Hydrogen bonding Watson-Crick type

Observation of the imino-proton resonances - albeit somewhat shifted and broadening at low temperatures - of the central G C base pairs, indicates that hydrogen bonding (Watson-Crick type or related) is still possible after platination. 

Authors of paper [48] studied the self-complementary duplexes A and B and compared them to their single strands, in order to compare helix or G-quadruplex. Clear differences in the UV spectra of the double heUx and G-quadruplex are observed, as compared to the corresponding single strands. The red shift upon higher-order structure formation is attributed to the absorption of clusters of bases interacting via hydrogen bonds (Watson-Crick type for the duplex and Hoogsteen... 

Figure 1. Catalysis and template action of RNA and proteins. Catalytic action of one RNA molecule on another one is shown in the simplest case, the "hammerhead ribozyme." The substrate is a tridecanucleotide forming two double-helical stacks together with the ribozyme (n = 34) in the confolded complex. Tertiary interactions determine the detailed structure of the hammerhead ribozyme complex and are important for the enzymatic reaction cleaving one of the two linkages between the two stacks. Substrate specificity of ribozyme catalysis is caused by secondary structure in the cofolded complex between substrate and catalyst. Autocatalytic replication of oligonucleotide and nucleic acid is based on G = C and A = U complementarity in the hydrogen bonded complexes of nucleotides forming a Watson-Crick type double helix. Gunter von Kiedrowski s experi-...

Base-pair hydrogen bonding of the Watson-Crick type is fundamental in all biological processes where nucleic acids are involved. These processes, which are chiefly DNA replication and protein biosynthesis [650, 651], were understood only at the molecular level when Watson and Crick discovered the three-dimensional structure of DNA [27, 527J. This structure consists of two polynucleotide chains running in opposite directions (antiparallel), and twisted into a right-handed double helix. The hydrophobic purine and pyrimidine bases are stacked in the center... 

Aida, M., Characteristics of the Watson-Crick type hydrogen-bonded DNA base pairs An ab initio molecular orbital study, J. Comput. Chem. 9, 362-368 (1988). 

Fig. 12.3. Adenine-thymine hydrogen-bonded pairs (a) found by Hoogsteen in a 1 1 complex of 3-N-methyllhymine and 9-Af-methyladenine (b) postulated by Watson and Crick (current version refined by Arnott) for part of the structure of DNA. Guanine-cytosine pairs (c) Hoogsteen type (d) Watson-Crick type (Wilkins and Arnott, 1965). (From Mahler and Cordes, 1966.)...

Basis set effect on hydrogen bond stabilization energy estimation of the Watson-Crick type nucleic acid base pairs using medium-size basis sets single point MP2... 

Combining these evidences one of the probable mechanisms seems to be keto-enol equilibrium in the hydrogen-bonded dimers. If so, only the imino protons and the conjugated amino proton in the cyclic hydrogen bond can exchange. Watson-Crick type base pairs contribute to it, but Hoogsteen type does not, which would result in the lower rate of exchange than that expected from total dimer concentration. 

Callahan et al. have used xanthine and its methylated derivatives as models for studying the two motifs [82, 83]. For the 7-methylxanthine dimer, they observed hydrogen bonding on the N3H position, suggesting three possible combinations, one that is reverse Watson-Crick type and two that are reverse Hoogsteen type. For the 3-7-dimethylxanthme dimer, they observed a stacked structure, as determined by the free NIH stretch frequency. For trimethylxanthine dimers they inferred a stacked structure as well. 

The triple helix is another type of superstructure of DNA [91]. A-T-T (A-T-U) and G-C-C base-trimers are formed by combination of Watson-Crick and Hoogsteen-type hydrogen bonding. Base-trimers are formed in the DNA-mimetic system at the air-water interface between the Watson-Crick-type monolayer and... 

From ethanol solution, needles of decyl 2-(thymin-l-yl)propionate (ESlO-2) were obtained. The crystal structure of ESlO-2 consists of two independent molecules forming a racemic pair. Figure 104.45 shows two kinds of conformations (I and II) in the crystal. The hydrogen bonds of the thymine bases in this crystal were formed between 04 and N3-H (Watson-Crick type) that is the same seen with derivatives with odd-numbered alkyl chain (Figure 104.44b). One base pair I (Figure 104.45a) shows a similar conformation to ESll where the alkyl chain is perpendicular to the thymine ring. The alkyl chains of the other base pair II (Figure 104.45b), however, were in an extended conformation. 

The exact nature of the lesion in DNA is unknown, and so is the type of DNA that is attacked. Recent X-ray crystallographic studies, as well as other physicochemical studies, have made it clear that DNA is not simply a polynucleotide, folded as Watson and Crick (106) proposed. There are three main conformational types of DNA they each keep the hydrogen-bonded bases in the center of the helix, but may tilt them by a "propellor twist," may slide them from the center of the helix in the plane of the base pairs, and may vary the amount of rotation from one base pair to the next up the helical axes. 

Figure 6.2. Watson-Crick (a) and reverse Watson-Crick (b) types of hydrogen bonding.

Watson-Crick base pairs. The type of hydrogen-bonded base pairs found in DNA, or comparable base pairs found in RNA. The base pairs are A-T, G-C, and A-U. 

Within the DNA double helix, the hydrogen-bonded pairs are of a very specific type termed Watson-Crick base pairs (after James Watson and Francis Crick who first described the structure of... 

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