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DNA backbone

DNA backbone showing chemical groups. Foldit atom numbering is in black. The blue numbers 1' to 4' refer to the carbons in the in deoxyribose ring.

DNA backbone is more complicated than the backbone of the amino acids in a protein.

DNA backbone is highly similar to RNA backbone. The difference is that RNA backbone contains the sugar ribose, while DNA backbone contains the sugar deoxyribose. This is why "RNA" stands for "ribonucleic acid", and "DNA" stands for "deoxyribonucleic acid".

Both DNA and RNA backbone consists of alternating groups phosphates and sugars. A phosphate group consists of a phosphorous atom bound to four oxygen atoms. Each segment of DNA or RNA is linked to the next by a phosphate.

The sugar group in the DNA backbone is always a form of deoxyribose, a pentagonal ring consisting of an oxygen atom and four carbon atoms. The carbon atoms are referred to as 1', 2', 3' and 4'. The DNA base is attached to carbon 1' of the deoxyribose.

In RNA, a hydroxyl group (oxygen and hydrogen) is attached to carbon 2'. This group is not present in DNA. The hydroxyl group is what distinguishes RNA from DNA.

Foldit atom numberingEdit

Caution: atom numbering for DNA has not been validated. DNA has only been found in intro puzzles to date, which don't allow the use of the recipes used to verify RNA atom numbering. The statements below are based on the similarities between RNA and DNA.

Just as in a protein, Foldit can identify atom numbers in DNA. The rules for numbering atoms are different in DNA, however. In a protein, the number of atoms in a segment is different depending on its position in the chain. For example, the C terminal of a chain has an extra backbone atom, so it's beta carbon, the first atom of the sidechain, is 6 instead of 5.

For DNA, the backbone atoms always have the same number, regardless position in the chain. Foldit starts numbering with the phosphorous in the phosphate group. Foldit considers one of the oxygen atoms of the phosphate to belong to the deoxyribose of the preceding segment, so only the oxygen atoms 2 through 4 are numbered.

Atom numbering continues with the dexoyribose group. Atom 9 is an oxygen which joins the phosphate group of the next DNA segment. Atom 10 is a carbon (carbon 1'), which is where the actual DNA base is attached.

For the first DNA segment in a chain, the phosphate group is missing. The first atom visible is atom 5, a carbon attached to the deoxyribose ring. Foldit still identifies atoms 1 through 4 as being present, and these "virtual atoms" can even be banded.

For the last DNA segment in a chain, numbering is more straightforward. Since there's no next DNA segment, the oxygen at atom 9 is not attached to a phosphate group. Atom numbering continues normally from there, and no "virtual atoms" are involved.

The first atom of the base in DNA is atom 12. In RNA, atom 12 is the oxygen in the hydroxyl group, and the first base atom is 13.

BondingEdit

Unlike the backbone of a protein, DNA backbone doesn't contain any nitrogen atoms, so hydrogen bonding must involve oxygen atoms. The oxygens at atom 7 can act as either a donor or an acceptor.. The other oxygens in the backbone can only act as hydrogen bond acceptors.

The table below summarizes the possibilities.

atom element acceptor donor
2 oxygen yes no
3 oxygen yes no
4 oxygen yes no
7 oxygen yes yes
9 oxygen yes no
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