Nucleic hydrogen bonding

When thinking about chemical reactivity, chemists usually focus their attention on bonds, the covalent interactions between atoms within individual molecules. Also important, hotvever, particularly in large biomolecules like proteins and nucleic acids, are a variety of interactions between molecules that strongly affect molecular properties. Collectively called either intermolecular forces, van der Waals forces, or noncovalent interactions, they are of several different types dipole-dipole forces, dispersion forces, and hydrogen bonds. 

A hypochromicity was observed between THPVP and APVP (or TPVP). Since theophylline is not a nucleic acid base and does not form hydrogen-bonding, these observations indicate that stacking-type hydrophobic forces are important. 

Poly A form a complex with a 4 1 stoichiometry. The apparent hypochromicities of various mixtures are listed in Table 4. The mixtures of A12 with Poly U and of T12 with Poly A showed large hypochromicities compared with other mixtures, which suggests the importance of the hydrogen-bonding formation between complementary nucleic acid bases such as A-U and T-A. 

Since these basic facts became known, a tremendous amount of research has been done on the structures and behaviors of these important substances. There has also been much research on the synthesis and study of other chain polyelectrolytes, containing hydrogen-bond-forming radicals (R) more-or-less like those in the natural nucleic acids. The primary aim of this research is, of course, to relate the behavior of the synthetic materials to the behavior of the natural ones. Okubo and Ise here present an excellent discussion on this research. 

Another class of molecules which are easily bound to hosts by hydrogen bonds are nucleic bases and related molecules like barbiturates (Hamilton and Little, 1990 Chang et al., 1991). The receptor arrays to bind such molecules often contain 2-acylaminopyridine units or related structures such... 

Three classes of nucleic acid triple helices have been described for oligonucleotides containing only natural units. They differ according to the base sequences and the relative orientation of the phosphate-deoxyribose backbone of the third strand. All the three classes involve Hoogsteen or reverse Hoogsteen-like hydrogen bonding interaction between the triple helix form-... 

Instead, this review seeks to cover less well-known and newly emerging aspects of metal-nucleobase chemistry. In addition to biomedical relevancies, nucleic acid chemistry offers a paradigm for organizing molecules via base pairing. Combining the hydrogen bonding... 

P2j Z = 2 DX = 1.43 R = 0.067 for 1269 intensities. The uracil residue is in the anti (63.4°) disposition. The conformation of the D-ribosyl group is 2T3 (176.8°, 37.5°). The orientation about the exocyclic, C-4 -C-5 bond is t (—174.2°). The phenyl and uracil ringsofthe same molecule lie in almost parallel planes, 120 pm apart. The phenyl group is disordered. The uracil ring is sandwiched by the phenyl rings, and vice versa. The 0-1 and N-a atoms of the peptide backbone are hydrogen-bonded to 0-4 and N-3 of atranslationally related uracil to form cyclic dimers. Such interactions serve as models for nucleic acid-protein interactions. [Coordinate errors H(02 ) x should be —1574, instead of —1474 H(Na)2 z should be —145 instead of— 645.]... 

Hardman SJO, Thompson KC (2006) Influence of base stacking and hydrogen bonding on the fluorescence of 2-aminopurine and pyrrolocytosine in nucleic acids. Biochem 45 9145-9155... 

We have now adjusted our molecular systems to provide a model in which both forces can operate simultaneously. The U-shaped relationship that exists between the imide function and amides of aryl amines creates a hydrogen bonding edge and a planar stacking surface that converge from perpendicular directions as in 44 to provide a microenvironment complementary to nucleic acid components. A large number of aromatic rings can be functionalized with this simple scaffold, and spacers (R) can also be incorporated. The imide function is a mimic of the thymine residues. 

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