The remodeling of phosphaticlylinositol polyphosphates in cellular membranes by phosphatases and kinases orchestrates the signaling by these lipids in space and time. To provide chemical tools to study the changes in cell physiology mediated by these lipids, three new metabolically stabilized (ms) analogues of phosphatidylinositol-3-phosphate (Ptdlns(3)P) were synthesized. We describe herein the total asymmetric synthesis of 3-methylphosphonate, 3-(monofluoromethyl)phosphonate and 3-phosphorothioate analogues of Ptdlns(3)P. From differentially protected D-myo-inositol key intermediates, a versatile phosphoramidite reagent was employed in the synthesis of PtdIns(3)P analogues with diacylglyceryl moieties containing dioleoyl, dipalmitoyl, and dibutyryl chains. In addition, we introduce a new phosphorylation reagent, (monofluoromethyl)phosphonyl chloride, which has general applications for the preparation of "pK(a)-matched" monofluorophosphonates. These ms-Ptdlns(3)P analogues exhibited reduced binding activities with N-15-labeled FYVE and PX domains, as significant H-1 and N-15 chemical shift changes in the FYVE domain were induced by titrating ms-Ptdlns(3)P analogues into membrane-mimetic dodecylphosphocholine micelles. In addition, the Ptdlns(3)P analogues with dioleoyl and dipalmitoyl chains were substrates for the 5-kinase enzyme PIKfyve; the corresponding phosphorylated ms-Pl(3,5)P-2 products were detected by radio-TLC analysis.