The Age of Genetics was created by remarkable advances in the use of biotechnology to manipulate plant and animal genomes. Given that the world population reached 7.5 billion people in 2017 and is expected to reach 9.7 billion in 2050, some scientists have proposed that only the worldwide introduction of genetically modified (GM) foods will increase crop yields enough to meet future nutritional demands. Pest resistance, herbicide, cold, drought, and salinity tolerance, along with increased nutrition, are seen as positive attributes of GM foods. However, others caution that unintended harm to other organisms, reduced effectiveness to pesticides, gene transfer to nontarget species, allergenicity, and as yet unknown effects on human health are potential concerns regarding GM foods. If you were in a position to control the introduction of a GM primary food product (rice, for example), what criteria would you establish before allowing such introduction?

You have recovered a cloned DNA segment from a vector and determine that the insert is 1300 bp in length. To characterize this cloned segment, you isolate the insert and decide to construct a restriction map. Using enzyme I and enzyme II, followed by gel electrophoresis, you determine the number and size of the fragments produced by enzymes I and II alone and in combination, as recorded in the following table. Construct a restriction map from these data, showing the positions of the restriction-enzyme cutting sites relative to one another and the distance between them in units of base pairs.

Enzyme   Restriction Fragment Sizes (bp)
     I           350, 950
    II           200, 1100
I and II      150, 200, 950

The restriction enzymes XhoI and SalI cut their specific sequences as shown below:

Xhol     5'-C             TCGAG-3'
            3'-GAGCT   C-5'
Sall      5'-G             TCGAC-3'
            3'-CAGCT   G-5'  

Can the sticky ends created by XhoI and SalI sites be ligated? If yes, can the resulting sequences be cleaved by either XhoI or SalI?

The bacteriophage ϕX174 has a single-stranded DNA genome of 5386 bases. During DNA replication, double-stranded forms of the genome are generated. In an effort to create a restriction map of ϕX174, you digest the z-stranded form of the genome with several restriction enzymes and obtain the following results. Draw a map of the ϕX174 genome.

Pstl     5386                PstI + PsiI      3078, 2308
Psil     5386                PstI + DraI      331, 1079, 3976
Dral    4307, 1079      PstI + DraI      898, 1079, 3409

To further analyze the CRABS CLAW gene (see Problems 19 and 20), you create a map of the genomic clone. The 11-kb EcoRI fragment is ligated into the EcoRI site of the MCS of the vector shown in Problem 18. You digest the double-stranded form of the genome with several restriction enzymes and obtain the following results. Draw, as far as possible, a map of the genomic clone of CRABS CLAW.

EcoRI                   11.0, 3.0                     XbaI     4.5, 9.5
EcoRI + XbaI        4.5, 6.5, 3.0               XhoI     13.2, 0.8
EcoRI + XhoI        10.2, 3.0, 0.8             SalI       6.0, 8.0
EcoRI + SalI          6.0, 5.0, 3.0              HindIII   12.0, 1.5, 0.5
EcoRI + HindIII      9.0, 3.0, 1.5, 0.5

What restriction digest would help resolve any ambiguity in the map?

To estimate the number of cleavage sites in a particular piece of DNA with a known size, you can apply the formula N/4ⁿ where N is the number of base pairs in the target DNA and n is the number of bases in the recognition sequence of the restriction enzyme. If the recognition sequence for BamHI is GGATCC and the  phage DNA contains approximately 48,500 bp, how many cleavage sites would you expect?