis through the catalytic inactivation of 60S ribosomal subunits by removing adenine from position 4,324 of 28S rRNA. Abrin-a is more toxic than ricin.

	Interaction ID	311
	Target type	Protein
	Target unique ID	P11140
	Activity	28 nM
	Binding Conditions/Buffer	20 mM HEPES (pH 7.35), 120 mM NaCl, 5 mM KCl, 1 mM CaCl2, 1 mM MgCl2
	Assay	Binding curve of TA6 (1 nM) with increasing concentrations of abrin in selection buffer. FP changes refer to the difference in steady-state polarization from the 5-FAM-labeled DNA in the absence and presence of abrin at RT. The line is a nonlinear least square fit using GraphPad Prism software and the fitted dissociation constant is 28 ± 9 nM
	PubMed ID	17055241

Aptamer ID	Aptamer chemistry	Sequence	Similarity
Apta_1065	DNA	CCTCGCTATGATGGAGTGCGTTTAGATCAGGGAACGGGTT	60.00%
Apta_517	DNA	ACCTTCGGGGAGTATTGCGGAGGAAGGT	58.82%
Apta_1023	DNA	CTCCTTCAACGAAGTGGGTCTCCTTCAACGAAGTGGGTCTC	56.10%
Apta_515	DNA	CCTGGGGGAGTATTGCGGAGGAAGG	55.88%
Apta_49	DNA	CTTCCATGTTGAGGCGTTTATACCAGTTATCATCGGACTA	55.00%
Apta_946	DNA	TACCGGGTAATATGCACACATGCTGATAGCAAGCAATGCA	55.00%
Apta_1022	DNA	CTCCTTCAACGAAGTGGGTTCCTTCAACGAAGTGGGTCTC	55.00%
Apta_60	DNA	GGAATGAGTGCCCTGCAAGCGAGGGCTAGC	52.94%
Apta_678	DNA	CGTACGGTGGGAACGGTTCCTCTTAGGGT	52.94%
Apta_680	DNA	ACATGCGACTGAGGCTCGGTTTATTGAGGG	52.94%
Apta_1019	DNA	ATCCCTGCAGTTTGGTAGGGTGCAGG	52.94%
Apta_1282	DNA	TCCTCTCACACATCTTATCCCCTAGGG	52.94%
Apta_1256	DNA	GATCGGGTGTGGGTGGCGTAAAGGGAGCATCGGACA	52.78%
Apta_58	DNA	GCACCTTGATGACATGATAGTCGTTGTGTATGCAGTTGGC	52.50%
Apta_160	DNA	CGGTGCAGTGGATACATGCCAGCCGTAGCCATCGTGGATA	52.50%
Apta_274	DNA	GATACTGAGCATCGTACATGATCCCGCAACGGGCAGTATT	52.50%
Apta_348	DNA	ACTTGCTCTGATGCGACAACCTTTTGCCCAGATAGTAAGT	52.50%
Apta_406	DNA	AAAGCCCACTGCATAGAGGCCGCTCAACATGCGAGCCGGT	52.50%
Apta_438	DNA	AGCCATGACGATGTCGTTACGTAGATGCAGAGACTCCTAA	52.50%
Apta_438	DNA	AGCCATGACGATGTCGTTACGTAGATGCAGAGACTCCTAA	52.50%

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