Although multiple molecules are important in modern molecularlabs, in Genetics Lab, we will be focusing on DNA. Throughout thesemester, our treatment of the DNA can determine if we aresuccessful or not in meeting our experimentalgoals.  

You are going to consider several treatments that might affectDNA shape/form/function. We use some of these treatments on purposein order to manipulate our DNA, but sometimes we avoid thesetreatments to keep from harming our DNA.

You will be considering these treatments across three types ofDNA:

1. pUC19 - pUC19 is a closed-circle plasmid (2686 bp) which usedin molecular cloning
2. Lambda phage - Linear DNA from a bacteriophage (viruses thatinfect bacteria - in this case E. coli). Lambda phage isapproximately 45,000 bps long.
3. Mammalian DNA - Eukaryotic mammalian DNA is arranged in verylarge linear chromosomes. Although this DNA is mechanically shearedto some extent during extraction, there are still pieces that maybe hundreds of thousands of bps long.

You will consider what the following treatments could do to theDNA listed above:

1. Severe agitation - aggressive mixing with a votex machine
2. NaOH - treatment with a base
3. High heat - heating to 100^oC
4. Nuclease treatment - treatment with endo- or exonucleases

Think about the structure of the DNA. Hydrogen bonds are holdingthe bases together, while phosphodiester bonds are holding thesugar-phosphate backbone together.

• Which treatments will break the hydrogen bonds (and denaturethe DNA-reduce it from double-stranded DNA (dsDNA) tosingle-stranded DNA (ssDNA)?
• What treatments might break the DNA into pieces(fragmentation).
• Do you think that all of the types of DNA will be affected thesame, or will certain treatments affect certain types of DNAmore?

Consider the above questions and write out hypotheses for eachtreatments. Make sure to also address whether or not you think thedifferent types of DNA will have different results.