Use of Specific Chemical Reagents for Detection of Modified Nucleotides in RNA

Table 1

Known RNA modifications and their abbreviations and symbols (modified nucleosides mentioned in the text are indicated in bold).

Number	Symbol	Common name
(1)	m^1A	1-methyladenosine
(2)	m^2A	2-methyladenosine
(3)	m^6A	N^6-methyladenosine
(4)	Am	𝟐^′ -O-methyladenosine
(5)	ms^2m^6A	2-methylthio-N^6-methyladenosine
(6)	i^6A	N^6-isopentenyladenosine
(7)	ms^2i^6A	2-methylthio- N^6 -isopentenyladenosine
(8)	io^6A	N^6-(cis-hydroxyisopentenyl)adenosine
(9)	ms^2io^6A	2-methylthio-N^6-(cis-hydroxyisopentenyl) adenosine
(10)	g^6A	N ^6-glycinylcarbamoyladenosine
(11)	t^6A	N ^6-threonylcarbamoyladenosine
(12)	ms^2t^6A	2-methylthio-N 6 -threonyl carbamoyladenosine
(13)	m^6t^6A	N ^6-methyl-N 6 -threonylcarbamoyladenosine
(14)	h 𝐧^6 A	N ^6-hydroxynorvalylcarbamoyladenosine
(15)	ms^2h 𝐧^6 A	2-methylthio-N 6 -hydroxynorvalyl carbamoyladenosine
(16)	Ar(p)	2′-O-ribosyladenosine (phosphate)
(17)	I	inosine
(18)	m^1I	1-methylinosine
(19)	m^1Im	1,2′-O-dimethylinosine
(20)	m^3C	3-methylcytidine
(21)	m^5C	5-methylcytidine
(22)	Cm	2 ′ -O-methylcytidine
(23)	s^2C	2-thiocytidine
(24)	ac^4C	N ^4-acetylcytidine
(25)	f^5C	5-formylcytidine
(26)	m^5Cm	5,2′-O-dimethylcytidine
(27)	ac^4Cm	N ^4-acetyl-2′-O-methylcytidine
(28)	k^2C	lysidine
(29)	m^1G	1-methylguanosine
(30)	m^2G	N^2-methylguanosine
(31)	m^7G	7-methylguanosine
(32)	Gm	2 ′ -O-methylguanosine
(33)	m^22G	N^2,N^2-dimethylguanosine
(34)	m^2Gm	N^2,2′-O-dimethylguanosine
(35)	m^22Gm	N^2,N^2,2′-O-trimethylguanosine
(36)	Gr(p)	2′-O-ribosylguanosine (phosphate)
(37)	yW	wybutosine
(38)	o2yW	peroxywybutosine
(39)	OHyW	hydroxywybutosine
(40)	OHyW*	undermodified hydroxywybutosine
(41)	imG	wyosine
(42)	mimG	methylwyosine
(43)	Q	queuosine
(44)	oQ	epoxyqueuosine
(45)	galQ	galactosyl-queuosine
(46)	manQ	mannosyl-queuosine
(47)	preQ0	7-cyano-7-deazaguanosine
(48)	preQ1	7-aminomethyl-7-deazaguanosine
(49)	G^+	archaeosine
(50)	Ψ	pseudouridine
(51)	D	dihydrouridine
(52)	m^5U	5-methyluridine
(53)	Um	2 ′ -O-methyluridine
(54)	m^5Um	5,2′-O-dimethyluridine
(55)	m^1Ψ	1-methylpseudouridine
(56)	Ψm	2′-O-methylpseudouridine
(57)	s^2U	2-thiouridine
(58)	s^4U	4-thiouridine
(59)	m^5s^2U	5-methyl-2-thiouridine
(60)	s^2Um	2-thio-2′-O-methyluridine
(61)	acp^3U	3-(3-amino-3-carboxypropyl)uridine
(62)	ho^5U	5-hydroxyuridine
(63)	mo^5U	5-methoxyuridine
(64)	cmo^5U	uridine 5-oxyacetic acid
(65)	mcmo^5U	uridine 5-oxyacetic acid methyl ester
(66)	chm^5U	5-(carboxyhydroxymethyl)uridine
(67)	mchm^5U	5-(carboxyhydroxymethyl)uridine methyl ester
(68)	mcm^5U	5-methoxycarbonylmethyluridine
(69)	mcm^5Um	5-methoxycarbonylmethyl-2′-O-methyluridine
(70)	mcm^5s^2U	5-methoxycarbonylmethyl-2-thiouridine
(71)	nm^5s^2U	5-aminomethyl-2-thiouridine
(72)	mnm^5U	5-methylaminomethyluridine
(73)	mnm^5s^2U	5-methylaminomethyl-2-thiouridine
(74)	mnm^5se^2U	5-methylaminomethyl-2-selenouridine
(75)	ncm^5U	5-carbamoylmethyluridine
(76)	ncm^5Um	5-carbamoylmethyl-2′-O-methyluridine
(77)	cmnm^5U	5-carboxymethylaminomethyluridine
(78)	cmnm^5Um	5-carboxymethylaminomethyl-2 ′ -O-methyluridine
(79)	cmnm^5s^2U	5-carboxymethylaminomethyl-2-thiouridine
(80)	m^62A	N^6,N^6-dimethyladenosine
(81)	Im	2′-O-methylinosine
(82)	m^4C	N^4-methylcytidine
(83)	m^4Cm	N^4,2′-O-dimethylcytidine
(84)	hm^5C	5-hydroxymethylcytidine
(85)	m^3U	3-methyluridine
(86)	m^1acp^3Ψ	1-methyl-3-(3-amino-3-carboxypropyl) pseudouridine
(87)	cm^5U	5-carboxymethyluridine
(88)	m^6Am	N^6,2′-O-dimethyladenosine
(89)	m^62Am	N^6,N^6,2′-O-trimethyladenosine
(90)	m^2,7G	N^2,7-dimethylguanosine
(91)	m^2,2,7G	N^2,N^2,7-trimethylguanosine
(92)	m^3Um	3,2′-O-dimethyluridine
(93)	m^5D	5-methyldihydrouridine
(94)	m^3Ψ	3-methylpseudouridine
(95)	f^5Cm	5-formyl-2′-O-methylcytidine
(96)	m^1Gm	1,2′-O-dimethylguanosine
(97)	m^1Am	1,2′-O-dimethyladenosine
(98)	τm^5U	5-taurinomethyluridine
(99)	τm^5s^2U	5-taurinomethyl-2-thiouridine
(100)	imG-14	4-demethylwyosine
(101)	imG2	isowyosine
(102)	ac^6A	N^6-acetyladenosine
(103)	inm^5U	5-(isopentenylaminomethyl)uridine
(104)	inm^5s^2U	5-(isopentenylaminomethyl)-2-thiouridine
(105)	inm^5Um	5-(isopentenylaminomethyl)-2′-O-methyluridine
(106)	m^2,7Gm	N^2,7,2′-O-trimethylguanosine
(107)	m^42Cm	N^4,N^4,2 ′-O-trimethylcytidine
(108)	m^8A	8-methyladenosine

Numbering and abbreviations of modified nucleosides are from “The RNA modification Database,” http://s59.cas.albany.edu/RNAmods/.