Heparan sulfate-N-deacetylase/N-sulfotransferase catalyzes both the N-deacetylation and N-sulfation reactions that initiate the modification of the oligosaccharide backbone of heparan sulfate (HS). The glycosaminoglycan polymer appears to modulate the activity of growth factors by mediating their initial binding. To understand how the biosynthesis of these binding sites is regulated, a rat liver-derived cDNA encoding the above activities was overexpressed in a COS cell mutant (CM-15) that has reduced levels of the enzyme and binds poorly to immobilized basic fibroblast growth factor (bFGF). This resulted in increased synthesis of sulfated blocks of decasaccharide size or longer. These blocks exhibited high affinity binding to bFGF and contained a high content of 2-O-sulfated iduronate and at least five consecutive N-sulfated disaccharides. An increase in the synthesis of these high affinity blocks was not seen in transfected wild-type COS cells even though they showed a 4-fold increase of both enzyme activities, suggesting that once sufficient levels of highly sulfated blocks of saccharides with high affinity for bFGF are attained, no further synthesis of these domains occurs.