Helix geometry, hydration, and G.A mismatch in a B-DNA decamer. 1987

G G Privé, and U Heinemann, and S Chandrasegaran, and L S Kan, and M L Kopka, and R E Dickerson
Molecular Biology Institute, University of California, Los Angeles 90024.

The DNA double helix is not a regular, featureless barberpole molecule. Different base sequences have their own special signature, in the way that they influence groove width, helical twist, bending, and mechanical rigidity or resistance to bending. These special features probably help other molecules such as repressors to read and recognize one base sequence in preference to another. Single crystal x-ray structure analysis is beginning to show us the various structures possible in the B-DNA family. The DNA decamer C-C-A-A-G-A-T-T-G-G appears to be a better model for mixed-sequence B-DNA than was the earlier C-G-C-G-A-A-T-T-C-G-C-G, which is more akin to regions of poly(dA).poly(dT). The G.A mismatch base pairs at the center of the decamer are in the anti-anti conformation about their bonds from base to sugar, in agreement with nuclear magnetic resonance evidence on this and other sequences, and in contrast to the anti-syn geometry reported for G.A pairs in C-G-C-G-A-A-T-T-A-G-C-G. The ordered spine of hydration seen earlier in the narrow-grooved dodecamer has its counterpart, in this wide-grooved decamer, in two strings of water molecules lining the walls of the minor groove, bridging from purine N3 or pyrimidine O2, to the following sugar O4'. The same strings of hydration are present in the phosphorothioate analog of G-C-G-C-G-C. Unlike the spine, which is broken up by the intrusion of amine groups at guanines, these water strings are found in general, mixed-sequence DNA because they can pass by unimpeded to either side of a guanine N2 amine. The spine and strings are perceived as two extremes of a general pattern of hydration of the minor groove, which probably is the dominant factor in making B-DNA the preferred form at high hydration.

UI MeSH Term Description Entries
D009690 Nucleic Acid Conformation The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape. DNA Conformation,RNA Conformation,Conformation, DNA,Conformation, Nucleic Acid,Conformation, RNA,Conformations, DNA,Conformations, Nucleic Acid,Conformations, RNA,DNA Conformations,Nucleic Acid Conformations,RNA Conformations
D009838 Oligodeoxyribonucleotides A group of deoxyribonucleotides (up to 12) in which the phosphate residues of each deoxyribonucleotide act as bridges in forming diester linkages between the deoxyribose moieties. Oligodeoxynucleotide,Oligodeoxyribonucleotide,Oligodeoxynucleotides
D010710 Phosphates Inorganic salts of phosphoric acid. Inorganic Phosphate,Phosphates, Inorganic,Inorganic Phosphates,Orthophosphate,Phosphate,Phosphate, Inorganic
D003460 Crystallization The formation of crystalline substances from solutions or melts. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed) Crystalline Polymorphs,Polymorphism, Crystallization,Crystal Growth,Polymorphic Crystals,Crystal, Polymorphic,Crystalline Polymorph,Crystallization Polymorphism,Crystallization Polymorphisms,Crystals, Polymorphic,Growth, Crystal,Polymorph, Crystalline,Polymorphic Crystal,Polymorphisms, Crystallization,Polymorphs, Crystalline
D004247 DNA A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine). DNA, Double-Stranded,Deoxyribonucleic Acid,ds-DNA,DNA, Double Stranded,Double-Stranded DNA,ds DNA
D001482 Base Composition The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid. Base Ratio,G+C Composition,Guanine + Cytosine Composition,G+C Content,GC Composition,GC Content,Guanine + Cytosine Content,Base Compositions,Base Ratios,Composition, Base,Composition, G+C,Composition, GC,Compositions, Base,Compositions, G+C,Compositions, GC,Content, G+C,Content, GC,Contents, G+C,Contents, GC,G+C Compositions,G+C Contents,GC Compositions,GC Contents,Ratio, Base,Ratios, Base
D001483 Base Sequence The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence. DNA Sequence,Nucleotide Sequence,RNA Sequence,DNA Sequences,Base Sequences,Nucleotide Sequences,RNA Sequences,Sequence, Base,Sequence, DNA,Sequence, Nucleotide,Sequence, RNA,Sequences, Base,Sequences, DNA,Sequences, Nucleotide,Sequences, RNA
D014867 Water A clear, odorless, tasteless liquid that is essential for most animal and plant life and is an excellent solvent for many substances. The chemical formula is hydrogen oxide (H2O). (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed) Hydrogen Oxide

Related Publications

G G Privé, and U Heinemann, and S Chandrasegaran, and L S Kan, and M L Kopka, and R E Dickerson
January 1983, Cold Spring Harbor symposia on quantitative biology,
G G Privé, and U Heinemann, and S Chandrasegaran, and L S Kan, and M L Kopka, and R E Dickerson
April 1984, Journal of molecular biology,
G G Privé, and U Heinemann, and S Chandrasegaran, and L S Kan, and M L Kopka, and R E Dickerson
December 1982, The Journal of biological chemistry,
G G Privé, and U Heinemann, and S Chandrasegaran, and L S Kan, and M L Kopka, and R E Dickerson
September 1981, Journal of molecular biology,
G G Privé, and U Heinemann, and S Chandrasegaran, and L S Kan, and M L Kopka, and R E Dickerson
June 1991, Biochemistry,
G G Privé, and U Heinemann, and S Chandrasegaran, and L S Kan, and M L Kopka, and R E Dickerson
November 1995, Proceedings of the National Academy of Sciences of the United States of America,
G G Privé, and U Heinemann, and S Chandrasegaran, and L S Kan, and M L Kopka, and R E Dickerson
January 1997, Biochemistry,
G G Privé, and U Heinemann, and S Chandrasegaran, and L S Kan, and M L Kopka, and R E Dickerson
January 1991, Journal of molecular biology,
G G Privé, and U Heinemann, and S Chandrasegaran, and L S Kan, and M L Kopka, and R E Dickerson
January 1991, Proceedings of the National Academy of Sciences of the United States of America,
G G Privé, and U Heinemann, and S Chandrasegaran, and L S Kan, and M L Kopka, and R E Dickerson
December 1992, Biochemistry,
Copied contents to your clipboard!