Applied Biosystems 7900HT User Manual

DRAFT
September 1, 2004 11:39 am, Glossary.fm
Applied Biosystems 7900HT Fast Real-Time PCR System and SDS Enterprise Database User Guide Glossary-5
minor groove
binder (MGB)
One of a class of molecules which form close atomic contacts in the deep, narrow
space formed between the two phosphate-sugar backbones in the DNA double helix.
Conjugation of a minor groove binder to oligonucleotides stabilizes nucleic acid
duplexes causing a dramatic increase in oligonucleotide T
m
. Fluorogenic probes with
the MGB attached to the 3′ end perform well in the 5′ nuclease assay. They are an
improvement over unmodified probes because shorter sequences (13- to 20-mers) can
be used to obtain probes that have an optimal T
m
. Thus, attachment of the MGB
enables the use of shorter fluorogenic probes, which results in improved mismatch
discrimination.
multicomponenting The analysis performed by the SDS software used to distinguish the contribution of
individual dyes to the raw spectral data collected by the 7900HT instrument. The
overlapping spectra from the individual dye components in a well generate the
composite spectrum that represents a raw data fluorescent reading.
multi-reporter
(multiplex) PCR
A technique that uses multiple fluorogenic dye-labeled TaqMan
®
probes to detect the
simultaneous amplification of two or more target nucleic acids within a DNA sample.
No Template
Control (NTC)
A control reaction with all PCR components included except DNA template. After a
detector is applied to a well, each detector must be assigned a task that describes its
purpose. One of the tasks is NTC and is applied to all detectors of negative control
wells containing PCR reagents but lacking samples.
normalized reporter
signal (R
n
)
See R
n
.
nucleotide One of the structural components, or building blocks, of DNA and RNA. A nucleotide
consists of a base (one of four chemicals: adenine, thymine, guanine, and cytosine)
plus a molecule of sugar and one of phosphoric acid.
outlier An unusually extreme value for a variable, given the statistical model in use. In the
SDS software, automatic outlier removal in RQ Studies is conducted to assist in the
elimination of data contamination occurring when a process or phenomenon other
than initial sample quantity affects the measured C
T
.
PCR master mix A reagent mix containing all components necessary for PCR except template DNA
and primers/probes. For example, the TaqMan
®
2✕ Universal PCR Master Mix
contains AmpliTaq Gold
®
DNA polymerase, AmpErase
®
UNG that protects against
carry-over contamination, Passive Reference I for signal normalization in all 5′
nuclease assays, dNTPs and optimized buffer components.
persist(ed) Stored in, and thus retrievable from, the database used by the SDS software.
pure dye Pure dye data is generated from the results of a pure dye run in which the SDS
software collects spectral data from a set of dye standards during a 2-min. hold at
60 °C. The software stores the spectral information for the pure dye standards within
a calibration file located in the SDS directory. This calibration file is used for
calculating multi-component data. After the run, the software extracts each
component dye spectrum from the collected data in the pure spectra run file. Because
the age and use of the instrument components can affect the pure spectra readings,
Applied Biosystems recommends updating the pure spectra data files once or twice
annually depending on instrument use.

Applied Biosystems 7900HT Specifications

General

Brand	Applied Biosystems
Model	7900HT
Category	Laboratory Equipment
Language	English