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 | 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 | 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 | |||
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 |
|
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 |
Amide moiety is vital to probe sensitivity.