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. 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 Applicationref 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
D659 Tat–TAR binding

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

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

6.28 tCo B483 Klenow fragment DNA polymerase
B661 Structural measurements on DNA using FRET

6.29 Çf A662 Discrimination of all 4 bases

6.30 8-oxoG-Clamp C488490 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 dChpp A664 A vs. G detection

6.39 dCppi 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 detectiona
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 UP 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 CP B685 Molecular beacon/Thermal denaturation

6.59 AP 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 GP B685 Molecular beacon/Thermal denaturation
B669 B to Z transition

6.61 APY B691 RNA hybridization

6.62 UPE C675,692 Charge transfer studies

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

6.67 dApymcm 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)
B/C696 Groove polarity (minor and major of Z-DNA)

6.80 danG B/C500 Groove polarity (minor and major of A/B
DNA)
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 UFL 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
C710712 Abasic site structure/dynamics
C713 Strength of BP interactions
D656,714717 Aminoglycoside/RNA binding
B/C718720 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
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
B/C11 Major groove polarity

6.136 5-(fur-2-yl)U D595 Tat/TAR binding
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
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
a

Amide moiety is vital to probe sensitivity.