Table 1.

Selected antibodies used to study biosynthesis and maturation of human MHC class II molecules.

Antibody	Isotype (murine)	Specificity in immunoprecipitation	Reference (original and application)
PIN 1.1	IgG1	Anti-Ii: Recognizes a cytoplasmic, N-terminal epitope of human Ii and co-immunoprecipitates any Ii-associated HLA class II αβ heterodimer. It also reacts with C-terminally truncated Ii fragments that retain the N terminus (Leupeptin-induced peptides, LIP, but not CLIP). Does not allow detection of Ii on the surface of intact cells by flow cytometry.	[26]
BU45	IgG1	Anti-Ii: Recognizes the C-terminal lumenal domain of Ii. Co-immunoprecipitates free and class II-associated Ii. Does not react with C-terminally truncated Ii fragments (LIP). Allows detection of Ii on the surface of intact antigen presenting cells (APCs) by flow cytometry.	[27–28]
CerCLIP.1	IgG1	Anti-CLIP: Recognizes the N-terminus of CLIP (Ii residues 81–105). Immunoprecipitates CLIP-loaded class II αβ heterodimers. Also allows detection of MHC class II-CLIP complexes on intact APC by flow cytometry. Staining intensity, relative to that with anti-class II mAbs, is inversely correlated with DM-catalysed CLIP release. CLIP levels also depend on the affinity of any given MHC allele(s) for CLIP.	[29–30]
6–39	IgG1	Recognizes DR3/CLIP complexes, but not free CLIP.	[31]
I-5	IgG1	Recognizes DR3/CLIP complexes, but not free CLIP.	[32]
DA6.147	IgG1	Anti-HLA-DR α chain: Recognizes a monomorphic (DR specific) determinant on the C-terminal cytoplasmic tail of DRα. The epitope is accessible for IP in Ii-associated DR but less so for mature DR molecules. It can also be used to immunoprecipitate DRα chain from denatured lysates. Also reacts with dissociated HLA-DR α chains on Western Blots. Not suitable for detection of DR on intact APCs by flow cytometry.	[33–34,30,35]
L243	IgG2a	Anti-HLA-DR: Recognizes a monomorphic, conformational determinant on the α chain of DR αβ heterodimers. DR molecules associated with intact Ii are immunoprecipitated poorly (presumably due to steric masking of the epitope by the Ii C terminus), but DR molecules associated with LIP, CLIP, or endosomal peptides are immunoprecipitated well (see Fig.10.1). The strength of the residual interaction with DR/Ii complexes may be dependent on the allele and the exact conditions for IP. L243 is poorly suited to the IP of SDS-stable DR/peptide complexes under non-denaturing conditions (without boiling), because these complexes are supershifted by L243, which fails to dissociate in SDS at room temperature. Such complexes (but not dissociated DR chains) are, however, detected by L243 on Western blots. Also detects DR molecules on the surface of intact APCs by flow cytometry and has been used for large-scale affinity chromatography to purify DR.	[12,34,36–37]
ISCR3	IgG2b	Anti-HLA-DR β chain: immunoprecipitates HLA-DR αβ dimers and is relatively insensitive to conformational maturation. Allows visualization of immunoprecipitated SDS-stable peptide-loaded DR αβ dimers, as it dissociates from antigen in reducing SDS-PAGE sample buffer at room temperature. Also, cross-reacts with MHC II molecules from other species.	[6,38–39]
LB3.1	IgG2a	Anti-HLA-DR α chain: Recognizes both empty and peptide-loaded HLA-DR 1 αβ heterodimer (monomorphic). Has been used for large-scale affinity chromatography of DR.	[40–43,38]
MEM-264	IgG2b	Anti-empty HLA-DR β chain: Recognizes an epitope on the β chain of empty HLA-DR1 αβ heterodimers. Binding of the antibody is abolished by association with CLIP, antigenic peptides, or truncated model peptides.	[40,44,43]
16.23	IgG3	Anti-HLA-DR3: Recognizes an allele-specific, DM-dependent epitope present on a subset of DR3 molecules. Empty DR3/DM complexes and DR3/peptide complexes have been reported to bind, but only after DM-mediated CLIP release and not after the alternative self-release exchange mechanism. CLIP-associated DR3 molecules are not recognised.	[45–48,32,49]
NFLD.D11	IgM	Anti-HLA-DR4: Recognizes an allele-specific, DM-dependent determinant on the HLA-DR0401 β chain.	[50]
SPVL3	IgG2a	Anti-HLA-DQ: Recognizes a monomorphic epitope on DQ αβ dimers, but not the denatured individual α or β chains. The epitope is maturation- and DM-dependent (see Fig. 10.2).	[51–53]
2.12.E11	IgG1	Anti-HLA-DQ2: Recognizes a conformation-dependent, polymorphic epitope on DQ αβ dimers, but not the denatured individual α or β chains. It is specific for DQB1*0201 or 0202 alleles.	[51,54–55]
Ia3	IgG2a	Anti-HLA-DQ: Recognizes a monomorphic epitope on DQ αβ dimers, but not the denatured individual α or β chains.	[51,56]
B7/21.2	IgG3	Anti-HLA-DP: Recognizes a monomorphic epitope on HLA-DP α and immunoprecipitates immature and mature DP heterodimers.	[57]
XD5.A11	IgG1	Anti-MHC class II β chain: Recognizes both intact and denatured DR, DP and DQ β chains and therefore all MHC class II αβ heterodimers.	[58]

Note that the studies cited here may describe the original derivation or informative uses of these antibodies, or both.