Editing RNA (section)

===Secondary and tertiary structures===
The functional form of single-stranded RNA molecules, just like proteins, frequently requires a specific spatial [[RNA Tertiary Structure|tertiary structure]]. The scaffold for this structure is provided by [[secondary structure|secondary structural]] elements that are hydrogen bonds within the molecule. This leads to several recognizable "domains" of secondary structure like [[hairpin loop]]s, bulges, and [[internal loop]]s.<ref>{{cite journal | vauthors = Mathews DH, Disney MD, Childs JL, Schroeder SJ, Zuker M, Turner DH | title = Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 101 | issue = 19 | pages = 7287–92 | date = May 2004 | pmid = 15123812 | pmc = 409911 | doi = 10.1073/pnas.0401799101 | bibcode = 2004PNAS..101.7287M | doi-access = free }}</ref> In order to create, i.e., design, RNA for any given secondary structure, two or three bases would not be enough, but four bases are enough.<ref>{{cite journal | vauthors = Burghardt B, Hartmann AK |
title = RNA secondary structure design | journal = Physical Review E | volume = 75 | issue = 2 | pages = 021920 | date = February 2007 | doi = 10.1103/PhysRevE.75.021920 |
pmid = 17358380 | url = https://link.aps.org/doi/10.1103/PhysRevE.75.021920| arxiv = physics/0609135 |
bibcode = 2007PhRvE..75b1920B |
s2cid = 17574854 }}</ref> This is likely why nature has "chosen" a four base alphabet: fewer than four would not allow the creation of all structures, while more than four bases are not necessary to do so. Since RNA is charged, metal ions such as [[Magnesium|Mg<sup>2+</sup>]] are needed to stabilise many secondary and [[RNA Tertiary Structure|tertiary structures]].<ref>{{cite journal | vauthors = Tan ZJ, Chen SJ | title = Salt dependence of nucleic acid hairpin stability | journal = Biophysical Journal | volume = 95 | issue = 2 | pages = 738–52 | date = July 2008 | pmid = 18424500 | pmc = 2440479 | doi = 10.1529/biophysj.108.131524 | bibcode = 2008BpJ....95..738T }}</ref>

The naturally occurring [[enantiomer]] of RNA is <small>D</small>-RNA composed of <small>D</small>-ribonucleotides. All chirality centers are located in the <small>D</small>-ribose. By the use of <small>L</small>-ribose or rather <small>L</small>-ribonucleotides, <small>L</small>-RNA can be synthesized. <small>L</small>-RNA is much more stable against degradation by [[ribonuclease|RNase]].<ref name="pmid25236655">{{cite journal | vauthors = Vater A, Klussmann S | title = Turning mirror-image oligonucleotides into drugs: the evolution of Spiegelmer(®) therapeutics | journal = Drug Discovery Today | volume = 20 | issue = 1 | pages = 147–55 | date = January 2015 | pmid = 25236655 | doi = 10.1016/j.drudis.2014.09.004 | doi-access = free }}</ref>

Like other structured [[biopolymer]]s such as proteins, one can define topology of a folded RNA molecule. This is often done based on arrangement of intra-chain contacts within a folded RNA, termed as [[circuit topology]].