This invention relates to methods and compositions for assessing an amount of total cell-free DNA, such as from a transplant subject. The methods and composition provided herein can be used to determine risk of complications following transplantation, including infection, cardiac arrest, and death, in a subject.

The carborhodamine dyes disclosed herein are novel reagents suitable for automated incorporation of carborhodamine dyes into oligonucleotides that can be used in detection methods for nucleic acid targets. This disclosure provides an efficient and simple process for the preparation of carborhodamine compounds and introduces previously unknown reagents for the automated synthesis of oligonucleotide-carborhodamine conjugates.

A lysis buffer comprising one non-ionic surfactant is provided which can be used as a one-step reagent of the preparation, storage, amplification, and/or detection of nucleic acids. Various embodiments of the lysis buffer of the invention comprise other substances that are compatible or useful in lysing cells, storing nucleic acids, amplifying nucleic acids, purifying nucleic acids, detecting nucleic acids, and/or other procedures for analysis of nucleic acids. Methods and kits based on the lysis buffer are also provided, including those for rapid lysis of cells and direct use of the resulting cell lysates in RT-PCR.

A lysis buffer comprising one non-ionic surfactant is provided which can be used as a one-step reagent of the preparation, storage, amplification, and/or detection of nucleic acids. Various embodiments of the lysis buffer of the invention comprise other substances that are compatible or useful in lysing cells, storing nucleic acids, amplifying nucleic acids, purifying nucleic acids, detecting nucleic acids, and/or other procedures for analysis of nucleic acids. Methods and kits based on the lysis buffer are also provided, including those for rapid lysis of cells and direct use of the resulting cell lysates in RT-PCR.

A method of identifying a first target nucleic acid comprising, providing a sample comprising the first target nucleic acid, providing a first set of paired oligonucleotides with complementarity to the first target nucleic acid, the first set of paired oligonucleotides comprising a first ratio of (a) first competitive oligonucleotides to (b) first signal oligonucleotides comprising a signal tag, wherein the competitive oligonucleotides compete with the signal oligonucleotides for binding to the first target nucleic acid, amplifying the first target nucleic acid with the polymerase chain reaction, thereby degrading the first signal oligonucleotide and permitting generation of a first signal, generating the first signal, measuring intensity of the first signal, and correlating the intensity of the first signal to the first ratio, thereby identifying the first target nucleic acid.

A method of identifying a first target nucleic acid comprising, providing a sample comprising the first target nucleic acid, providing a first set of paired oligonucleotides with complementarity to the first target nucleic acid, the first set of paired oligonucleotides comprising a first ratio of (a) first competitive oligonucleotides to (b) first signal oligonucleotides comprising a signal tag, wherein the competitive oligonucleotides compete with the signal oligonucleotides for binding to the first target nucleic acid, amplifying the first target nucleic acid with the polymerase chain reaction, thereby degrading the first signal oligonucleotide and permitting generation of a first signal, generating the first signal, measuring intensity of the first signal, and correlating the intensity of the first signal to the first ratio, thereby identifying the first target nucleic acid.

The present invention relates to the detection of a target nucleic acid sequence from a DNA or a mixture of nucleic acids by a PCE-hCTO (PTO Cleavage and Extension using hCTO) assay on a solid phase. According to the present invention, the extended duplex is formed in a liquid phase in a target-dependent manner and then its presence is detected on a solid phase. Since hCTO is not immobilized onto a solid phase, the extended duplex is more effectively formed in a liquid phase.

The present invention relates to the detection of a target nucleic acid sequence from a DNA or a mixture of nucleic acids by a PCE-hCTO (PTO Cleavage and Extension using hCTO) assay on a solid phase. According to the present invention, the extended duplex is formed in a liquid phase in a target-dependent manner and then its presence is detected on a solid phase. Since hCTO is not immobilized onto a solid phase, the extended duplex is more effectively formed in a liquid phase.

Disclosed are novel genetic arrays for use in the molecular detection of multiple Salmonella serovars, common food-borne and water-borne pathogens. The arrays may be used to simultaneously detect multiple food safety Salmonella serovars. The multiplex-detection methods have improved sensitivity and specificity for the detection of multiple high-impact food-borne pathogens simultaneously. Real-time PCR assaying techniques using such serovars include microarrays.

The present invention relates to the detection of a target nucleic acid sequence by a PTOCE (PTO Cleavage and Extension) assay. The present invention detects a target nucleic acid sequence in which the PTO (Probing and Tagging Oligonucleotide) hybridized with the target nucleic acid sequence is cleaved to release a fragment and the fragment is hybridized with the CTO (Capturing and Templating Oligonucleotide) to form an extended duplex, followed by detecting the presence of the extended duplex. The extended duplex provides signals (generation, increase, extinguishment or decrease of signals) from labels indicating the presence of the extended duplex and has adjustable T.sub.m value, which are well adoptable for detection of the presence of the target nucleic acid sequence.