Specific Topics (not all will necessarily be covered):

Gel Electrophoresis Techniques

• Denaturing
• Non-denaturing (Native)
• Gradient
• Gel retardation
• Pulsed gradient
• 2-D gels

Sequencing of DNA and RNA

• Maxam Gilbert base-specific - Methods in Enzymology
• Sanger dideoxy
• Automated Sequencing with fluorescence detection
• Nucleases (RNA)
• Mass Spectrometry
• DNA chip sequencing
• Nucleic acid sequence encoded tags

Chemical Synthesis

• Nucleosides
• Condensation
• Deoxygenation
• DNA
• Phosphodiester
• Phosphotriester
• Phosphoramdite
• RNA
• 2'-OH protecting group problem
• Modification
• 5' and 3'-derivatized DNA and RNA
• C5 derivatized
• Biotin-Avidin Affinity System
• Photolithographic synthesis, DNA chips
• PNA synthesis

Enzymatic synthesis/degradation

• nucleotides
• de novo pathways
• salvage pathways
• restriction enzymes
• kinases
• polymerases
• DNA
• polymerase
• proofreading
• RNA
• ligases
• exonucleases
• endonucleases
• excinucleases
• in vivo systems, cloning
• site-directed mutagenesis
• PCR
• DNA/RNA structure

Conformational analysis

• Five-membered rings
• Pseudorotation
• Sugar pucker
• Syn-anti
• Molecular modeling
• Force fields
• Molecular dynamics

Base-pairing

• Watson-Crick
• Hoogsteen
• Alternate

RNA

• A form
• Hairpins
• Bulge loops
• Interior loops
• Pseudoknots

DNA

• B DNA - Calladines rules
• Helix=coil transitions
• Z DNA
• H DNA
• Triple helices
• Bending
• Circular DNA
• Supercoiled
• Telomeres

Structure probes

• General probes
• Major groove probes
• Minor groove probes
• Backbone probes
• 3D structure determination
• NMR Sequential assignment strategy
• X-ray crystallography
• Electron microscopy
• Atomic Force Microscopy

DNA/RNA chemistry

• Spontaneous reactions
• Depurination
• Deamination
• Photochemistry
• Radiation chemistry
• Ribozymes

DNA drug/probe interactions

• Intercalators
• Ethidium bromide
• Anthracyclines
• echinomycin, triostin
• Minor groove binders
• Distamycin/netropsin
• Hoechst
• bis-benzamide
• Covalent modifiers
• AAF - carcinogen
• Aflatoxin - carcinogen
• BPDE - carcinogen
• anthramycin - toxin
• crosslinkers
• mustards (chemical warfare and anticancer)
• cis-platin (inorganic complex)
• mitomycin (bioreductively activated, anticancer)
• psoralen (phototoxin)
• mapping sites (polymerase termination and footprinting)

Oxidative degradation

• bleomycin
• enediyne class
• calicheamycin
• esperamycin
• neocarcinostatin
• mapping cleavage sites (sequencing gels)
• Designed drugs/probes
• MPE footprinting
• DE affinity cleaving
• oligo-x (x=EDTA, enzyme, alkylator)
• duplex (anti-sense)
• triplex (anti-duplex)
• protein-X (x=EDTA, enzyme, alkylator)

Nucleic Acid protein-interactions

• helix-turn-helix motif of repressors
• zinc finger of transcription factors
• leucine zipper (Jun and Fos)

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