Hydrogen bonds, in DNA

Figure 7.7 Color codes for the recognition patterns at the edges of the base pairs in the major (a) and minor (b) grooves of B-DNA. Hydrogen-bond acceptors are red hydrogen-bond donors are blue. The methyl group of thymine is yellow, while the corresponding H atom of cytosine is white.

Especially, the subdivision in different hydrogen bond acceptor atom sets improves the performance of the SEN approach while a subdivision depending on the hydrogen bond donor atom showed only a minor improvement compared to the general fit of Reiher et al. Thus, the SEN approach has proven as a tool to investigate hydrogen bonds of, e.g., transition metal compounds (171,174-177), peptides (178), enzymes (179), DNA and RNA (173), molecular switches (180), ionic liquids (181,182), and rotaxanes (183). However, the SEN approach is not solely restricted to hydrogen bond detection. This approach can also be apphed to determine the covalent interaction between metal atoms (184) or phosphorus atoms (162,185). Therefore, it is suitable for different kind of interactions. 

Netropsin lying in the minor groove of B-DNA hydrogen-bonded to bases in the central ATAT tetranucleotide. From Coll et al,r... 

Alkaline treatment. Some authors have used this procedure [26,27,48]. It consists of adding to DNA an alkaline solution (e.g., 0.5 M NaOH solution). An increase in pH affects the ionisation of the functional groups of bases implied in the hydrogen bonds, thus decreasing the number of these bonds between the strands. It is a rapid and simple method. 

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