Abstract: Provided herein are synthetic size standards that allow one to detect size bias in a sample that includes a plurality of polynucleotides. The size standards can provide an internal control to detect and correct for size bias in data obtained after manipulating and/or processing of sample polynucleotide. Also provided herein are methods for detecting size bias in a sample or in a sequencing run.

Abstract: Abstract: Provided herein are synthetic size standards that allow one to detect size bias in a sample that includes a plurality of polynucleotides. The size standards can provide an internal control to detect and correct for size bias in data obtained after manipulating and/or processing of sample polynucleotide. Also provided herein are methods for detecting size bias in a sample or in a sequencing run.

Abstract: Methods for amplifying nucleic acids (e.g., symmetric and asymmetric PCR methods) using a combination of linear and hairpin primers to enhance specificity are provided. The hairpin primer can be a fluorogenic hairpin primer, which facilitates detection of a nucleic acid target. Attendant compositions, systems, devices and kits are also provided.

Abstract: This invention provides methods for performing combined asymmetric amplification (e.g., asymmetric PCR amplification) and detection of nucleic acid targets using molecular beacons to detect the products. Methods using a polymerase having reduced or eliminated 5′ to 3′ nuclease activity are provided, as are methods using nuclease-resistant molecular beacons. Asymmetric amplifications using nuclease-free polymerase or nuclease-resistant molecular beacons provide dramatic improvements in signal intensity detected as a result of molecular beacon binding to a target nucleic acid, e.g., during asymmetric PCR. Attendant compositions, systems, devices and kits are also features of the invention.

Abstract: Ligation-based assembly of oligonucleotides to produce molecular beacons is provided. Formation of molecular beacons is monitored to improve reaction yield and efficiency and to permit optimization of structurally similar molecular beacons. Ligation mixtures and libraries of molecular beacon components are also provided. Methods of detecting juxtaposed nucleic acids using modular molecular beacons such as intron-exon junctions are provided.

Abstract: This invention provides methods for the assembly and cloning of target DNAs. Methods for cloning long chemically synthesized oligonucleotides without prior purification are provided. Compromised vectors are used to allow screening or selection for the desired target DNAs. Methods for assembling full-length target DNAs from smaller subsequences are provided, as are methods for purifying oligonucleotides.

Abstract: Ligation-based assembly of oligonucleotides to produce molecular beacons is provided. Formation of molecular beacons is monitored to improve reaction yield and efficiency and to permit optimization of structurally similar molecular beacons. Ligation mixtures and libraries of molecular beacon components are also provided. Methods of detecting juxtaposed nucleic acids using modular molecular beacons such as intron-exon junctions are provided.