• alkyl sulfate/sulfite
• 2-napthylamine (dyes)
• N,N dimenthylnitrosamine
• N-methyl-N-ethylnitrosamine
• MNNG
• MNU

• cytosine coverted to uracil (uracil should not be in DNA)
• 5-methylcytosine converted to thymine (genome that was suppose to be silenced, but is expressed)

• sodium nitrite (salt cured ham) when it is converted to nitrous acid in the stomach
• sodium bisulfide (wine)

• causes formation of thymine dimers
  • disrupts base pairing, so it put kink in DNA phosphodiester backbone
  • leads to corruption of molecular symmetry and DNA protein interactions
  • cause altering of chromatine structure

• ethidium bromide
• adriamycin
• actinomycin D
• psoralen

Clinical use and action of adriamycin/doxorubicin

• clinical use- leukemia treatment
• action- block DNA and RNA polymerase

• action
  • less than 10 uM block RNA Pol.
  • more than 10 uM blocks both RNA and DNA Pol.

Action of psoralen

1. psoralen intercalate within DNA
2. expose it to UV light
3. cause covalent bonds to form btw DNA strands
4. this cause DNA to be unable to denature

• direct reversal
  • photoreactivation
  • strand break repair
  • demethylase-transferase (takes methyl from where it shouldnt be and puts it where it should be)
  • apurinic site repair (fill hole)
• exision repair- short or long patch repair
• recombination repair
• post-replication repair (SOS repair)

photoreactivation, where we will use energy from visible light to split bonds forming dimer

• single strand via ligase
• double strand (more complex)
  • double strand rejoining
  • homologous recombination (chromosome crossing over)

1. damage recognition system
2. damage specific endonuclease recruitment (nick DNA strand 5' of damage site
3. 5'-3' exonucleasue activity to clear out damaged region (3 ways to do so)
   1. part of DNA polymerase I
   2. unique enzyme
   3. helicase mechanism
4. two options
   1. 5'-3' DNA Pol. I replaces dNTP's
   2. DNA Pol. II fills gaps
5. ligase seals strand break
6. repair mechansim goes back to monitoring for additional changes

• occurs between highly specific recombination sequencs in various regions of DNA
• sequences treated like cassettes of genetic information
• these sequences move from one genetic domain to another, controlling gene expression through chromatin reorganizing and repackaging

Holliday model for homologous recombination

1. nicks introduces at same position in both parental models
2. nicked strands exchange by complementary base pairing and ligation
3. this produces a cross stranded inermediate called holiday junction

1. The nicked strand will displace one strand and bind to the other strand via base pairing.
2. This loop is cleaved and will pair with first parental molecule, yielding Holliday junction.

• leads to genetic instability
• faulty or unprogrammed DNA recombinations
• cancer
• cell death

1. RecA protein sense ssDNA and tightly binds to ssDNA
2. RecA protein change confirmation upon binding and activates latent protease activity
3. RecA protease specifically cleaves Lex A protein
   1. LexA is transcriptional silencing protein that sits on promotor elements
4. inactivation of Lex A permit expression of previously repressed genes
   1. these genes are for DNA damage repair and stabilization genes
   2. many of these induced DNA repair systems are lower fidelity than constituitively expressed counterparts
5. DNA damage is repaired (error prone)
6. ssDNA signal activating RecA removed
7. RecA reverts to original confirmation (no protease activity)
8. LexA protein builds up and block transcription of DNA damage repair genes

1. binds to ssDNA to stabilize (SSBP)
2. leads to confirmation change in p53
3. leads to activation of TF's that serve as DNA repair genes
   1. blocks G1/S entry
4. but if repair system cant keep up with damage, it activates cell death system

• ionitation make ATM to activate p53
  • activate kinase which activate p53
  • directly activate p53
• UV make ATM to activate p53

1. p21 bind to cyclin dependent kinase (CDK) (as inhibitor of cell cycle)
2. along with cyclin and CDK, form PCNA
   1. loss of DNA pol. processivity (shut down replication)
   2. switch from replication to repair mode

Role of triplet repeat in disease

a certain sequence is repeated, causing expansion (makes disease worse) 

• autosomal dominant neurological disorder
• abnormal brain protein
  • CAG triplet repeats (glutatmine)
• repeats will increase with familial generations
• excess glutamine leads to protein aggregation and neurological dysfunction/ apoptosis

• CGG repeat triplet sequences in FMR1 gene, which is methylation site
  • leads to chromatin condensation, which will silence FMR1 gene
    • inhibited signal transduction
    • RNA trafficking from nucleus
    • neural development

Examples of faulty DNA repair mechanisms

• Xeroderma pigmentosum- bad UV repair (eye, nerve problems, skin cancer)
• Ataxia Telanglectasia- no strand break repair (X rays lethal, many leukemias and nerve problems, sensitive to ionizing radiation)
• Falconi's anemia- no X link repair (hemorrhage, mental retardation, fetal Hb, infection)