Method of producing a DNA library using positional amplification based on the use of adaptors and nick translation
Patent 6828098 Issued on December 7, 2004. Estimated Expiration Date: May 18, 2021. Estimated Expiration Date is calculated based on simple USPTO term provisions. It does not account for terminal disclaimers, term adjustments, failure to pay maintenance fees, or other factors which might affect the term of a patent.
The disclosed invention relates to general and specific methods to use the Primer Extension/Nick Translation (PENT) reaction to create an amplifiable DNA strand, called a PENTAmer. A PENTAmers can be made for the purpose of amplifying a controlled length of DNA located at a controlled position within a DNA molecule, a process referred to as Positional Amplification by Nick Translation (PANT). In contrast to PCR, which amplifies DNA between two specific sequences, PANT can amplify DNA between two specific positions. PENTAmers can be created to amplify very large regions of DNA (up to 500,000 bp) as random mixtures (unordered positional libraries), or as molecules sorted according to position (ordered positional libraries). PANT is fast and economical, because PENTAmer preparation can be multiplexed. A single PENTAmer preparation can include very complex mixtures of DNA such as hundreds of large-insert clones, complete genomes, or cDNA libraries. Subsequent PCR amplification of the preparation using a single specific primer can positionally amplify contiguous regions along a specific clone, along a specific genomic region, or along a specific expressed sequence.
Other References
Guilfoyle, Richard A., et al., Ligation-mediated PCR amplification of specific fragments from a Class-II restriction endonuclease total digest, Nucleic Acids Research vol. 25, No. 9 (1997), pp. 1854-1858.
Hagiwara, Koichi and Harris, Curtis C., ‘Long distance sequencer’ method: a novel strategy for large DNA sequencing projects, Nucleic Acids Research, vol. 24, No. 12 (1996), pp. 2460-2461.
Makorov, Vladimir L., et al., Long G. Tails at Both Ends of Human Chromosomes Suggest a C Strand Degradation Mechanism for Telomere Shortening, Cell, vol. 88 (1997), pp. 657-666.
Rosenthal, Andre, et al., Genomic walking and sequencing by oligo-cassette mediated polymerase chain reaction, Nucleic Acids Research, vol. 18, No. 10 (1990), pp. 3095-3096.
Smith, Douglas R., Ligation-mediated PCR of Restriction Fragments from Large DNA Molecules, PCR Methods and Applications, vol. 2 (1992), pp. 21-27.
Unrau, Paul and Deugau, Kenneth V., Non-cloning amplification of specific DNA fragments from whole genomic DNA digests using DNA ‘indexers’, Gene, 145 (1994), pp. 163-169.
Walker, G. Terrance, et al., Isothermal in vitro amplification of DNA by a restriction enzyme/DNA polymerase system, Proc. Natl. Acad. Sci. USA vol. 89 (1992), pp. 392-396, Applied Biological Sciences.
Walker G. Terrance, et al., Strand displacement amplification—an isothermal, in vitro DNA amplification technique, Nucleic Acids Research, vol. 20, No. 7 (1992), pp. 1691-1696.
Currently Pending Claims in U.S. patent application No. 09/801,346, Filed Mar. 6, 2001, Entitled “Compositions and Methods for Analysis of Nucleic Acids”.
Fu, Doug-Jing, et al., Sequencing Double-Stranded DNA by Strand Displacement, Nucleic Acids Research vol. 25, No. 3 (1997), pp. 677-679.