Question: What base is most commonly modified in RNA?
About the article "Nucleic acid sequence", section "Notation".

Candidate passages:
Each nucleotide in RNA contains a ribose sugar, with carbons numbered 1' through 5'.
A base is attached to the 1' position, in general, adenine (A), cytosine (C), guanine (G), or uracil (U).
Adenine and guanine are purines, cytosine and uracil are pyrimidines.
A phosphate group is attached to the 3' position of one ribose and the 5' position of the next.
The phosphate groups have a negative charge each at physiological pH, making RNA a charged molecule (polyanion).
The bases form hydrogen bonds between cytosine and guanine, between adenine and uracil and between guanine and uracil.
However, other interactions are possible, such as a group of adenine bases binding to each other in a bulge,or the GNRA tetraloop that has a guanine–adenine base-pair.
An important structural feature of RNA that distinguishes it from DNA is the presence of a hydroxyl group at the 2' position of the ribose sugar.
The presence of this functional group causes the helix to adopt the A-form geometry rather than the B-form most commonly observed in DNA.
This results in a very deep and narrow major groove and a shallow and wide minor groove.
A second consequence of the presence of the 2'-hydroxyl group is that in conformationally flexible regions of an RNA molecule (that is, not involved in formation of a double helix), it can chemically attack the adjacent phosphodiester bond to cleave the backbone.RNA is transcribed with only four bases (adenine, cytosine, guanine and uracil), but these bases and attached sugars can be modified in numerous ways as the RNAs mature.
Pseudouridine (Ψ), in which the linkage between uracil and ribose is changed from a C–N bond to a C–C bond, and ribothymidine (T) are found in various places (the most notable ones being in the TΨC loop of tRNA).
Another notable modified base is hypoxanthine, a deaminated adenine base whose nucleoside is called inosine (I).
Inosine plays a key role in the wobble hypothesis of the genetic code.
There are more than 100 other naturally occurring modified nucleosides, The greatest structural diversity of modifications can be found in tRNA, while pseudouridine and nucleosides with 2'-O-methylribose often present in rRNA are the most common.
The specific roles of many of these modifications in RNA are not fully understood.
However, it is notable that, in ribosomal RNA, many of the post-transcriptional modifications occur in highly functional regions, such as the peptidyl transferase center and the subunit interface, implying that they are important for normal function.
The functional form of single-stranded RNA molecules, just like proteins, frequently requires a specific tertiary structure.
The scaffold for this structure is provided by secondary structural elements that are hydrogen bonds within the molecule.
This leads to several recognizable "domains" of secondary structure like hairpin loops, bulges, and internal loops.
Since RNA is charged, metal ions such as Mg2+ are needed to stabilise many secondary and tertiary structures. 
RNA extraction is the purification of RNA from biological samples.
This procedure is complicated by the ubiquitous presence of ribonuclease enzymes in cells and tissues, which can rapidly degrade RNA.
Several methods are used in molecular biology to isolate RNA from samples, the most common of these is Guanidinium thiocyanate-phenol-chloroform extraction.RNA extraction in liquid nitrogen, commonly using a mortar and pestle, or specialised motorized grinding device cell lysis device is also useful in preventing ribonuclease activity. 
The northern blot is used to study the expression patterns of a specific type of RNA molecule as relative comparison among a set of different samples of RNA.
It is essentially a combination of denaturing RNA gel electrophoresis, and a blot.
In this process RNA is separated based on size and is then transferred to a membrane that is then probed with a labeled complement of a sequence of interest.
The results may be visualized through a variety of ways depending on the label used; however, most result in the revelation of bands representing the sizes of the RNA detected in sample.
The intensity of these bands is related to the amount of the target RNA in the samples analyzed.
The procedure is commonly used to study when and how much gene expression is occurring by measuring how much of that RNA is present in different samples.
It is one of the most basic tools for determining at what time, and under what conditions, certain genes are expressed in living tissues. 
The most commonly used and commercially available fluorescent base analogue, 2-aminopurine (2-AP), has a high-fluorescence quantum yield free in solution (0.68) that is considerably reduced (appr.
100 times but highly dependent on base sequence) when incorporated into nucleic acids.
The emission sensitivity of 2-AP to immediate surroundings is shared by other promising and useful fluorescent base analogues like 3-MI, 6-MI, 6-MAP, pyrrolo-dC (also commercially available), modified and improved derivatives of pyrrolo-dC, furan-modified bases and many other ones (see recent reviews).
This sensitivity to the microenvironment have been utilized in studies of e.g.
structure and dynamics within both DNA and RNA, dynamics and kinetics of DNA-protein interaction and electron transfer within DNA.
A newly developed and very interesting group of fluorescent base analogues that has a fluorescence quantum yield that is nearly insensitive to their immediate surroundings is the tricyclic cytosine family.
1,3-Diaza-2-oxophenothiazine, tC, has a fluorescence quantum yield of approximately 0.2 both in single- and in double-strands irrespective of surrounding bases.
Also the oxo-homologue of tC called tCO (both commercially available), 1,3-diaza-2-oxophenoxazine, has a quantum yield of 0.2 in double-stranded systems.
However, it is somewhat sensitive to surrounding bases in single-strands (quantum yields of 0.14–0.41).
The high and stable quantum yields of these base analogues make them very bright, and, in combination with their good base analogue properties (leaves DNA structure and stability next to unperturbed), they are especially useful in fluorescence anisotropy and FRET measurements, areas where other fluorescent base analogues are less accurate.
Also, in the same family of cytosine analogues, a FRET-acceptor base analogue, tCnitro, has been developed.
Together with tCO as a FRET-donor this constitutes the first nucleic acid base analogue FRET-pair ever developed.
The tC-family has, for example, been used in studies related to polymerase DNA-binding and DNA-polymerization mechanisms. 
Pseudouridine (abbreviated by the Greek letter psi- Ψ) is the "C"-glycoside isomer of the nucleoside uridine, and it is the most prevalent of the over one hundred different modified nucleosides found in RNA.
Ψ is found in all species and in many classes of RNA except mRNA.
Ψ is formed by enzymes called Ψ synthases, which post-transcriptionally isomerize specific uridine residues in RNA in a process termed "pseudouridylation".
It is commonly found in tRNA, associated with thymidine and cytosine in the TΨC arm and is one of the invariant regions of tRNA.
The function of it is not very clear, but it is expected to play a role in association with aminoacyl transferases during their interaction with tRNA, and hence in the initiation of translation.
Recent studies suggest it may offer protection from radiation.