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Chemical structure of nucleic acids

Last update on the 18th of September, 2017

In this work we lear to draw nucleotides, dsDNA and base pairs in MarvinSketch.

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Base pairs final.mrv

Nucleotides and dsDNA

nucl.mrv

Exercises are shown in figures 1 and 2.

Fig. 1. Several nucleotides drawn in MarvinSketch.
Fig. 2. Sample double strand DNA fragment.

Non-canonical base pairs

final.mrv

Usually nucleotides in nucleic acids connect in "canonical" base pairs (see example in figure 3): A=T and G≡C — with hydrogen bonds. Moreover, preferred tautomeric forms are lactamic and amino rather then lactimic and imino, respectively. However, we can guess non-canonical structures: various tautomeric forms, numerous interaction sites provide almost combinatorial number of possible pairs. Sample interactions of (deoxy)cytidine with other (deoxy)nucleosides are shown below.

Fig. 3. Canonical C≡G pair.

Deoxyadenosine

Fig. 3. Non-canonical C-A pairs.

The most plausible C-A pair is shown in fig. 3A: "normal" tautomers and good connectivity of hydrogen bonds in terms of distance and angles. The next is 3E because of normal tautomeric forms. Despite that, the distance between interacting atoms are bigger then in canonical pairs so this pair might be less stable. The 3A form exhibits good distance almost as in A-T pair but imino form if C makes it less possible. Forms 3B and 3D seem rather improbable as angles between hydrogen bonds are larger then in canonical pairs.

Deoxycytidine

Fig. 4. Non-canonical C-C pairs.

Cytidine dimers are shown in fig. 4. None of possible interaction are between normal tautomers. So that, 4B and 4C seem plausible as they contain one normal form and interacting atoms in both bases are neighbouring to each other. Then goes 4D and, finally, 4A. The last one is the least stable because of possible mutual repulsion of 4-imino groups. It ought to be said, that in regular dsDNA such interactions will lead to structure infractions.

Deoxyguanosine

Fig. 5. Non-canonical C-G pairs.

Interactions of C with G (fig. 5) are vast as both bases contain numerous donors and acceptors of hydrogen bonds. A form 5B seems most plausible because of three bonds although these tautomers are not likely to occur. 5A, 5D and 5F forms lose in stability to canonical C-G pair as 3N and 1N atoms in C and G, respectively, suffer loss of connection. 5C, 5E and 5G might be as stable as tautomeric forms are because of neighbouring interacting atoms in both bases. 5H is similar to 3E form in terms of geometry.

Deoxythymidine

Fig. 6. Non-canonical C-T pairs.

C-T interactions (fig. 6) are as less stable as C-C ones concernig dsDNA stability. Despite that, 6B and 6H pairs show significant strength due to three hydrogen bonds and normal tautomeric form of T in latter. Pairs 6A and 6D will suffer repulsion of 2-keto groups in spite of neighbouring atoms interaction. Form 6C will be less stable as 3N atoms suffer similar repulsion. In contrast, pairs 6E, 6F and 6G are better at placement of interacting atoms in bases. The most stable of them might be 6F as of normal T tautomer. As thymine is 5-methyluracil there is no purpose in studying C-U pairs.

Pseudouridine

Fig. 7. Non-canonical C-Ψ pairs.

Yet an interaction between C and Ψ might take place in some exotic situations. However, I came up with only interactions with abnormal tautomeric forms (see fig. 7). Both of them seem stable because of three hydrogen bonds looking quite similar to canonical C-G interaction. Taking into account normality of tautomers, pairs show parity as each pair contains one normal tautomer.