Oligonucleotide sizing using cleavable primers

Abstract

The present invention provides modified oligonucleotide primers designed to incorporate a cleavable moiety so that a 3′ portion of the primer (linked to an extension product) can be released from an upstream 5′ portion of the primer. Upon selective cleavage of the cleavable site, primer extension products that contain about five or fewer base pairs of the primer sequence are released, to provide more useful sizing and sequence information per fragment than extension products containing the entire primer.

Description

[0001] The present application is a divisional of U.S. application Ser. No. 09 / 139,386 filed Aug. 25, 1998, allowed, which is a continuation-in-part of U.S. patent application Ser. No. 08 / 639,363 filed Apr. 26, 1996, which has since issued as U.S. Pat. No. 5,830,655, which is a continuation-in-part of U.S. patent application Ser. No. 08 / 445,751 filed May 22, 1995 which has since issued as U.S. Pat. No. 5,700,642. The entire text of each of the above-referenced disclosures is specifically incorporated by reference herein without disclaimer.1.0 BACKGROUND OF THE INVENTION [0002] 1.1 Filed of the Invention [0003] The present invention relates to oligonucleotide compositions containing cleavable primers and diagnostic and analytical methods employing such primers. [0004] 1.2 Description of Related Art [0005] DNA, the primary genetic material, is a complex molecule consisting of two intertwined polynucleotide chains, each nucleotide containing a deoxyribose unit, a phosphate group and a ...

AI Technical Summary

Benefits of technology

[0119] Read length is typically method dependent (i.e., a function of the detection method being employed). In some analytical methods size resolution may have an essentially finite upper limit, (e.g., up to 100 nucleotides. One advantage of the present invention is the ability to improve the amount of new or useful information about a target DNA sequence that can be obtained from a primer extension product, when the products are analyzed using such a method.

[0120] For example, using the modified primers of the present invention, the read length of an exemplary extension segment would be determined as follows. A modified primer composed of nucleotides complementary to a DNA target and having a cleavable linkage between nucleotides 17 and 18 (e.g., with a polymerase or ligase), and the resulting primer extension product (subsequent to immobilization) is cleaved at the cleavable site to produce an extension segment containing only one nucleotide derived from the primer. In carrying out sizing of the extension products, the read length is equal to the total number of nucleotides detected (X) minus the one nucleotide derived from the second region of the primer, or X−1.

[0121] In contrast, prior to cleavage at the cleavable site, the product composed of the primer and the same set of extension segments would have a read length of X−18, where 18 equals the number of bases in the primer. Thus the amount of new or useful sequencing or size information for primer extension products obtained using the modified primers of the present invention is improved. 4.2 Oligonucleotide Compositions: Synthesis of Modified Primers 4.2.1 Feature of the Modified Primer

[0122] The oligonucleotide primers of the present invention (i) are designed for optional attachment to a solid support in a manner that does not block the ability to extend the primer from its 3′ end, and (ii) incorporate a cleavable moiety so that a 3′ portion of the primer linked to an extension segment can be released from an upstream portion of the primer, 5′ to the cleavable site. The upstream portion of the timer, referred to herein as the first primer region, typically contains a sigNificant number of the total number of nucleotides present in the primer, so that upon cleavage at the cleavable site, the amount of new fragment information for primer extension products is maximized.

[0123] The modified primers of the invention preferable contain an immobilization attachment site for attaching the primer to a solid support. For modified primers containing an internal immobilization attachment site (i.e., a site contained with the primer itself), the immobilization attachment site or IAS is generally separated from the cleavable site by at least three nucleotides. Upon selective cleavage of the cleavable site, a large portion of the primer fragment remains affixed to the solid support. This enables the release of primer extension products that contain about five or fewer base pairs of the primer sequence, to extend the useful size analysis range (e.g., increased read lengths), as illustrated in FIG. 15A and FIG. 15B.

[0124]FIG. 15A and FIG. 15B are mass spectra of products from primer extension reactions, illustrating the difference in fragment information obtained for cleaved primer extension segments according to the invention (FIG. 15B) versus non-cleaved full primer-extension segments (FIG. 15A). The details of the primer extension reactions and primer cleavable are described in Example 8. For sequencing applications, the modified primers can also provide more useful sequence information per fragment than extension products containing the entire primer.

Problems solved by technology

Standard detection, sizing, DNA sequencing methods as described above, while providing useful information, are often tedious and costly.

Further, the most common method of fragment analysis—gel electrophoresis—is a relatively time-consuming process.

In contrast, electrophoretic methods require significantly longer lengths of time (minutes to hours) and can only measure the size of DNA fragments as a function of relative mobility to comigrating standards.

Gel-based separation systems also suffer from a number of artifacts that reduce the accuracy of size measurements.

Existing gel-based protocols for the analysis of DNA often do not work with TOF-MS because the PCR® product size range, typically between 100 and 800 nucleotides, is outside the current resolution capabilities of TOF-MS.

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