An instrument is provided that can monitor nucleic acid sequence amplification reactions, for example, PCR amplification of DNA and DNA fragments. The instrument includes a multi-notch filter disposed along one or both of an excitation beam path and an emission beam path. Methods are also provided for monitoring nucleic acid sequence amplifications using an instrument that includes a multi-notch filter disposed along a beam path.

To minimize cross talk in systems and methods for detecting two or more different optical signals emitted from each of a plurality of reaction receptacles, an excitation signal associated with each of the optical signals has a known excitation frequency, and any detected signal having a frequency that is inconsistent with the excitation frequency is discarded. The receptacles are moved relative to optical sensors configured to detect each unique optical signal from an associated receptacle, and to further minimize cross talk, the optical sensors are arranged so that only one reaction receptacle at a time is in a signal detecting position with respect to one of its associated optical sensors, and the optical sensors are grouped by the optical signal they are configured to detect so that a first optical signal is detected from each of the reaction receptacles before a second optical signal is detected from the reaction receptacles.

A thermal cycling device for thermally cycling samples of biological material contained in a microcard having a top and bottom surface. The thermal cycling device can include a sample block having an upper surface configured for engaging the bottom surface of a microcard, a vacuum device, and a temperature control system operatively connected with the sample block. The upper surface of the sample block may include a plurality of channels, the channels defining spaces between the sample block and the bottom surface of a microcard that may be positioned thereon. The vacuum device may be in fluid communication with the sample block for drawing gas out of the spaces defined by the channels in the sample block. The vacuum device may be configured for substantially maintaining a vacuum between the sample block and microcard so that a retention force is imparted on the microcard to urge the microcard toward the sample block. Methods of maintaining a microcard on a sample block of a thermal cycling device are also provided.

A method of determining the presence or amount of a target nucleic acid in each of a plurality of reaction mixtures. In the method, a first plurality of reaction mixtures are provided to a heater and subjected to conditions for performing a first amplification reaction. The presence or amount of a first target nucleic acid in each of the first plurality of reaction mixtures is determined during the first amplification reaction. During the first amplification reaction, a second plurality of reaction mixtures are provided to the heater and subjected to conditions for performing a second amplification reaction. The presence or amount of a second target nucleic acid in each of the second plurality of reaction mixtures is determined during the second amplification reaction. At least a portion of the second plurality of reaction mixtures are removed from the heater during the second amplification reaction.

A continuous process for performing multiple nucleic acid amplification assays, where at least a portion of a second subset of reaction mixtures are transferred to a heater while a first subset of reaction mixtures are being subjected to conditions for performing a nucleic acid amplification assay. During the process, a plurality of reaction mixtures from the first and second subsets of reaction mixtures are simultaneously subjected to conditions sufficient to perform multiple nucleic acid amplification assays in the reaction mixtures. The presence or absence of a target nucleic acid in the first subset of reaction mixtures is determined while the reaction mixtures are in the heater.

A continuous process for performing multiple nucleic acid amplification assays, where at least a portion of a second subset of reaction mixtures are transferred to a heater while a first subset of reaction mixtures are being subjected to conditions for performing a nucleic acid amplification assay. During the process, a plurality of reaction mixtures from the first and second subsets of reaction mixtures are simultaneously subjected to conditions sufficient to perform multiple nucleic acid amplification assays in the reaction mixtures. The presence or absence of a target nucleic acid in the first subset of reaction mixtures is determined while the reaction mixtures are in the heater.