Chapter 1. Structure, Nomenclature and Properties of Nucleic Acids
Structure and nomenclature of bases, nucleosides, nucleotides
Hybridization
Aromaticity
H-bonding
Acid/Base properties
Tautomerization
Stability
UV spectroscopy
NMR spectroscopy
Chapter 2. Conformational Analysis of Nucleosides and Nucleotides
Molecular mechanics
Sugar pucker, envelope and twist forms
Pseudorotation
Other torsion angles
Anomeric effect
Chapter 3. Conformational analysis of DNA duplexes, triplexes and quadruplexes, tRNA
Base pairing motifs
Watson Crick base pair
Helical parameters
A and B DNA duplexes
Sequence-dependent variations in structure: Calladine’s rules
Z DNA
Triplexes
Quadruplexes
Chapter 4. Thermodynamics of duplex formation
Base pairing in water
Pi-stacking in water
Helix = coil equilibria
helix initiation and propagation
extracting thermodynamic parameters from melting temperature curves
thermodynamics of RNA folding
Chapter 5. Chemical and Spectroscopic Probes of NA structure and Interactions
Chemical probes
2D NMR spectroscopy (NOESY and COSY)
Chapter 6. Small molecule – DNA interactions
Intercalators
Ethidium bromide
Anthracyclines
echinomycin, triostin
Minor groove binders
Distamycin/netropsin
Hoechst
bis-benzamide
polyamides
Chapter 7. Protein – DNA interactions
protein secondary structure
helix-turn-helix
leucine zippers
zinc fingers
other motifs
Chapter 8. Supercoiling
Circular DNA forms
Electrophoresis
knots and catenanes
free energy of supercoiling
driving structural transitions
topoisomerases
Chapter 9. DNA bending
Discovery of DNA bending
Circular permutation assay
Sequence-specificity of bending
Determining bending and unwinding angles
Determining bending direction
Bending by assymetric charge neutralization
Chapter 10. Chemical synthesis of nucleic acids
synthesis of nucleosides
synthesis of nucleotides
Chapter 11. Solution and solid phase synthesis of DNA, RNA
Chapter 12. DNA chips, Chemical Synthesis of Modified nucleic acids
2D photolithographic synthesis of DNA (DNA chips)
thiolated DNA
synthesis of peptide nucleic acids
Chapter 13. Enzymatic synthesis of nucleotides, de novo, salvage
Chapter 14. Enzymatic synthesis of DNA, RNA, and protein, PCR,
Chapter 15. Physical, chemical, and enzymatic sequencing of DNA and RNA
Maxam Gilbert base-specific
Sanger dideoxy
Automated Sequencing with fluorescence detection
Nucleases (RNA)
Mass spectrometry
Chapter 16. In vitro evolution, SELEX, catalytic DNA, nucleic acid encoded tags
Chapter 17. Genetic engineering, site-directed mutagenesis
Chapter 18. Protein expression, unnatural mutagenesis, semi-synthetic proteins
Chapter 19. Photochemistry of DNA
cyclobutane dimers
cytosine hydrates
(6-4) products
Dewar isomers
TA* photoproducts
AA photoproducts
sensitized reactions
Chapter 20. Radiation Chemistry
Chemistry of ionizing radiation in water
DNA strand cleavage
DNA adducts
Chapter 21. Radiomimetic Agents, Footprinting and affinity cleaving
bleomycin
enediyne class
calicheamycin
esperamycin
neocarcinostatin
MPE footprinting
DE affinity cleaving
oligo-x (x=EDTA, enzyme, alkylator)
duplex (anti-sense)
triplex (anti-duplex)
protein-X (x=EDTA, enzyme, alkylator)
Chapter 22. Covalent Binders/Xenobiotics
AAF - carcinogen
Aflatoxin - carcinogen
BPDE - carcinogen
anthramycin - toxin
crosslinkers
mustards (chemical warfare and anticancer)
cis-platin (inorganic complex)
mitomycin (bioreductively activated, anticancer)
psoralen (phototoxin
Chapter 23. DNA Repair Enzymes
Direct repair
Glycosylases
Excinucleases
Chapter 24. RNA cleavage chemistry