A method of preparing DNA molecules, comprising: (a) providing one or more DNA molecules; (b) incorporating a nucleic acid molecule, which is resistant to bisulfite conversion, into the DNA molecules by one of the following to provide first modified DNA molecules: attaching first adaptors having a nonblocked 3' end to the ends of the DNA molecule to produce first adaptor-linked DNA molecules, wherein the 5' end of the DNA molecule is attached to the nonblocked 3' end of the adaptor, leaving a nick site between the juxtaposed 3' end of the DNA molecule and a 5' end of the first adaptor, and extending the 3' end of the DNA molecule from the nick site; or blunt-end ligating an oligonucleotide comprising an inverted repeat and a loop to one strand of the DNA molecule, thereby producing an oligonucleotide-linked DNA molecule comprising a nick having a 3' hydroxyl group, permitting polymerization from the 3' hydroxyl group of at least part of the oligonucleotide-linked DNA molecule; (c) providing sodium bisulfite to said first modified DNA molecules, wherein the unmethylated cytosines in said DNA molecules are converted to uracil, thereby producing bisulfite-converted single-stranded DNA molecules; and (d) amplifying one or more of the bisulfite-converted DNA molecules. (a) providing one or more DNA molecules; (b) incorporating a nucleic acid molecule, which is resistant to bisulfite conversion, into the DNA molecules by one of the following to provide first modified DNA molecules: attaching first adaptors having a nonblocked 3' end to the ends of the DNA molecule to produce first adaptor-linked DNA molecules, wherein the 5' end of the DNA molecule is attached to the nonblocked 3' end of the adaptor, leaving a nick site between the juxtaposed 3' end of the DNA molecule and a 5' end of the first adaptor, and extending the 3' end of the DNA molecule from the nick site; or blunt-end ligating an oligonucleotide comprising an inverted repeat and a loop to one strand of the DNA molecule, thereby producing an oligonucleotide-linked DNA molecule comprising a nick having a 3' hydroxyl group, permitting polymerization from the 3' hydroxyl group of at least part of the oligonucleotide-linked DNA molecule; attaching first adaptors having a nonblocked 3' end to the ends of the DNA molecule to produce first adaptor-linked DNA molecules, wherein the 5' end of the DNA molecule is attached to the nonblocked 3' end of the adaptor, leaving a nick site between the juxtaposed 3' end of the DNA molecule and a 5' end of the first adaptor, and extending the 3' end of the DNA molecule from the nick site; or blunt-end ligating an oligonucleotide comprising an inverted repeat and a loop to one strand of the DNA molecule, thereby producing an oligonucleotide-linked DNA molecule comprising a nick having a 3' hydroxyl group, permitting polymerization from the 3' hydroxyl group of at least part of the oligonucleotide-linked DNA molecule; (c) providing sodium bisulfite to said first modified DNA molecules, wherein the unmethylated cytosines in said DNA molecules are converted to uracil, thereby producing bisulfite-converted single-stranded DNA molecules; and (d) amplifying one or more of the bisulfite-converted DNA molecules.