Barcoded Nucleotides

Abstract

DNA as an information storage system is simple and at the same time complex owing to the various different arrangements of the four natural nucleotides.[1] The DNA synthesis by DNA polymerases is intriguing, since these enzymes are able to catalyze the elongation of the primer strand by recognizing the DNA template and selecting the corresponding nucleotide.[1b, 2] This feature can be exploited to diversify the four-base-code by substitution of the natural substrates with modified analogues.[3] Nucleotide analogues equipped with various marker groups (e.g. dyes, tags, or spin labels[4])can be employed in DNA polymerase catalyzed reactions to increase the application scope of DNA (e.g. sequencing,structural characterization, and immobilization[4d, 5]). The “information” embedded in the marker groups allow conclusions to be drawn from the evaluation of the resulting signals. A significant gain in information would result by embedding a marker that exhibits the properties of a barcode. Typically, the barcode label bears no descriptive data but it consists of a series of signs which code for the deposited information (the term was used in other contexts with DNA before).[6] For universal adoption the barcode should be simple, affixed easily, and allow a reliable assignment of the deposited information. Oligodeoxynucleotides (ODNs) meet the requirements of a barcode label to a great extent, since they have a simple code and can be distinguished bycharacteristics such as self-assembly and hybridization specificity. For a simple introduction of these DNA barcode labels into DNA, an enzyme-mediated approach utilizing ODN-modified nucleotides would be desirable.[7] However, the acceptance of these modified nucleotides by DNA polymerases should be hampered by the steric demand of the ODN-modified nucleotides. Herein, we show that despitethe steric demand the enzymatic synthesis of barcoded DNA is feasible by using ODN-modified nucleoside triphosphatesthat are about 40-times larger than the natural nucleotides and longer than the diameter of a DNA polymerase (Figure 1A).