Cellular processes can only be understood as the dynamic interplay of molecules. There is a need for techniques to monitor interactions of endogenous proteins directly in individual cells and tissues to reveal the cellular and molecular architecture and its responses to perturbations. Here we report our adaptation of the recently developed proximity ligation method to examine the subcellular localization of protein-protein interactions at single-molecule resolution. Proximity probes-oligonucleotides attached to antibodies against the two target proteins-guided the formation of circular DNA strands when bound in close proximity. The DNA circles in turn served as templates for localized rolling-circle amplification (RCA), allowing individual interacting pairs of protein molecules to be visualized and counted in human cell lines and clinical specimens. We used this method to show specific regulation of protein-protein interactions between endogenous Myc and Max oncogenic transcription factors in response to interferon-gamma (IFN-gamma) signaling and low-molecular-weight inhibitors.

The advent of in vitro DNA amplification has enabled rapid acquisition of genomic information. We present here an analogous technique for protein detection, in which the coordinated and proximal binding of a target protein by two DNA aptamers promotes ligation of oligonucleotides linked to each aptamer affinity probe. The ligation of two such proximity probes gives rise to an amplifiable DNA sequence that reflects the identity and amount of the target protein. This proximity ligation assay detects zeptomole (40 x 10(-21) mol) amounts of the cytokine platelet-derived growth factor (PDGF) without washes or separations, and the mechanism can be generalized to other forms of protein analysis.

Several platelet-derived growth factor (PDGF) and vascular endothelial growth factor (VEGF) family members display C-terminal protein motifs that confer retention of the secreted factors within the pericellular space. To address the role of PDGF-B retention in vivo, we deleted the retention motif by gene targeting in mice. This resulted in defective investment of pericytes in the microvessel wall and delayed formation of the renal glomerulus mesangium. Long-term effects of lack of PDGF-B retention included severe retinal deterioration, glomerulosclerosis, and proteinuria. We conclude that retention of PDGF-B in microvessels is essential for proper recruitment and organization of pericytes and for renal and retinal function in adult mice. Received April 3, 2003; revised version accepted May 23, 2003. The control of cell migration and the formation of specific patterns during embryonic development are believed to depend, at least in part, on the precise spatial distribution of secreted growth and differentiation factors (GDFs). This is achieved by strictly localized and regulated synthesis and secretion of GDFs, but also by binding of the secreted GDFs to cell surface-and extracellular matrix molecules. One type of molecule strongly implicated in the regulation of GDF activities in vivo is the heparan sulphate proteoglycans ( Certain isoforms of platelet-derived growth factor (PDGF) and vascular endothelial growth factor (VEGF) family members display positively charged stretches of amino acids residues at the C terminus. These stretches are included or excluded depending on alternative splicing or proteolytic processing (Eriksson and Alitalo 1999; Heldin and Westermark 1999). For VEGF-A, the long splice isoforms, which carry HSPG-binding domains, accumulate on the cell surface or in the extracellular matrix, whereas short VEGF-A is diffusible following cellular release (Park et al. 1993). The developmental role of HSPG binding of VEGF-A was recently addressed using mice in which the long VEGF-A splice isoforms were selectively ablated (Carmeliet et al. 1999;Ruhrberg et al. 2002;Stalmans et al. 2002). In these mice, extracellular VEGF-A distribution becomes more widespread, leading to changes in endothelial sprouting and branching, and to the formation of abnormal vascular patterns (Ruhrberg et al. 2002). In PDGF-A and PDGF-B, the HSPGbinding motifs do not affect receptor binding or biological activity of the recombinant proteins (Östman et al. 1989). However, in transfected cells, these motifs confer retention of the secreted growth factor to the surface of the producing cells. Conversely, absence of the retention motif leads to increased secretion of a diffusible protein that readily accumulates in the cell culture medium (LaRochelle et al. 1991;Östman et al. 1991;Raines and Ross 1992;Andersson et al. 1994). The retention motif also appears to limit the action range of PDGF-B in vivo, as suggested from experiments with transplanted keratinocytes transfected with PDGF-B expression vectors (Eming et al. 1999). ...

Nucleotide sequence information derived from DNA segments of the human and other genomes is accumulating rapidly. However, it frequently proves difficult to use such short DNA segments to identify clones in genomic libraries or fragments in blots of the whole genome or for in situ analysis of chromosomes. Oligonucleotide probes, consisting of two target-complementary segments, connected by a linker sequence, were designed. Upon recognition of the specific nucleic acid molecule the ends of the probes were joined through the action of a ligase, creating circular DNA molecules catenated to the target sequence. These probes thus provide highly specific detection with minimal background.

An assay for the presence of given DNA sequences has been developed, based on the ability of two oligonucleotides to anneal immediately adjacent to each other on a complementary target DNA molecule. The two oligonucleotides are then joined covalently by the action of a DNA ligase, provided that the nucleotides at the junction are correctly base-paired. Thus single nucleotide substitutions can be distinguished. This strategy permits the rapid and standardized identification of single-copy gene sequences in genomic DNA.