DNA duplex is not totally inflexible ABZs of DNA secondary structure Triple helix and G-quartets - Hoogsteen base pairing Problems: textbook Ch.8: 1, 2, 4, 5 Study guide, p.107:#3 The double helix is not totally inflexible 1. X-ray analysis of crystallized dodecamer (12mer) - overall structure is very much like a Watson-Crick double helix, but there are a lot of local deviations. Base sequence determines local structure 2. Neighboring bases rotate between 28° to 42° rather than a fixed 36°. 3. Opposing bases are not perfectly coplanar - assume ?propellar twist. 4. Sequence can determine local structure (run of As can bend DNA) A DNA backbone can rotate about 6 bonds in each monomer pair 3? end 3? end Note: 2 strands of the helix are antiparallel Sugar phosphate backbone is fexible N-glycosidc bond Propellar twists - Anti or syn conformation Interaction with EcoRI changes conformation of DNA Run of As bends DNA AAAAAAAA TTTTTTTT Comparison of A, B, Z DNA A: right-handed, short and broad, 2.6 A, 11 bp per turn. Formed in dehydrated DNA fibers, RNA/DNA hybrids, and RNA/RNA duplexes. 2?OH of ribose causes puckering of sugar. B: right-handed, longer, thinner, 3.4 A, 10.5 bp per turn. Natural form of DNA found in prokaryotes and eukaryotes. Z: left-handed, longest, thinnest, 3.7 A, 12 bp per turn. Existence in nature presumed. A form duplex is more stable than B form duplex Tm RNA/RNA > RNA/DNA > DNA/DNA 24 bp in each helix A B OH Conditions for Z DNA formation 1. First identified in synthetic deoxynucleotide dCpGpCpGpCpG at salt conditions of ? 3M. The N- glycosidic bonds of G residues in the alternating copolymer is in the syn conformation. Stretches of alternating GC occur frequently in euk. genomes. 2. If a substantial fraction of the C residues are methylated to form 5-methylcytosine, will adopt Z conformation at physiological ionic strengths. 3. Mg++ or small positively charged molecules such as spermine and spermidine also favors Z form. Hypermethylation of CpG islands is associated with gene silencing and epigenetic regulation in mammalian cells. Deoxyguanosine in B- DNA (anti position) Deoxyguanosine in Z- DNA (syn position) Note zigzag of the sugar-P backbone of Z-DNA See fig. 8-18 H-bonds 2 2 Madam Nurses run Anna 5? 5? 3? 3? Palindromes can form hairpins. Double-stranded palindromes can form cruciforms What kind of structures do mirror repeats form? Hoogsteen (non Watson-Crick) pairing The N-7, O6 and N6 that participate in the H-bonding of triplex are often referred to as Hoogsteen positions 7 6 6 7 3 4 4 3 3 4 3 2 Hoogsteen pairing allows the formation of triplex DNA from mirror repeats Triple helix or H-DNA usually consists of one strand of purines and two strands of pyrimidines or vice versa The third purine strand (green) binds to the major groove of pyrimidine.purine duplex DNA to form a triple-stranded DNA Structure of Triplex DNA py pu pu Triple helix formation is sensitive to the length of the third strand, single base mismatches, pH, cation concentration and valence - requires Mg++ and inhibited by K+ temperature, backbone composition (DNA or RNA) of the three strands. Potential application in gene therapy: Design oligonucleotides that recognize unique base pair sequence and form a stable triplex in a promoter region of the human genome to inactivate a specific gene. 6 7 6 7 6 6 7 7 G4 or G quartet DNA Structure extremely stable, can withstand boiling (quadruplex) Possible cellular functions for G quartet or G4 DNA Stabilizes telomere structure - so far, no good evidence Human topoisomerase I interacts with G quartet structure promotes synapsis of double-stranded DNA helices via the formation of guanine quartets
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