Nowadays, several dioxygenases with complementary substrate profiles have become available for synthetic applications by creation of efficient recombinant whole-cell expression systems. In particular with such delicate enzyme complexes, production of the required biocatalyst within its natural environment inside of an intact host cells (predominantly Escherichia coli) is highly advantageous, as this strategy allows the utilization of such catalytic entities within asymmetric synthesis with a minimum expertise in enzymology and also proteins from pathogenic organisms can be studied in a benign and safe environment. The most abundantly utilized type of aryl dioxygenases (2,3-dioxygenases) incorporates the additional oxygen functionalities in ortho- and meta-position to an existing substituent at the aromatic core exclusively in cis-configuration usually in very high optical purity. There are three different prototype enzymes distinguished by the nature of the preferably converted aromatic ring system toluene (TDO, from Pseudomonas putida F39/D), naphthalene (NDO, from Pseudomonas putida 119), and biphenyl dioxygenases (BPDO, from Sphingomonas yanoikuyae B8/36). The biocatalyst originated from Pseudomonas putida and was utilized within recombinant whole-cells of E. coli. The whole cell mediated biotransformations were carried out with three different enzymes E. coli JM109 (pDTG601A) expressing TDO, E. coli JM109 (DE3)(pDTG141) and E. coli JM109 (PVL1343-PMS13) expressing NDO. Within this contribution we have focused our attention to substituted quinolines and isoquinolines and the scope of the biotransformation of a series was explored. While such systems have been investigated in the past, the chosen substituents (Cl, Br, OMe) adjacent to the ring nitrogen atom represented labile functionalities, which led to subsequent hydrolytic processes and ultimately to complicated compound mixtures. Based on rich chemistry associated to carboxylic acid derivatives and nitrile groups and the hydrolytic stability of the corresponding quinoline and isoquinoline derivatives, we investigate a small collection of such compounds in dioxygenase mediated biooxygenations. The present study establishes that several bicyclic azaarenes are good substrates in the dioxygenase catalyzed reaction, giving cis-dihydrodiol derivatives. In case of alkyl substituents monohydroxylated products were also observed. Complete structural assignment of novel metabolites was carried out using NMR and diffraction techniques. The regio- and stereo-selectivity of the cis-dihydroxylation was found to be in accordance with the literature. Regioselective cis-dihydroxylation of the carbocyclic and the heterocyclic rings in the quinolines and isoquinolines (5,6 and/or 7,8 bonds), occurred to give the corresponding cis-dihydrodiol metabolites. The cis-diol metabolites formed by biooxygenations were isolated, purified, characterized and absolute configuration established by using heavy halogen assisted crystallographic studies of corresponding 4-iodobenzoate esters. The structures and absolute configurations of metabolites have been determined by NMR analysis and correlation to the existing data for similar compounds. It was discovered that trichloroacetyl chloride could be used to protect the cis-diols as 5-membered cyclic carbonates. The scope and limitation of trichloroacetyl chloride towards 5-membered cyclic carbonate synthesis was elaborated with selected reactions with different classes including catechol, aliphatic, and cyclic diols. Cyclic carbonate synthesis was not selective in case of aliphatic diols. The aliphatic diols gave both cyclic carbonates and diesters with trichloroacetyl chloride. The diester was the major product of reaction as compared to the carbonate. This indicates that aromatic cis-diols can be protected as 5-membered cyclic carbonates with trichloroacetyl chloride whereas the aliphatic diols are not completely converted to cyclic carbonates. Keywords: biotransformation; naphthalene dioxygenase (NDO); toluene dioxygenase (TDO); chemoenzymatic synthesis; catalytic hydrogenation; desymmetrization; cis-dihydrodiols.