Arrays with modified oligonucleotide and polynucleotide compositions

Abstract

The present invention provides arrays having associated modified oligonucleotides that selectively bind to DNA or RNA, methods of making such arrays, assays for using such arrays, and the like. In one embodiment, the arrays of the invention exhibit an increased binding affinity with complementary nucleic acids, and in particular with complementary RNA. In another embodiment, the associated nucleic acids of the array of the invention exhibit substantial acid resistance, allowing the arrays to be treated with low pH solutions. In another embodiment, the modified associated nucleic acids of the array of the invention exhibit substantial resistance to nuclease degradation.

Description

[0001] This application is a continuation-in-part of our earlier filed application Ser. No. 09 / 408,088, filed Sep. 29, 1999, which is a continuation-in-part of application Ser. No. 09 / 223,498, filed Dec. 30, 1998, to each of which we claim priority under 35 U.S.C. .sctn. 120 and which are each incorporated herein by reference in their entirety.[0002] The field of this invention is arrays having associated modified oligonucleotides and / or polynucleotides, methods of producing such arrays, and uses thereof.[0003] Arrays of binding agents, such as oligonucleotides and polynucleotides, have become an increasingly important tool in the biotechnology industry and related fields. These arrays, in which a plurality of binding agents are deposited onto a solid support surface in the form of an array or pattern, find use in a variety of applications, including drug screening, nucleic acid sequencing, mutation analysis, and the like. One important use of arrays is in the analysis of differenti...

AI Technical Summary

Benefits of technology

[0043] Acid stable associated modified oligonucleotides and / or polynucleotides of the invention are preferably stable when exposed to a pH of 1-2, while their binding partners are not. This allows an array having associated acid stable oligonucleotides and / or polynucleotides to be exposed to a first sample, treated with an acidic solution applied in any of several possible protocols to free the array from the first binding partner, and reused with a second sample. Direct comparison of two different samples of binding partners using a single array has the advantage of limiting potential experimental variation present when comparing multiple arrays. Performing the experiment with the same sample on the same array allows a confirmation of the results obtained in the first instance, thus effectively confirming results without having variation in the array composition.

[0121] A number of different methods can be used to isolate the beads following exposure to the sample. Relatively large field strengths may be generated by a small diameter wire that creates a high field gradient when placed in an external magnetic field. The small diameter wire acts as an antenna to concentrate the magnetic fields near it. A number of existing immunomagnetic separation and detection methods and apparatus rely on this observation. One method has been to place steel wool inside a collecting vessel and then place the vessel inside a strong magnetic field. Another method has been to place paperclip-shaped bent metal pins inside microtiter wells and then move the holder for the microtiter wells inside a strong magnetic field. In the presence of the enhanced magnetic gradients, magnetic beads can be captured-from any fluid samples inside the vessel or microtiter wells onto the steel wool or the bent metal pins. After the magnetic fields are removed, the captured magnetic beads can be removed from the steel wool or bent pins by various techniques. A third method described in the prior art for concentrating magnetic fields is a quadrupole magnetic arrangement which concentrates a magnetic field near the intersection of two north and two south poles of four bar magnets brought in close proximity. These and other methods, as will be apparent to one skilled in the art, can be used to separate the beads following exposure to a sample. Alternatively non-magnetic beads with density >water, i.e. <1.0 can be used. These can be isolated easily by centrifuging briefly in a benchtop centrifuge. The beads will be pelleted. They can be easily washed and then centrifuged again. This step can be repeated as many times as needed.

Problems solved by technology

Despite the wide variety of array technologies currently in preparation or available on the market, there is currently no technique for distinguishing the type of binding partner that recognizes a probe sequence on an array (i.e. the ability to distinguish the difference between a target RNA and target DNA sequence).

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