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Composition and method for optimized hybridization using modified solutionsRelated Patent Categories: Chemistry: Molecular Biology And Microbiology, Measuring Or Testing Process Involving Enzymes Or Micro-organisms; Composition Or Test Strip Therefore; Processes Of Forming Such Composition Or Test Strip, Involving Nucleic AcidComposition and method for optimized hybridization using modified solutions description/claimsThe Patent Description & Claims data below is from USPTO Patent Application 20060228746, Composition and method for optimized hybridization using modified solutions. Brief Patent Description - Full Patent Description - Patent Application Claims
FIELD OF THE INVENTION [0001] The present invention relates to the field of nucleic acids and more particularly to a modified solution containing a denaturant for application with biopolymers and micro arrays. BACKGROUND OF THE INVENTION [0002] Various arrays of polynucleotides (such as RNA and DNA) are known and used in genetic testing, screening and diagnostics. Arrays are defined by the regions of different biopolymers or nucleotides arranged in a predetermined configuration on a substrate. Most importantly, the arrays when exposed to a population of analytes will exhibit a pattern indicative of the presence of the various components separated spatially. Array binding patterns of polynucleotides and/or peptides can be detected by using a variety of suitable target labels. Once bound to the array, these target labels can then be quantified and observed and the overall pattern on the array determined. [0003] DNA micro arrays are particularly useful for analyzing large sets of genes through "gene expression profiling". However, for the micro arrays to be effective in binding target sequences, they must be capable of annealing. In addition, the detection of optimal "sensitivity" and "specificity" of hybridization for biopolymers (probes) to complimentary sequences in complex cRNA is complicated by the fact that the characteristic melting temperature (Tm) for this interaction rises with increasing probe length. However, increasing the stringency of hybridization comes with the cost of losing sensitivity. Moreover, the higher temperatures needed to reach the Tm (>60.degree. C.) are detrimental to the array surface. Previous researchers have determined that including 30% formamide in the hybridization solution can significantly reduce the Tm and allow for hybridization to take place at a lower temperature while maintaining an acceptable balance between specificity and sensitivity. Formamide is often used in Southern and Northern blotting as a hybridization modifier, because it is effective and because it is easily washed out of the nitrocellulose or modified nylon materials used to perform porous filter-based hybridization assays. However, formamide is a highly toxic and hazardous to ship (the US Department of Transportation requires double-containment of formamide-containing solutions). For these reasons it would be desirable to create an effective solution system that maintains specificity, sensitivity and allows for hybridizations at lower temperature, yet is not toxic, does not effect the central nervous system of the operator, is not a fetal poison or does not require special handling or transportation costs. These and other problems with the prior art systems and solutions are obviated by the present invention. The references cited in this application infra and supra, are hereby incorporated by reference. However, cited references or art are not admitted to be prior art to this application. SUMMARY OF THE INVENTION [0004] The invention provides a composition, kit and method for use with micro arrays. The composition, kit and method allow a probe and target to hybridize at a temperature lower than their standard hybridization temperature. The composition has a chemical component of the formula: R(NH.sub.2)C.dbd.O where R is an amino or alkyl group. The kit of the present invention comprises a micro array, a composition for use with the micro array and a target for detection. The kit may further comprise an optional set of instructions. The composition in the kit contains the chemical component. The chemical component may or may not be in solution. The method provides the steps of adding to a probe and target the chemical component, heating the probe and target in the presence of the added component and then allowing the biopolymers to hybridize. BRIEF DESCRIPTION OF THE DRAWINGS [0005] Embodiments of the invention will now be described with reference to the drawings in which: [0006] FIG. 1 illustrates a single nucleotide polymorphic array. [0007] FIG. 2 is an enlarged view of a portion of FIG. 1 showing multiple spots or regions of an array. [0008] FIG. 3 shows a duplex hybridization curve without the addition of the denaturant. Percentage of single stranded DNA is plotted against temperature. [0009] FIG. 4 shows a plot of percentage of single stranded DNA against temperature. The plot shows a series of melting curves (25, 60 and 60 mer with denaturant added). [0010] FIG. 5 shows a contour plot of the observed optimal conditions using urea concentrations with varying probe lengths (L=60, T=50.degree. C.). Probe length has been plotted against urea concentration. [0011] FIG. 6 shows a plot of optimal urea concentrations of 50.degree. C. probe length series. The plot shows average GCN4 specificity plotted against urea concentration. [0012] FIG. 7 shows the extrapolated optimal urea concentration for a probe length of 60-mer at a temperature of 50.degree. C. Optimum urea concentration at 50.degree. C. is plotted against probe length. [0013] FIG. 8 shows a contour plot of the extrapolation to predicted optimum for the probe having a length of 60 and 50.degree. C. Probe length has been plotted against urea concentration. [0014] FIG. 9 shows the results of various arrays with the addition of the denaturant. DETAILED DESCRIPTION OF THE INVENTION [0015] Before describing the present invention in detail, it is to be understood that this invention is not limited to specific compositions, process steps, or equipment, as such may vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to be limiting. [0016] It must be noted that, as used in this specification and the appended claims, the singular forms "a", "an" and "the" include plural referents unless the context clearly dictates otherwise. Thus, for example, reference to "an array" includes more than one array, reference to "a polynucleotide primer" includes a plurality of polynucleotide primers and the like. [0017] In describing and claiming the present invention, the following terminology will be used in accordance with the definitions set out below. [0018] A "biopolymer" is a polymer of one or more types of repeating units. This includes traditional polynucleotides, the case in which the conventional backbone has been replaced with a non-naturally occurring or synthetic backbone, and nucleic acids in which one or more of the conventional bases have been replaced with a synthetic base capable of participating in Watson-Crick type hydrogen bonding interactions. Polynucleotides include single or multiple stranded configurations, where one or more of the strands may or may not be completely aligned with another. While probes and targets of the present invention will typically be single-stranded, this is not essential. Specifically, a "biopolymer" includes DNA (including cDNA), RNA and polynucleotides, regardless of the source. [0019] An "alkyl" group includes aliphatic and aromatic hydrocarbon molecules as well as substituted hydrocarbons and their derivatives. Continue reading about Composition and method for optimized hybridization using modified solutions... 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