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This is due, on the one hand, to the smallness of the dimensions on which we are moving

here, namely a few angstroms (Å, i.e. ten billionths of a metre), as well as to the special

properties of RNA. It is not as stable as deoxyribonucleic acid, i.e. DNA, which is therefore

very suitable as a long-term storage medium. RNA stores for shorter times, after which it can

either be digested with its additional OH group or otherwise continue to react. And this is

also the reason for its “magic” activity, it can accelerate or advance a reaction at the same time.

This also makes it clear what existed before today’s division of labor between genetic

information (DNA) and enzymatic action (proteins): namely, the RNA world. That was

more than 3 billion years ago. The first cells were just coming into being, and it was there

that RNA nucleotides of varying lengths both stored information and accelerated reac­

tions. The oldest molecule was an RNA polymerase made of RNA, which catalytically

transcribed its description, faster than it was destroyed by environmental stresses. If you

still want to know what was before RNA: metabolism on surfaces that held certain mole­

cules and obtained energy from sulfur compounds until the first membranes and first

nucleotides accumulated more and more on these surfaces (Scheidler et al. 2016).

Since that time, RNA has been essential for all life. The protein factories (ribosomes)

of the body consist of RNA in their central parts. All peptide bonds in the ribosome are

made by catalytic ribosomal RNA (rRNA), and many vitamins and excipients in our

enzymes are still made of nucleotides (especially adenine, e.g. FAD, NAD, NADH, NADP,

NADPH, cAMP, ATP, etc.).

But that’s not all: RNA can not only build proteins (with the help of tRNA and rRNA),

whereby the genes are transcribed via mRNA (messenger RNA), but there are also numer­

ous regulatory functions of RNA. As microRNA (miRNA), it degrades messenger RNA

more quickly (and one small molecule directs many, sometimes hundreds of messenger

RNAs), as long non-coding RNA (lncRNA) it even switches off entire chromosomes, as

smallRNA (sRNA) in bacteria it switches off or on promoters or individual genes, as a

riboswitch (e.g. riboswitch finder [https://riboswitch.bioapps.biozentrum.uni-­wuerzburg.

de/]) it allows or rejects the translation of genes.

It can be seen that an important part of bioinformatics is trying to identify and describe

the function and hidden signals in RNA molecules. The basic question is: Where is the

signal in the RNA molecule? First, in the order of its building blocks, i.e. in the nucleotides

(the so-called sequence), but then also in the folding of the RNA, the secondary structure,

how the RNA forms. In addition, one can also look at how stable the folding of the RNA

is, the so-called folding energy.

So, with these three characteristics, I can check a wide range of RNA molecules if I know

what sequence, secondary structure, and energy the RNA molecule must have for a particu­

lar property. For example, one can check all three characteristics for a number of molecules

using the RNAAnalyzer program or look up exciting RNA types in the Rfam database.

2  Magic RNA