Hydrogen bonding base pairing

Section 28 8 The most common form of DNA is B DNA which exists as a right handed double helix The carbohydrate-phosphate backbone lies on the outside the punne and pyrimidine bases on the inside The double helix IS stabilized by complementary hydrogen bonding (base pairing) between adenine (A) and thymine (T) and guanine (G) and cytosine (C)... 

The results of the various semi-empirical calculations on the reference structures contained within the JSCH-2005 database (134 complexes 31 hydrogen-bonded base-pairs, 32 interstrand base pairs, 54 stacked base pairs and 17 amino acid base pairs) are summarised in Table 5-10. The deviations of the various interaction energies from the reference values are displayed in Figure 5-5. As with the S22 training set, the AMI and PM3 methods generally underestimate the interactions whereas the dispersion corrected method (PM3-D) mostly over-estimates the interactions a little. Overall the PM3-D results are particularly impressive given that the method has only... 

The duplex with the normal HBB gene has one hydrogen-bonded base pair more than the duplex with the mutated HBB gene, and therefore the first duplex has more double-helical region. The single-nucleotide mismatch has a significant effect on the structure of the duplexes, which in turn strongly influences the local environment where the clusters could form. 

Most DNA occurs in nature as a right-handed double-helical molecule known as Watson-Crick DNA or B-DNA (Fig I-1-9). The hydrophilic sugar-phosphate backbone of each strand is on the outside of the double helix. The hydrogen-bonded base pairs are stacked in the center of the molecule. There are about 10 base pairs per complete turn of the helix. A rare left-handed double-helical form of DNA that occurs in G-C-rich sequences is known as Z-DNA. The biologic function of Z-DNA is unknown, but may be related to gene regulation. 

Figure 12.3 The double hehx of DNA. The sugar-phosphate backbones wind about the periphery of the molecule in opposite directions. The hydrogen-bonded base pairs occupy the core of the structure and are basically flat and lie perpendicular to the long axis of the helix. (Illustration, Irving Geis/Geis Archives Trust. Howard Hughes Medical Institute. Reproduced with permission.)...

Pranata J, Wierschkem SG, Jorgensen WL. OPLS potential functions for nucleotide bases— relative association constants of hydrogen-bonded base-pairs in chloroform. J Am Chem Soc 1990 113 2810-2819. 

A. Hydrogen-bonded base pairing of adenine and thymine... 

Hydrogen-bonded base pair inside micelle with hydrocarbon tails anchoring the bases to the micelle. 

Figure 5-2 A distorted (flattened) view of the Watson-Crick structure of DNA showing the hydrogen-bonded base pairs.

Figure 5.19 Schematic representation of the two strands of a nucleic acid. P = phosphate and S = sugar bases are as in Figure 5.18. The two strands of the double helix are held together through specific hydrogen bonds (base pairing)...

While searching for the meaning of these equalities, James Watson noted that hydrogen-bonded base pairs with the same overall dimensions could be formed between A and T and between G and C (fig. 25.4). The A-T base-paired structure has two hydrogen bonds, whereas the G-C base pair has three. The hydrogen-bonded pairs are formed between bases of opposing strands and can only arise if the directional senses of the two interacting chains are opposite or antiparallel (fig. 25.5). With this notion in mind Francis Crick took a closer look at the x-ray diffraction pattern produced by DNA and was able to interpret the diffraction pattern in terms of a helix (see Methods of Biochemical... 

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. 

Figure 2.27 (a) The DNA double helix. Dotted lines represent hydrogen bonded base-pair interac-... 

Guanosine 10 make a hydrogen-bonded base pair, but other nucleobase positions are poorly constrained by NMR data (Addess et al, 1997 Laing and Hall, 1996 McCallum and Pardi, 2003). To better characterize the loop structure and nucleotide motions, 2AP replaced A7 and G8 in the IRE (Fig. 13.4). 

R.R. Toczylowski, S. Cybulski, An analysis of the interactions between nucleic acid bases Hydrogen-bonded base pairs. J. Phys. Chem. A 107, 418 126 (2003)... 

The implication is that under the conditions of deep UV irradiation, which likely existed on the early earth, selective chemistry may have taken place in favor of species with the shortest excited state lifetimes. Benner and coworkers, for example, have proposed a molecular lexicon of 12 alternate bases that can produce 6 base pairs with virtually identical geometries as the guanine-cytosine (GC) triply hydrogen bonded base pair [1], Several of these alternate bases have been observed as products in simulation experiments that test the feasibility of synthesis of such compounds under primitive conditions [77, 78], This raises the... 

Where cyclic hydrogen-bond configurations occur, they are referred to as base pairs. They can be of the homo type, if the bases self-associate, or of the hetero type, if different bases interact with each other. The hydrogen-bonded base pairs can form isolated dimers and in many cases this dimerization is extended to two-dimensional ribbon patterns or to three-dimensional networks of hydrogen bonds (see Chap. 16). 

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