Abstract: The invention includes a method of determining the level of Type I collagen fragments in a biological fluid using an antibody which is immunospecific for an epitope contained in one of the following sequences:(1) Ala-Hyp-Gly-Asp-Arg-Gly-Glu-Hyp-Gly-Pro-Hyp-Gly-Pro-Ala, or(2) Gly-Asn-Ser-Gly-Glu-Hyp-Gly-Ala-Hyp.under conditions effective to allow determination of the level of collagen fragments in the sample which contain the epitope. The method is useful for assessing the level of bone collagen degradation, particularly in humans. Also disclosed are antibodies and kits which can be used in the method.

Abstract: An improved fluorescence monitoring apparatus for measuring fluorescent emission from a sample in response to sample irradiation by an emission beam is disclosed. The apparatus employs a sample tube having surface roughness characteristics which substantially reduce background fluorescence emission due to contamination of the tube holder in the apparatus. Also disclosed is a method of reducing such background, by texturing of a sample tube to produce desired roughness characteristics.

Abstract: Substantially-isolated polynucleotides encoding human RAD50 polypeptides, human RAD50 genomic sequences, and methods of use thereof.

Abstract: The invention provides a method for diagnosis of genetic abnormalities or other genetic conditions which can be readily automated. The method is used to determine the presence or absence of a target sequence in a sample of denatured nucleic acid and entails hybridizing the sample with a probe complementary to a diagnostic portion of the target sequence (the diagnostic probe), and with a probe complementary to a nucleotide sequence contiguous with the diagnostic portion (the contiguous probe), under conditions wherein the diagnostic probe remains bound substantially only to the sample nucleic acid containing the target sequence. The diagnostic probe and contiguous probe are then covalently attached to yield a target probe which is complementary to the target sequence, and the probes which are not attached are removed.

Abstract: The invention is directed to a method for sequencing multiple target polynucleotide segments in parallel, and to compositions and kits therefor. In the method, a plurality of sample polynucleotide fragments are used to form a mixture of different-length sequencing fragments. The sequencing fragments are complementary to at least two different sample fragments, wherein (1) each sequencing fragment terminates at a predefined end with a known base or bases, and (2) each sequencing fragment contains an identifier tag sequence that identifies the sample fragment to which the sequencing fragment corresponds. The sequencing fragments are then separated on the basis of size to produce a plurality of resolved, size-separated bands. Resolved bands are collected in separate aliquots, which, in a preferred embodiment, are then subjected to an amplification step to amplify the complements of the tag sequences in each aliquot, and preferably, the tag sequences too. Amplification is preferably by PCR.

Abstract: A method and system for polynucleotide synthesis are provided which employ solid phase synthesis on a nonswellable porous polystyrene support by phosphoramidite or hydrogen phosphonate chemistries. The polystyrene support gives rise to fewer tritylated failure sequences caused by chain growth from extraneous support sites, and allows lower amounts of monomer reactants to be used to achieve equal or better coupling efficiencies as those achieveable with CPG. The method and system also employ nucleoside intermediates whose exocyclic amines are protected by base-labile groups which permit simultaneous cleavage and deprotection of the completed polynucleotide chain in the presence of the solid phase support. This latter feature allows practical automation of both the synthesis and purification of polynucleotides.

Abstract: Disclosed is a method for measuring or detecting inorganic phosphate ion in a sample. In the method, a sample is reacted with a phosphate-binding protein containing (i) an inorganic phosphate ion binding site and (ii) a detectable label that produces a signal whose amplitude changes detectably upon the binding of inorganic phosphate ion to the binding site, under conditions effective to allow binding of phosphate in the sample to the binding site. From a change in signal, the level of inorganic phosphate ion is measured or detected. Also disclosed are phosphate binding proteins for use in the method.

Abstract: The invention provides a method of synthesizing oligonucleotide N3'.fwdarw.P5' phosphoramidates using an amine-exchange reaction of phosphoramidites in which a deprotected 3'-amino group of a solid phase supported oligonucleotide chain is exhanged for the amino portion of a 5'-phosphoramidite of an incoming monomer which has a protected 3'-amino group. The resulting internucleotide phosphoramidite linkage is then oxidized to form a stable protected phosphoramidate linkage. The method of the invention greatly improves product yields and reduces reagent usage over currently available methods for synthesizing the above class of compound.

Abstract: A method of screening for the presence of a periodontal disease condition is disclosed. The method involves obtaining an oral fluid sample from a human subject being tested, and determining the level of native free pyridinium crosslinks (free pyridinoline and/or free deoxypyridinoline) from the subject. An above-normal level of crosslinks, when compared with a predetermined level characteristic of normal subjects, is an indication of the presence of a periodontal disease condition.

Abstract: Method and compositions are provided for analyzing nucleic acid sequences based on repeated cycles of duplex extension along a single stranded template. Preferably, such extension starts from a duplex formed between an initializing oligonucleotide and the template. The initializing oligonucleotide is extended in an initial extension cycle by ligating an oligonucleotide probe to its end to form an extended duplex. The extended duplex is then repeatedly extended by subsequent cycles of ligation. During each cycle, the identity of one or more nucleotides in the template is determined by a label on, or associated with, a successfully ligated oligonucleotide probe. Preferably, the oligonucleotide probe has a blocking moiety, e.g. a chain-terminating nucleotide, in a terminal position so that only a single extension of the extended duplex takes place in a single cycle. The duplex is further extended in subsequent cycles by removing the blocking moiety and regenerating an extendable terminus.

Abstract: A method of screening for the presence of a bone resorption abnormality is disclosed. The method includes obtaining a sweat sample from the subject, and determining the level of native free pyridinoline (Pyd) and/or deoxypyridinoline (Dpd) in the sample. The determined level is compared with a predetermined level characteristic of normal subjects, and an above-normal level is an indication that the subject has a bone resorption abnormality.