Maxim D Frank‐Kamenetskii, Boston University, Boston, Massachusetts, USA
Published online: May 2005
DOI: 10.1038/npg.els.0002976
DNA sequence significantly affects the local stability of the DNA double helix. In addition, depending on their particular sequence, different DNA sites are capable of adopting various unusual structures.
Keywords: kinetic stability; thermodynamic stability; DNA melting; supercoiling; Gibbs free energy; DNA unusual structures
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Figure 1. Schematics of (a) B-DNA and some of DNA unusual structures: (b) Z-DNA; (c) intermolecular triplex; (d) cruciform; (e) H-DNA; (f) G-quadruplex and its various folding modes.
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Figure 2. DNA base triads. (a) The Hoogsteen base triads. The Watson–Crick and Hoogsteen pairings are indicated by arrows. Note that to form the Hoogsteen pair with G, C must be protonated at the N3 position. (b) The reverse Hoogsteen base triads.
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| References | |
| Anshelevich VV, Vologodskii AV, Lukashin AV and Frank-Kamenetskii MD (1984) Slow relaxational processes in the melting of linear biopolymers. A theory and its application to nucleic acids. Biopolymers 23: 39–58. | |
| Craig ME, Crothers DM and Doty P (1971) Relaxation kinetics of dimer formation by self complementary oligonucleotides. Journal of Molecular Biology 62: 383–401. | |
| Crothers DM and Drak J (1992) Global features of DNA structure by comparative gel electrophoresis. Methods in Enzymology 212: 46–71. | |
| Frank-Kamenetskii MD (1971) Simplification of the empirical relationship between melting temperature of DNA, its GC content and concentration on sodium ions in solution. Biopolymers 10: 2623–2624. | |
| book Frank-Kamenetskii MD (1990) "DNA supercoiling and unusual structures". In: Cozzarelli NR and Wang JC (eds) DNA Topology and its Biological Effects, pp. 185–215. Cold Spring Harbor: Cold Spring Harbor Laboratory Press. | |
| Frank-Kamenetskii MD and Mirkin SM (1995) Triplex DNA structures. Annual Review of Biochemistry 64: 65–95. | |
| Ivanov VI and Krylov DY (1992) A-DNA in solution as studied by diverse approaches. Methods in Enzymology 211: 111–127. | |
| Marmur J and Doty P (1962) Determination of the base composition of deoxyribonucleic acid from its thermal melting temperature. Journal of Molecular Biology 5: 109–118. | |
| Rippe K and Jovin JM (1992) Parallel-stranded duplex DNA. Methods in Enzymology 211: 199–220. | |
| SantaLucia J (1998) A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proceedings of the National Academy of Sciences of the USA 95: 1460–1465. | |
| Schwartz T, Rould MA, Lowenhaupt K, Herbert A and Rich A (1999) Crystal structure of the Z-alpha domain of the human editing enzyme ADAR1 bound to left-handed Z-DNA. Science 284: 1841–1845. | |
| Further Reading | |
| book Bloomfield VA, Crothers DM and Tinoco I (2000) Nucleic Acids: Structure, Properties, and Function. Sausalito, CA: University Science Books. | |
| book Cantor CR and Smith CL (1999) Genomics. New York: Wiley-Interscience. | |
| book Cozzarelli NR and Wang JC (eds) (1990) DNA Topology And Its Biological Effects. Cold Spring Harbor: Cold Spring Harbor Laboratory Press. | |
| book Frank-Kamenetskii MD (1997) Unraveling DNA. Reading, MA: Perseus Books. | |
| book Lilley MJ and Dahlberg JE (eds) (1992) DNA Structure. Parts A and B. Methods in Enzymology, vols 211, 212. London: Academic Press. | |
| book Malvy C, Harel-Bellan A and Pritchard LL (eds) (1999) Triple Helix Forming Oligonucleotides. Boston: Kluwer Academic. | |
| book Nelson DR and Cox MM (2000) Lehninger Principles of Biochemistry. New York: Worth Publishers. | |
| book Sinden RR (1994) DNA Structure and Function. San Diego: Academic Press. | |
| book Soyfer VN and Potaman VV (1996) Triple Helical Nucleic Acids. New York: Springer. | |
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