IgG aptamer

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Timeline

2008

The aptamer is initially acquired through the SELEX[1]

2008

RNA aptamer complex with the Fc fragment of human IgG1, X-ray diffraction studies revealed 2.2 A resolution[2]

2010

Determined the 2.15 Å crystal structure of the Fc fragment of human IgG1 (hFc1) complexed with an anti-Fc RNA aptamer[3]

2012

Reported a lightly cross-linked (2%) N-isopropyl acrylamide (NIPAm) synthetic polymer NP (50-65 nm) incorporating hydrophobic and carboxylate groups that binds with high affinity to the Fc fragment of IgG[4]

2013

Efficiently select and identify novel DNA aptamers against the Fc region of mouse IgG by EXponential enrichment (SELEX)[5]

Description

 In 2008, Yamazaki, S., & Nakamura, Y. RNA aptamers against the Fc portion of human IgG1 subclass (hIgG1-Fc) were selected from a library of RNA sequences by modified SELEX with 2′-fluoro pyrimidines. In 2008, Nakamura, Y., & Matsumura, H. solved a crystal structure of an RNA aptamer bound to hIgG1-Fc，diffracted X-rays to 2.2 Å resolution. moreover, In 2012, they determined the 2.15 Å crystal structure of the Fc fragment of human IgG1 (hFc1) complexed with an anti-Fc RNA aptamer[1,2,3].

SELEX

In 2008, Yamazaki, S., & Nakamura, Y. RNA aptamers against the Fc portion of human IgG1 subclass (hIgG1-Fc) were selected from a library of 5 × 1014 different RNA molecules randomized over 40 nucleotides (40N RNA pool) by modified SELEX with 2′-fluoro pyrimidines. After 10 rounds of selection, we obtained six sets of RNA sequences of 71–74 nucleotides (nt) long, Apt1 through Apt6[1].
Detailed information are accessible on SELEX page.



Structure

2D representation

Here we use ribodraw to complete the figure, through the 3D structure information. Apt8 aptamer was the aptamer sequence studied in SELEX article[3].

5'-GGGAACAAAGCUGAAGUACUUACCC-3'

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3D visualisation

Nakamura, Y., & Matsumura, H. determined the crystal structure of Apt8-2 aptamer bound to the Fc fragment of human IgG1 at 2.15 Å resolution. The PDB ID of this structure is 3AGV. The final model, an asymmetric unit including homodimeric hFc1 residues 241–262, 272–296, 302–321 and 334–443 for chain A and 237–444 for chain B, two RNA aptamer molecules (G1-C11 and G16-C23 and G1-A24), two carbohydrate chains , two Ca2+ ions, and 254 water molecules[3].
Additional available structures that have been solved and detailed information are accessible on Structures page.

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Binding pocket

Left: Surface representation of the binding pocket of the aptamer generated from PDB ID: 3AGV at 2.15 Å resolution. the Fc fragment of human IgG1 (shown in vacuumm electrostatics), blue is positive charge, red is negative charge. Right: The hydrogen bonds of binding sites of the aptamer bound with the Fc fragment of human IgG1.

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Ligand information

SELEX ligand

The affinity of the selected aptamers to hIgG1-Fc was examined by surface plasmon resonance (SPR) using BIAcore 2000. We chose association rate constants 1(Ka1) and dissociation rate constants1(Kd1) to Calculate affinity constant (KD) in the document[1]. This result is for reference only.

Name Sequence Ligand Affinity
apt2 AGUUACAGGUGCUCCAUCAACAAAAUGUUACAUGGAACUG Human IgG1 Fc portion 5.6 nM
apt7 GGAGGUGCUCUGCGAGCCACGCGGAACUCC Human IgG2 Fc portion 7.5 nM
apt8 GGAGGUGCUCCGAAAGGAACUCC(U and C are modified with fluorine) Human IgG3 Fc portion 75 nM
apt8-1 GGAGGUGCUCCGAAAGGAACUCC(U and C are modified with fluorine, some bases used deoxynucleotide) Human IgG4 Fc portion 25.5 nM
apt8-2 GGAGGUGCUCCGAAAGGAACUCC(some U and C was modified with fluorine, some bases used deoxynucleotide) Human IgG5 Fc portion 110 nM

Structure ligand

The basic structure of immunoglobulin (Ig) molecules is a tetramer of two light chains and two heavy chains linked by disulphide bonds. There are two types of light chains: kappa and lambda, each composed of a constant domain (CL) and a variable domain (VL). There are five types of heavy chains: alpha, delta, epsilon, gamma and mu, all consisting of a variable domain (VH) and three (in alpha, delta and gamma) or four (in epsilon and mu) constant domains (CH1 to CH4). Ig molecules are highly modular proteins, in which the variable and constant domains have clear, conserved sequence patterns. The domains in Ig and Ig-like molecules are grouped into four types: V-set, C1-set, C2-set and I-set. Structural studies have shown that these domains share a common core Greek-key β-sandwich structure, with the types differing in the number of strands in the β-sheets as well as in their sequence patterns.-----from Pfam(Interpro)
Uniprot ID Pfam MW Amino acids sequences PDB ID GenBank
P01857 IPR003597 23.89 KDa GPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK 1FC1 9606
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Similar compound

We used the Dail server website to compare the structural similarities of ligand proteins, and chose the top 10 in terms of similarity for presentation. The Dali server is a network service for comparing protein structures in 3D. Dali compares them against those in the Protein Data Bank (PDB). Z-score is a standard score that is converted from an original score. The list of neighbours is sorted by Z-score. Similarities with a Z-score lower than 2 are spurious. RMSD(Root Mean Square Deviation) value is used to measure the degree to which atoms deviate from the alignment position.
PDB Z-score RMSD Description
3AGV-B 31.6 0 Ig gamma-1 chain c region
1OQO-A 29.2 0.5 Immunoglobulin gamma-1 heavy
7Q3P-B 29.1 0.6 IgG1-Fc-MST-HH
5D4Q-A 29 0.7 Ig gamma-1 chain c region
5IW6-A 29 0.7 Ig gamma-1 chain c region
3AVE-B 29 0.7 Ig gamma-1 chain c region
6FGO-A 29 0.7 Immunoglobulin gamma-1 heavy
6GFE-H 29 0.8 Immunoglobulin gamma-4 heavy
4KU1-B 28.9 0.9 Ig gamma-1 chain c region
5U4Y-A 28.9 0.6 IgG1 Fc


References

[1] Structural and molecular basis for hyperspecificity of RNA aptamer to human immunoglobulin G.
Miyakawa, S., Nomura, Y., Sakamoto, T., Yamaguchi, Y., Kato, K., Yamazaki, S., & Nakamura, Y.
RNA (New York, N.Y.), 14(6), 1154–1163. (2008)
[2] Crystallization and preliminary X-ray diffraction studies of an RNA aptamer in complex with the human IgG Fc fragment.
Sugiyama, S., Nomura, Y., Sakamoto, T., Kitatani, T., Kobayashi, A., Miyakawa, S., Takahashi, Y., Adachi, H., Takano, K., Murakami, S., Inoue, T., Mori, Y., Nakamura, Y., & Matsumura, H.
Acta crystallographica. Section F, Structural biology and crystallization communications, 64(Pt 10), 942–944. (2008)
[3] Conformational plasticity of RNA for target recognition as revealed by the 2.15 A crystal structure of a human IgG-aptamer complex.
Nomura, Y., Sugiyama, S., Sakamoto, T., Miyakawa, S., Adachi, H., Takano, K., Murakami, S., Inoue, T., Mori, Y., Nakamura, Y., & Matsumura, H.
Nucleic acids research, 38(21), 7822–7829. (2010)
[4] Engineered synthetic polymer nanoparticles as IgG affinity ligands.
Lee, S. H., Hoshino, Y., Randall, A., Zeng, Z., Baldi, P., Doong, R. A., & Shea, K. J.
Journal of the American Chemical Society, 134(38), 15765–15772. (2012)
[5] Target replacement strategy for selection of DNA aptamers against the Fc region of mouse IgG.
Ma, J., Wang, M. G., Mao, A. H., Zeng, J. Y., Liu, Y. Q., Wang, X. Q., Ma, J., Tian, Y. J., Ma, N., Yang, N., Wang, L., & Liao, S. Q.
Genetics and molecular research : GMR, 12(2), 1399–1410. (2013)