ch. 17 (recombinant DNA tech)

Question 1

Method for using electrical current to separate DNA or RNA molecules through agarose as a matrix.

Answer 1

agarose gel electrophoresis

Question 2

Cloning vectors derived from bacterial chromosomes; designed to replicate larger fragments of cloned DNA than plasmids.

Answer 2

bacterial artificial chromosomes (BACs)

Question 3

DNA cloning technique used to distinguish host bacterial cells containing recombinant plasmids (white colonies) from host cells containing nonrecombinant plasmids (blue colonies).

Answer 3

‘blue-white’ screening

Question 4

In recombinant DNA, an agent such as a phage or plasmid into which a foreign DNA segment will be inserted and used to transform host cells.

Answer 4

cloning vector

Question 5

A collection of cloned cDNA sequences.

Answer 5

complementary DNA (cDNA) libraries

Question 6

Computer automated DNA sequencing technique that can produce large amounts (high-throughput) of DNA sequence in relatively short periods of time compared to manual sequencing.

Answer 6

computer-automated high-throughput DNA sequencing

Question 7

One of the first DNA sequencing techniques; also referred to as Sanger sequencing. Technology relies on modified nucleotides called dideoxynu cleotides (ddNTPs), which terminate a newly synthesized strand of DNA when incorporated during a sequencing reaction.

Answer 7

dideoxy chain-termination sequencing

Question 8

A nucleotide containing a deoxyribose sugar lacking a hydroxyl group. It stops further chain elongation when incorporated into a growing polynucleotide and is used in the Sanger method of DNA sequencing

Answer 8

dideoxynucleotide

Question 9

Collections of cloned DNA in host cells; cDNA or genomic libraries are common types of libraries. Can be screened to identify particular genes of interest.

Answer 9

DNA libraries

Question 10

An enzyme that forms a covalent bond between the 5` end of one polynucleotide chain and the end of another polynucleotide chain. It is also called polynucleotide-joining enzyme

Answer 10

DNA ligase

Question 11

Used for genome editing by CRISPR-Cas; an experimentally introduced DNA molecule carrying a sequence with desired edits flanked by ‘homology arms’ with sequences that match regions of the genome adjacent to the target sequence to be edited.

Answer 11

donor template

Question 12

Cells derived from the inner cell mass of early blastocyst mammalian embryos. These cells are pluripotent, meaning they can differentiate into any of the embryonic or adult cell types characteristic of the organism.

Answer 12

embryonic stem (ES) cells

Question 13

Plasmids or phages carrying promoter regions designed to cause expression of inserted DNA sequences.

Answer 13

expression vectors

Question 14

A method of in situ hybridization that utilizes probes labeled with a fluorescent tag, causing the site of hybridization to fluoresce when viewed using ultraviolet light.

Answer 14

fluorescence in situ hybridization (FISH)

Question 15

A transgenic technique used to create and introduce a specifically ­altered gene into an organism. In mice, gene targeting often involves the induction of a specific mutation in a cloned gene that is subsequently introduced into the genome of a gamete involved in fertilization. The organism produced is bred to produce adults homozygous for the mutation, for example, the creation of a gene knockout.

Answer 15

gene targeting

Question 16

Method for removing, replacing, or modifying a specific sequence in the genome; CRISPR-Cas is one of the most effective approaches to genome editing.

Answer 16

genome editing

Question 17

A collection of clones that contains all the DNA sequences of an organism’s genome.

Answer 17

genomic library

Question 18

A collection of DNA-equencing methods that outperform the standard (Sanger) method of DNA sequencing by a factor of 100-1000 and reduce sequencing costs by more than 99 percent. Also called next-generation sequencing.

Answer 18

high-throughput DNA sequencing

Question 19

A genomic DNA repair mechanism that is induced by double-strand DNA breaks. In this type of repair, an intact molecule of DNA, such as a homologous chromosome in diploid eukaryotes, is used as a template for repair of a damaged homolog.

Answer 19

homology-directed repair (HDR)

Question 20

An organism whose genome has been modified by the introduction of external DNA sequences into the germ line.

Answer 20

knock-in animals (transgenic animal)

Question 21

A collection of DNA-equencing methods that outperform the standard (Sanger) method of DNA sequencing by a factor of 100-1000 and reduce sequencing costs by more than 99 percent. Also called next-generation sequencing.

Answer 21

next-generation sequencing (NGS) technologies (high-throughput DNA sequencing)

Question 22

A genomic DNA repair mechanism that is induced by double-strand DNA breaks. This type of repair is error prone because broken ends of DNA molecules are randomly ligated together, which may lead to insertions, deletions, translocations, or inversions.

Answer 22

nonhomologous end joining (NHEJ)

Question 23

Electrophoresis, blotting, and hybridization technique for detecting and quantifying RNA expression.

Answer 23

Northern blot analysis

Question 24

An analytic technique in which RNA molecules are separated by electrophoresis and transferred by capillary action to a nylon or nitrocellulose membrane. Specific RNA molecules can then be identified by hybridization to a labeled nucleic acid probe.

Answer 24

Northern blotting

Question 25

In genetics, a sequence of DNA base pairs that read the same on complementary strands. Because the strands run antiparallel to one another in DNA, the base sequences on the two strands read the same backwards and forward when read from the 5` end.

Answer 25

palindrome

Question 26

A method for amplifying DNA segments that depends on repeated cycles of denaturation, primer annealing, and DNA polymerase-directed DNA synthesis.

Answer 26

polymerase chain reaction (PCR)

Question 27

A short (2-6 basepair) DNA segment immediately adjacent to the DNA sequence that is targeted by a Cas nuclease of the CRISPR-Cas system. In the well-described CRISPR-Cas system of Streptococcus pyogenes, the PAM sequence is 5-NGG-3 immediately downstream of the target sequence on the non-complementary strand of the DNA.

Answer 27

protospacer adjacent motif (PAM)

Question 28

A variation of PCR (polymerase chain reaction) that uses fluorescent probes to quantitate the amount of DNA or RNA product present after each round of amplification.

Answer 28

quantitative real-time PCR (qPCR)

Question 29

Method for amplifying and quantifying PCR products without the need for gel electrophoresis; quantification of PCR products occurs at the end of each PCR cycle and is captured by software; thus, analysis occurs in ‘real-time.’

Answer 29

real-time PCR

Question 30

A DNA sequence, often palindromic, recognized by a restriction endonuclease. The enzyme binds to and cleaves DNA at the restriction site.

Answer 30

recognition sequence (restriction site)

Question 31

A recombinant DNA tool that detects gene expression. The regulatory sequence of a gene of interest is fused to a coding sequence that confers an easily observable phenotype, such as fluorescence, and is inserted into an organism to learn when, where, and under what conditions the gene of interest is expressed.

Answer 31

reporter gene

Question 32

Physical map displaying the number, order, and distances between restriction enzyme digestion sites in a particular segment of DNA.

Answer 32

restriction map

Question 33

Method for synthesizing DNA from RNA through the actions of the enzyme reverse transcriptase.

Answer 33

reverse transcription PCR (RT_PCR)

Question 34

DNA sequencing by synthesis of DNA chains that are randomly terminated by incorporation of a nucleotide analog (dideoxynucleotides) followed by sequence determination by analysis of resulting fragment lengths in each reaction.

Answer 34

Sanger sequencing

Question 35

Marker gene such as one that encodes a gene for antibiotic resistance allowing specific cells to be chosen or selected by phenotype or characteristics (for example, antibiotic resistance) provided by the marker gene.

Answer 35

selectable marker gene

Question 36

Next-generation sequencing platform that uses DNA fragments to synthesize new strands which are sequenced.

Answer 36

sequencing-by-synthesis (SBS)

Question 37

An engineered hybrid RNA molecule that combines sequences of the crRNA and tracrRNA of type II CRISPR-Cas systems into a single RNA. This makes CRISPR-Cas-mediated genome editing more convenient because two separate components are integrated into one.

Answer 37

single guide RNA (sgRNA)

Question 38

Electrophoresis, blotting, and hybridization technique for detecting specific DNA fragments; pioneered by Edwin Southern.

Answer 38

Southern blot analysis

Question 39

Developed by Edwin Southern, a technique in which DNA fragments produced by restriction enzyme digestion are separated by electrophoresis and transferred by capillary action to a nylon or nitrocellulose membrane. Specific DNA fragments can be identified by ­hybridization to a complementary radioactively labeled nucleic acid probe using the technique of autoradiography.

Answer 39

Southern blotting

Question 40

A display of all the chromosomes in an organism as a karyotype with each chromosome stained in a different color.

Answer 40

spectral karyotype

Question 41

DNA-sequencing technologies based largely on methods for sequencing individual molecules of single-stranded DNA.

Answer 41

third-generation sequencing (TGS)

Question 42

A bacterial plasmid used as a vector to transfer foreign DNA to plant cells

Answer 42

Ti plasmid

Question 43

An analytical technique in which proteins are separated by gel electrophoresis and transferred by capillary action to a nylon membrane or nitrocellulose sheet. A specific protein can be identified through hybridization to a labeled antibody.

Answer 43

Western blotting

Question 44

Artificial DNA-cleaving ­enzymes created by combining DNA-­binding motifs (transcription activator-like effectors or TALES) from plant pathogenic bacteria to a DNA-cutting domain from a nuclease. This method can produce restriction enzymes for any DNA sequence

Answer 44

transcription activator-like effector nucleases (TALENs)

Question 45

A cloning vector in the form of a yeast artificial chromosome, constructed using chromosomal components including telomeres (from a ciliate) and centromeres, origin of replication, and marker genes from yeast. YACs are used to clone long stretches of eukaryotic DNA.

Answer 45

yeast artificial chromosomes (YACs)