Chapter 7: Amplification by Polymerase Chain Reaction

The RNA template is then degraded by an ______ activity of reverse transcriptase during the reverse transcription reaction.

________ is the most commonly used enzyme for routine PCR applications.

________ are the oligonucleotides that are complementary to the sequences that flank the target region of the template.

The ________ serves as the template for DNA replication.

________ can hybridize to any mRNA sequence in a sample to convert all mRNAs to cDNA.

Extraction ________, which contain all extraction reagents but no sample, monitor contamination from extraction to PCR.

________ is carried out by a reverse transcriptase that forms the basis of reverse transcriptase PCR.

________ forms the basis of many forensic DNA assays such as DNA quantitation, STR profiling and mtDNA sequencing.

also known as translation, is directed by an RNA template.

The temperature at which 50% of DNA strands are denatured

The single strands in a solution of denatured DNA can reanneal into double-stranded DNA

The catalytic function of cDNA synthesis requires a primer that ______ to a complementary mRNA template.

This process allows the monitoring of amplicon production at each cycle of the PCR process

A modified enzyme, remains in an inactive form until activated with a pH below 7 prior to the PCR cycling in which the inhibitory motif is inactivated

and double-stranded DNA can be used as a template for PCR

The substrates for DNA synthesis

denaturation, annealing, and extension

Instrument that carries out PCR amplification

The two alleles in a heterozygous individual are unequally detected at a low level of starting DNA template

The pathway for the flow of genetic information

The flow of genetic information from RNA to DNA

A domain of the viral reverse transcriptase enzyme

Double-stranded DNA is maintained by _______ between the bases of complementary pairs.

Occurs when the hydrogen bonds of DNA are disrupted, and the strands are separated.

Can be obtained from measuring DNA denaturation by slowly heat- ing a solution of DNA.

The polymerase chain reaction (PCR) allows the exponential amplification of specific sequences of DNA to yield sufficient amplified products, also known as _______, for various downstream applications.

An _____ is obtained and divided into an exponential phase, a linear phase, and a plateau.

A modified enzyme, remains in an inactive form until activated with a pH below 7 prior to the PCR cycling in which the inhibitory motif is inactivated.

A primer must be specific to the ______ ; otherwise, nonspecific products that might interfere with the proper interpretation of a DNA profile might be produced.

A primer should not contain _______ that may form hairpin structures interfering with the annealing of primers and the template.

These annealed primers may then be amplified during PCR, creating products known as _____, which compete with the target DNA template for PCR components.

is the simultaneous amplification of more than one region of a DNA template in a single reaction to achieve high-throughput analysis.

are required for the enzymatic activity of DNA polymerases.

are usually recommended, and a buffer is often utilized to maintain pH between 8.3 and 8.8 at room temperature.

A ______ shows that PCR components such as reagents and PCR cycle parameters are working properly during a PCR.

At the beginning of each cycle, the two complementary DNA template strands are separated at high temperatures (94°C–95°C) in a process called _______.

The temperature is then decreased to allow _____ between the oligonuclers and the template. The temperature for annealing is usually 3°C–5°C.

causes DNA to break into smaller fragments.

If the damage occurs at a region to be ______, the result can be a failure in PCR amplification.

The two alleles in a heterozygous individual are unequally detected at a low level of starting DNA template.

The presence of PCR inhibitors can be detected using an _______.

If PCR inhibitors are not eliminated during the extraction process, additional procedures such as the use of _______ devices can be used.

With _______ or transcription, the process is carried out using the DNA as a template.

RNA chains can be used as templates for the synthesis of a DNA strand of complementary sequence, in which the end product is referred to as ______

The most common reverse transcriptases used for cDNA synthesis are encoded by the _______ from the avian myeloblastosis virus (AMV) and the Moloney strain of the murine leukemia virus (MMLV).

are an essential component for a reverse transcriptase reaction.

can hybridize to the 3′ termini poly (A) tails of eukaryotic mRNAs.

are nonspecific primers that can hybridize, at mul- tiple sites, to any RNA sequence including non-mRNA templates such as ribosomal RNA.

combines the reverse transcription reaction and PCR in a single tube.

During a ______, the reverse transcription reaction and PCR are carried out in separate tubes.

The ______ measures the amount of amplified product synthesized during PCR at the end of the PCR amplification.

With the ______, the amplified product is quantified during the exponential phase of PCR.

The ______ strategy is typically used to increase sensitivity, specificity, and yield.