RecA protein catalyzes the homologous pairing and strand exchange between single stranded circular and homologous linear duplex DNA substrates forming nicked circular heteroduplex products. Effects of alkylated DNA substrates on RecA mediated strand exchange reaction were studied. Methylation of single stranded circular DNA by dimethylsulfate blocks strand exchange completely. Dimethylsulate reacts with amino groups of DNA bases to produce N-methylated products, which cannot form stable hydrogen bond. Thus pairing and strand exchange cannot occur between modified ssDNA and homologous intact duplex. In contrast to methylation, ethylated ssDNA by ethylnitrosourea reacts with homologous linear duplex to form stable nicked circular DNA products. However, the products were reduced with increase of degree of ethylation. When strand exchange was proceeded with ethylnitrosourea treated duplex DNA, similar results were obtained, although large amount of slow moving reaction intermediates were detected. Since less than 1% of nucleotides in DNA substrates is ethylated in the given reaction condition and most of the reaction products are ethylphosphotriesters (Singer et al., 1978), ethylated ssDNA may inhibit the formation of initiation complex, whereas ethylated dsDNA probably decrease the rate of homologous pairing and/or strand exchange.