Rna backbone.stickpolarh

RNA backbone showing chemical groups. Foldit atom numbering is in black. The blue numbers 1' to 4' refer to the carbons in the in ribose ring. (Stick + polar H view.)

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

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

The sugar group in the RNA backbone is always a form of ribose, 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 RNA base is attached to carbon 1' of the ribose. A hydroxyl group (oxygen and hydrogen) is attached to carbon 2'. The hydroxyl group is what distinguishes RNA from DNA.

Foldit atom numberingEdit

Just as in a protein, Foldit can identify atom numbers in RNA. The rules for numbering atoms are different in RNA, 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 RNA, 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 ribose of the preceding segment, so only the oxygen atoms 2 through 4 are numbered.

Atom numbering continues with the ribose group. Atom 9 is an oxygen which joins the phosphate group of the next RNA segment. Atom 10 is a carbon (carbon 1'), which is where the actual RNA base is attached. Atom 12 is the oxygen in the hydroxyl group, which Foldit considers to be the first "sidechain" atom, meaning it's not part of the backbone.

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

For the last RNA segment in a chain, numbering is more straightforward. Since there's no next RNA 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 RNA is atom 13. In DNA, the oxygen at atom 12 is not present, and the first base atom is 12.


Unlike the backbone of a protein, RNA backbone doesn't contain any nitrogen atoms, so hydrogen bonding must involve oxygen atoms. The oxygens at 7 and 12 can act as either donors or acceptors. 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
12 oxygen yes yes
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