. Author manuscript; available in PMC: 2011 May 12.

Published in final edited form as: Chem Rev. 2010 May 12;110(5):2579–2619. doi: 10.1021/cr900301e

Table 20.

Fluorescent Nucleosides and Some of Their Typical Applications

	#	Probe name	Application^ref	Remarks
Chromophoric base analogs	6.9	Coumarin		Time resolved Stokes shift:
			C⁴²⁸	Helix interior
			C⁴⁴⁶	Sequence dependence
			C⁴⁴⁷,⁴⁴⁸	Counter ions
			C⁴⁵⁰	Structural changes/probe position
			C⁴⁴⁴,⁴⁴⁵,⁴⁵¹	Probe position
			B⁴⁴⁹	Endonuclease APE1

	6.14	M	B⁶⁵⁴	Denaturation

	6.15	O	B⁶⁵⁴	Denaturation

	6.18	Nile red nucleoside	E⁴³¹	Influence of β-cyclodextrin on emission maximum

Pteridines	6.19	3-MI	B⁴⁵⁶,⁴⁵⁷	HIV-1 Intergrase activity
			B/C⁴⁵⁶,⁶⁵⁵	DNA-HU interactions
			B/C⁴⁵⁶	Interaction of DNA with RNA polymerase
			D⁶⁵⁶	Aminoglycoside/RNA binding
			B⁴⁵⁶,⁶⁴³	Detection of complementary strand
			C⁴⁵⁶	Alkyl transferase
			E⁴⁵⁶,⁶⁴³	Cellular uptake of oligonucleotides

	6.20	6-MI	B⁶⁵⁷	RecA-DNA interactions
			B/C⁴⁵⁶	Interaction of DNA with RNA polymerase
			D⁶⁵⁶	Monitoring Aminoglycoside/RNA binding

	6.22	6-MAP	C⁴⁵⁶,⁶⁵⁸	Investigating A-tracts

Expanded nucleobases	6.23	Etheno-A	B⁶⁵⁷	RecA-DNA interactions

	6.24	Benzo-A	C⁴⁷⁰	Base pairing/stacking effects

	6.25	BgQ	B⁴⁷⁶,⁴⁷⁷	Triplex formation
	6.25	BgQ	D⁶⁵⁹	Tat–TAR binding

	6.26	C_f	B⁴⁷⁶,⁴⁷⁷	Triplex formation
	6.26	C_f	D⁶⁶⁰	Bleomycin analogs cleavage of DNA

	6.27	tC	B⁴⁸³,⁴⁸⁵	Klenow fragment DNA polymerase
	6.27	tC	B⁶⁶¹	Structural measurements on DNA using FRET

	6.28	tC^o	B⁴⁸³	Klenow fragment DNA polymerase
	6.28	tC^o	B⁶⁶¹	Structural measurements on DNA using FRET

	6.29	Ç^f	A⁶⁶²	Discrimination of all 4 bases

	6.30	8-oxoG-Clamp	C⁴⁸⁸–⁴⁹⁰	Detection of 8-oxoG (free nucleoside and incorporated into an oligonucleotide)

	6.31	BPP	A⁴⁹²	A vs. G detection

	6.32	NPP	A⁴⁹³,⁶⁶³	A vs. G detection

	6.33	^MDA	A⁴⁹⁴	T vs. C detection

	6.34	^MDI	A⁴⁹⁴	T vs. C detection

	6.35	dC^hpp	A⁶⁶⁴	A vs. G detection

	6.39	dC^ppi	A⁶⁶⁵	A vs. G detection

Extended nucleobases	6.51	^PYU	A⁶⁶⁶	A vs. C detection
			B⁶⁶⁷	RNA poly(A) tracts
			C⁶⁶⁸	Detection of T•Hg•T base pairs

	6.52	^PYC	A⁶⁶⁶	G vs. T detection^a
	6.52	^PYC	B⁶⁶⁹	B to Z transition

	6.53	DMAP-^PYU	B⁵¹⁴	Dual emission

	6.54	5-(1-pyrenyl)-dU	B⁶⁷⁰	Multiple consecutive modified nucleosides

	6.55	8-(1-pyrenyl)-dG	A/B⁴²²	Mismatch vs. perfect complement Detection/Charge transfer studies

	6.57	U^P	B⁶⁷¹	B to Z transition
			B⁶⁷²	Molecular beacons
			B⁶⁷³	Probe base pairing interactions
			C⁵¹⁰,⁶⁷⁴,⁶⁷⁵	Charge transfer studies
			C⁶⁷⁶	HIV TAR RNA base conformations
			B⁶⁷⁷	Hybridization detection
			A⁶⁷⁸	Mismatch vs perfect complement detection
			B⁶⁷⁹	Multiple consecutive modified nucleosides
			A⁶⁸⁰	A vs. C/G/T detection
			C⁶⁸¹	Ultrafast structural dynamics
			B⁶⁸²	Duplex stability
			A⁶⁸³	Mismatch detection
			E⁶⁸⁴	White-light-emitting DNA

	6.58	C^P	B⁶⁸⁵	Molecular beacon/Thermal denaturation

	6.59	A^P	B⁶⁷¹	B to Z transition
			B⁶⁷²,⁶⁸⁶	Molecular beacons
			B⁶⁷³	Probe base pairing interactions
			B⁶⁷⁸,⁶⁸⁸	G-quadruplex transition
			A⁶⁸⁰	A vs. C/G/T detection
			A⁶⁸⁹	Homoadenine signalling system for SNP typing
			B⁶⁹⁰	Photophysics of modified poly-A oligonucleotides

	6.60	G^P	B⁶⁸⁵	Molecular beacon/Thermal denaturation
	6.60	G^P	B⁶⁶⁹	B to Z transition

	6.61	A^PY	B⁶⁹¹	RNA hybridization

	6.62	U^PE	C⁶⁷⁵,⁶⁹²	Charge transfer studies

	6.66	5-(perylen-3-ylethynyl)dU	B⁶⁸²	Duplex stability
	6.66	5-(perylen-3-ylethynyl)dU	A⁶⁸³	Mismatch detection

	6.67	dA^pymcm	A and B⁶⁹³	Mismatch vs. perfect complement detection Hanging vs. blunt ends detection

	6.68	^MMeU	B⁴⁹⁷	Hybridization detection

	6.69	^PHU	B⁴⁹⁷	Hybridization detection

	6.70	^MeOPhU	B⁴⁹⁷	Hybridization detection

	6.71	^PYA	A⁶⁹⁴	C vs. T detection

	6.74	^DNCU	B/C⁶⁹⁵	Polarity inside DNA-binding protein (KF)

	6.75	^PDNU	A⁴⁹⁹	Mismatch vs. perfect complement detection

	6.76	^PDNC	A⁴⁹⁹	Mismatch vs. perfect complement detection

	6.77	^PDNA	A⁴⁹⁹	Mismatch vs. perfect complement detection

	6.78	^PDNG	A⁴⁹⁹	Mismatch vs. perfect complement detection

	6.79	^danC	B/C⁵⁰⁰	Groove polarity (minor and major of A/B DNA)
	6.79	^danC	B/C⁶⁹⁶	Groove polarity (minor and major of Z-DNA)

	6.80	^danG	B/C⁵⁰⁰	Groove polarity (minor and major of A/B DNA)
	6.80	^danG	B/C⁶⁹⁶	Groove polarity (minor and major of Z-DNA)

	6.81	5-aminodansyl-dU	B/C⁵⁰¹,⁶⁹⁷,⁶⁹⁸	Groove polarity (major/minor interactions and sequence dependence)

	6.82	2-Anthracenecarboxamide-dU	A⁶⁹⁹	Mismatch vs. perfect complement detection

	6.83	9-Anthracenecarboxamide-dU	A⁶⁹⁹	Mismatch vs. perfect complement detection

	6.84	NeT	A/B⁷⁰⁰	A vs. G detection/Hybridization detection

	6.85	AeT	A/B⁷⁰⁰	A vs. G detection/Hybridization detection

	6.86	AeeT	A/B⁷⁰⁰	A vs. G detection/Hybridization detection

	6.87	U^FL	A⁵⁰²	Mismatch vs. perfect complement detection

	6.96.c	5-[3(phen)ethynyl]dU	A⁵³¹	Discrimination of all 4 bases

	6.98.g	5-[5-Ru(bpy)₃ethynyl] dU-TP	A⁵³⁸	Luminescent and electrochemical detection

	6.104.g	5-[5-Ru(bpy)₃ethynyl] dC-TP	A⁵³⁸	Luminescent and electrochemical detection

	6.111.g	7-[7-deaza-5-Ru(bpy)₃ ethynyl]dG-TP	A⁵³⁸	Luminescent and electrochemical detection

	6.116.g	7-[7-deaza-5-Ru(bpy)₃ ethynyl]dA-TP	A⁵³⁸	Luminescent and electrochemical detection

Isomorphic nucleobases	6.123	2-AP	B⁷⁰¹	Molecular beacon
			B⁷⁰²	Duplex denaturation
			B⁷⁰³	Helicase activity
			B⁷⁰⁴	Hammerhead ribozyme
			B⁷⁰⁵	DNA polymerase fidelity in vitro
			B⁶⁵⁷	RecA-DNA interactions
			B⁷⁰⁶	HIV-I DIS RNA structure
			B/D⁷⁰⁷	G-quadruplex structure and ligand binding
			C⁷⁰⁸	Local conformation via CD
			C⁷⁰²,⁷⁰⁹	Base flipping
			C⁷¹⁰–⁷¹²	Abasic site structure/dynamics
			C⁷¹³	Strength of BP interactions
			D⁶⁵⁶,⁷¹⁴–⁷¹⁷	Aminoglycoside/RNA binding
			B/C⁷¹⁸–⁷²⁰	Interaction of DNA with RNA polymerase

	6.126	8-vinyl-6-aminopurine	A⁷²¹	short/long excited state lifetimes

	6.127	2-amino-6-(2-thienyl)purine	B⁵⁷¹	Detection of fluorescently labeled complementary strand
	6.127	2-amino-6-(2-thienyl)purine	B⁵⁶⁹	Denaturation of RNA (hairpin and tRNA)

	6.128	2-amino-6-(2-thiazolyl)purine	B⁵⁷¹	Detection of fluorescently labeled complementary strand

	6.129	m⁵K	B⁶⁵⁷,⁷²²	ssDNA–Escherichia coli RecA binding

	6.130	pC	A⁶⁰⁹	Mismatch vs. perfect complement detection
			B²⁰	Duplex denaturation
			B⁷⁰¹	Molecular beacon
			B⁶⁰⁸	Hybridization detection
			C⁷²³	Local conformation via CD
			C/D⁷²⁴	Metal ion biosensors
			B⁷²⁵	DNA–reverse transcriptase binding
			B⁶⁰⁷,⁷²⁶	T-7 RNA polymerase
			C⁷²⁷	Base flipping
			B⁷²⁸	tRNA conformations

	6.131	^MMepC	B⁶⁰⁸	Hybridization detection

	6.132	^PhpC	A⁶⁰⁹	Mismatch vs. perfect complement detection

	6.133	^PyIpC	B⁷²⁹	Molecular beacon

	6.134	^PyIIpC	B⁷²⁹	Molecular beacon

	6.135	5-(fur-2-yl)dU	C⁵⁸⁹	Abasic site detection
	6.135	5-(fur-2-yl)dU	B/C¹¹	Major groove polarity

	6.136	5-(fur-2-yl)U	D⁵⁹⁵	Tat/TAR binding
	6.136	5-(fur-2-yl)U	D⁵⁹¹	aminoglycoside/A-site binding

	6.141	5-(fur-2-yl)dC	C⁵⁹⁶	Detection of 8-oxoG and its transverse mutation product

	6.161	Thieno[3,4-d]-U	A⁵⁹⁷	C mismatch detection
	6.161	Thieno[3,4-d]-U	B/C⁵⁹⁹	Activity of toxic ribosome-inactivating protiens

	6.162	^BTU	B⁵⁴⁸	Hybridization detection

	6.168	5-MeOQuinazolinedione	D⁶⁰⁰	FRET enabled detection of aminglycoside- RNA binding

Amide moiety is vital to probe sensitivity.