AptaDB: Result

Interaction ID: 156

Aptamer sequence: UUACCACGCGCUCUUAACUGCUAGCGCCAUGGC

Target unique ID: P03355

Aptamer ID	Aptamer descriptor	Target chemistry	Target name	Affinity	Binding Conditions/Buffer	PubMed ID
Apta_152	m.1.1	Protein	POL_MLVMS	6.9 nM	50 mM Tris-HC1 (pH 7.7), 200 mM potassium acetate, and 10 mM DTT	7518691

Aptamer Sequence:	UUACCACGCGCUCUUAACUGCUAGCGCCAUGGC
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_152	Description	m.1.1
Aptamer chemistry	RNA	Length	33 nt
GC content	57.6%	Molecular weight	10,681.15 Da
Molarity of 1 μg/μl solution	93.62 μM	Number of G-quadruplexes	No QGRS found
G-Score	N/A	Function	Targeted binding
Sequence	UUACCACGCGCUCUUAACUGCUAGCGCCAUGGC
Applications	Inhibition of cDNA Synthesis and RNase H Activity

Type	Detail	Type	Detail
Uniprot ID	P03355	Protein name	Gag-Pol polyprotein (Pr180gag-pol) [Cleaved into: Matrix protein p15 (MA); RNA-binding phosphoprotein p12 (pp12); Capsid protein p30 (CA); Nucleocapsid protein p10-Pol (NC-pol); Protease (PR) (EC 3.4.23.-) (p14); Reverse transcriptase/ribonuclease H (RT) (EC 2.7.7.49) (EC 2.7.7.7) (EC 3.1.26.4) (p80); Integrase (IN) (EC 2.7.7.-) (EC 3.1.-.-) (p46)]
Gene name(s)	gag-pol	Organism	Gag-Pol polyprotein (Pr180gag-pol) [Cleaved into: Matrix protein p15 (MA); RNA-binding phosphoprotein p12 (pp12); Capsid protein p30 (CA); Nucleocapsid protein p10-Pol (NC-pol); Protease (PR) (EC 3.4.23.-) (p14); Reverse transcriptase/ribonuclease H (RT) (EC 2.7.7.49) (EC 2.7.7.7) (EC 3.1.26.4) (p80); Integrase (IN) (EC 2.7.7.-) (EC 3.1.-.-) (p46)]
Status	reviewed in uniprot database	Length	1738
Mass	194,912	Activity regulation	Most efficiently inhibited by Amprenavir, which is able to block Gag-Pol processing in infected cells
Involvement in disease	N/A	Catalytic activity	Reaction=a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = diphosphate + DNA(n+1)
PDB ID(s)	1D0E;1D1U;1I6J;1MML;1N4L;1NND;1QAI;1QAJ;1ZTT;1ZTW;2FJV;2FJW;2FJX;2FVP;2FVQ;2FVR;2FVS;2HB5;2M9U;2MQV;2MS0;2MS1;2R2R;2R2S;2R2T;2R2U;3FSI;3NNQ;4M94;4M95;4MH8;4NZG;4XO0;4XPC;4XPE;5DMQ;5DMR;5VBS;6B1Q;6B1R;6B1S;6GZA;6MIG;6MIH;6MIK;7JQ8;
Function	Plays a role in budding and is processed by the viral protease during virion maturation outside the cell.

No relevant experimental diagram	Interaction ID	156
	Target type	Protein
	Target unique ID	P03355
	Activity	6.9 nM
	Binding Conditions/Buffer	50 mM Tris-HC1 (pH 7.7), 200 mM potassium acetate, and 10 mM DTT
	Assay	N/A
	PubMed ID	7518691

Aptamer ID	Aptamer chemistry	Sequence	Similarity
Apta_374	RNA	GUCCCGUGCGCAAAAGUUCUUAGCGCUAGCAGUCCUAGUUGC	59.52%
Apta_51	RNA	GCCUUAGUAACGUGCUUUGAUGUCGAUUCGACAGGAGGC	53.85%
Apta_379	RNA	UACGACACGAUUGGGACGUGUCUAUGGGAC	51.52%
Apta_1292	RNA	GGCACGUGUAUUACCCUAGUGGUCGACGUGCC	51.52%
Apta_87	RNA	UACCGACUAGCAAAACCUGCUGGCGACGUUUAGAU	51.43%
Apta_313	RNA	UGCCCUGCCCUCACCCGUUAGCCUGAGCGCCCCGCA	50.00%
Apta_384	RNA	AUGAUCAAUCGCCUCAAUUCGACAGGAGGCUCAC	50.00%
Apta_603	RNA	CUUGUCUGAACAAUUUCGUCUGCCUUUGCGUUCCGACGGC	50.00%
Apta_632	RNA	GACGAGAAGGAGUGCUGGUUAUACUAGCGGUUAGGUCACUCGUC	50.00%
Apta_658	RNA	CUGCGAUCAGGGGUAAAUUUCCGCGCAGGCUCCACGCCGC	50.00%
Apta_709	RNA	AGUGAUACCAGCAUCGUCUUGAUGCCCUUGGCAGCACU	50.00%
Apta_1211	RNA	ACUAGCCUCAUCAGCUCAUGUGCCCCUCCGCCUGGAUCAC	50.00%
Apta_520	RNA	GGGAGAUCUACGGAUCUCAGGGCUCUUACGGGAGCUACAUGGAAGGAGUCCAUGUGU	49.12%
Apta_849	RNA	UCCCGAUUACUGUACAUACCUUAGCCCAUAGCUGGCUGC	48.72%
Apta_237	RNA	UUCAACGCUGUGAAGGGCUUAUACGAGCGGAUUACCC	48.65%
Apta_630	DNA	GACCAGGGCAAACGGTAGGGAGTGGTC	48.48%
Apta_927	RNA	UUACAAUGAGGUGGGACGCGGGUUGUGGUG	48.48%
Apta_366	RNA	GGUUAGAGGCGACGUCCCGGAAUCCGCGCCCAUUGCCCCC	47.50%
Apta_660	RNA	UGGGAGGAGUGCUGCUCUCCAGGCACUCUUGUUGCUCGGA	47.50%
Apta_370	RNA	GGGAGGACGCGUCGCCGUAAUGGAUGUUUUGCUCCCUG	47.37%

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