Abstract: The present invention provides improved compositions and methods of sequence detection and single nucleotide (“SNP”) genotyping. The methods of the present invention are related to combining sequence or allelic specific ligation on a solid phase platform with specific and efficient solid phase signal amplification. The methods for sequence detection include a first, second and third oligonucleotide. The methods of SNP genotyping include four oligonucleotides for SNPs associated with two alleles and additional oligonucleotides may be added for SNPs associated with more than two alleles. The usefulness of the present method is that it results in the determination of thousands of genotypes simply, rapidly and inexpensively on a solid support from a single genomic DNA sample.

Abstract: The present invention provides methods for determining the number of tandem repeat units in a region of double stranded DNA based on the use of RecA-like recombinase protein and oligonucleotide ligation. The methods of the present invention provide RecA coated, specific DNA oligonucleotide probes (RecA filaments) for homology searching in duplex DNA where the location of homologous sequences results in the formation of D-loop structures containing a duplex region comprising the oligonucleotide probe and one strand of the target DNA.

Abstract: A method for detecting a specific sequence, a mutation and/or a polymorphisms, including a single nucleotide polymorphism (SNP), is based on the use of RecA-like recombinase protein and primer extension (PE) or oligonucleotide ligation assays (OLA). RecA coated, specific DNA oligonucleotide probes (RecA filaments) are used for homology searching in duplex DNA. Location of homologous sequences results in the formation of D-loop or double D-loop structures containing a duplex regions comprising the oligonucleotide probe and one strand of the target DNA. In the case of the PE methods, probes are selected to terminate with their 3? end adjacent to the site of mutation or SNP such that a single nucleotide or terminator addition to the primer will be diagnostic of the mutation or SNP.

Abstract: The invention is directed to a method for detection of single nucleotide polymorphisms utilizing a solid phase RFLP-based method of detection. The invention further relates to a method of detecting a single nucleotide polymorphism (SNP) comprising providing a sample test DNA molecule containing an SNP site of interest; detectably labeling the DNA molecule at or near each of its ends with different labels and containing the SNP site of interest; providing at least two different immobilization oligonucleotides capable of immobilization to a solid support; digesting the test DNA molecule with a restriction endonuclease, whose cut site contains the SNP site in at least one allele of the SNP site; separating strands of the test DNA molecule; annealing the strands to the immobilization oligonucleotides; and detecting the labels of DNA strands annealed to the immobilization oligonucleotide.

Abstract: A method for detecting a specific sequence, a mutation and/or a polymorphisms, including a SNP, is based on the use RecA or a RecA-like recombinase protein and the process of allele specific oligonucleotide extension. RecA coated, specific DNA oligonucleotide probes (RecA filaments) are used for homology searching in duplex DNA. Location of homologous sequences results in the formation of D-loop or double D-loop structures containing a duplex regions comprising the oligonucleotide probe and one strand of the target DNA. Probes are selected to terminate with their 3′ end at the site of the mutation or the SNP, such that extension depends on correct nucleotide pairing, which occurs only when the probe is annealed to a target DNA which comprises the allele complementary to the 3′ end of the probe. Successful extension is diagnostic of the specific sequence, mutation or SNP. Also provided are compositions and kits useful for practicing the above methods.

Abstract: A method for detecting mutations, such as a single base change or an addition or deletion of about one to four base pairs, is based on the use of an immobilized DNA mismatch-binding protein, such as MutS, which binds to a nucleic acid hybrid having a single base mismatch or unpaired base or bases, thereby allowing the detection of mutations involving as little as one base change in a nucleotide sequence. Such a method is useful for diagnosing a variety of important disease states or susceptibilities, detecting the presence of a mutated oncogene and for isolating or removing by affinity chromatography duplex DNA molecules containing mismatches such as error-containing molecules in PCR-amplified DNA samples. Also provided are kits useful for practicing the methods of the present invention.