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Method and Apparatus to Increase Hybridization Rate of DNA Microarrays

IP.com Disclosure Number: IPCOM000198213D
Publication Date: 2010-Jul-30
Document File: 4 page(s) / 70K

Publishing Venue

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Method and Apparatus to Increase Hybridization Rate of

DNA

Microarrays

Described herein is a method and apparatus to increase the hybridization rate of a nucleic acid sample to a microarray, where a microarray is a two-dimensional arrangement of spatially addressable regions bearing nucleic acids, e.g.,

RNA

or

DNA

oligonucleotides. The nucleic acids are covalently or non-covalently attached to a planer substrate at any point in the nucleic acid. The method may be applied to arrays that are fabricated using either precursor units (such as nucleotide monomers) in the case of in situ fabrication (using, e.g., pulse-jet or photolithography), or using previously made nucleic acid. 

One of the causes that limit the rate of nucleic acid (

DNA

or

RNA

) hybridization or binding in microarray assays is that the targets in solution near the probes of the surface attach quickly relative to the diffusion rate of the targets in the remainder of the solution. This results in a concentration gradient of complimentary targets to the probes on the surface. The reaction rate is directly proportional to the concentration of the targets. As the targets near the probes are depleted, the reaction rate becomes limited by the diffusion rate of the targets in the remainder of the solution.

One way of increasing the hybridization rate of a microarray is to mechanical mix the solution that is on the microarray surface, during hybridization. Mechanical mixing replenishes the targets in the area near the probes on the surface with those in the remainder of the solution. In effect, mixing maintains a uniform concentration of the targets throughout the entire solution. Mechanical mixing can be of the form of: shaking the solution, moving a bubble within the solution, ultrasonic energy, moving a flexible surface to cause fluid movement, moving the fluid into and out of the hybridization chamber, and moving particles in the solution

Mixing does increase the hybridization rate compared to relying on diffusion, but since the reaction rate is proportional to the concentration of targets in solution, one is still limited by the target concentration and in many applications, the concentration of targets in solution still limits the reaction rate.

The use of an electric field to concentrates the

DNA

at specific sites to allow rapid hybridization has also been disclosed. The limitation of this method is that special arrays are required, and the fabrication process for those arrays is slow and there is a practical limitation to the total number of features on the array. The surface of this type of array is difficult to make since in order for this type of system to work, there must be a flow of current in the solution. That means that the surface of the array must have an electrical contact for each specific site. An addition problem arises since if there is a current path in solution, hydrolysis can occur at the site forming gas bubbles.

The method described below seeks to increase t...