FRET - Förster Resonance Energy Transfer || Data

Part FourSupporting Information and Conclusions

FRET – Förster Resonance Energy Transfer: From Theory to Applications, First Edition.Edited by Igor Medintz and Niko Hildebrandt.� 2014 Wiley-VCH Verlag GmbH & Co. KGaA. Published 2014 by Wiley-VCH Verlag GmbH & Co. KGaA.

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14DataAlice G. Byrne, Matthew M. Byrne, George Coker III, Kelly B. Gemmill,Christopher Spillmann, Igor Medintz, Seth L. Sloan, and B. Wieb van der Meer

In this chapter, we present FRET data using the following tables:

These tables contain F€orster distances and other information about donorsand acceptors. The chromophores, donors, and/or acceptors belong to threegroups:

1) Traditional probes (i.e., probes that are neither fluorescent proteins nor quantumdots)

2) Fluorescent proteins3) Quantum dots

Table Description

Table 14.1 The Steinberg R0 tableTable 14.2 The Fairclough–Cantor R0 tableTable 14.3 The Kawski R0 tableTable 14.4 The 17 “families” of traditional dyesTable 14.5 The official names of the dyes in Table 14.6Table 14.6 Donor–acceptor pairsTable 14.7 Acceptor–donor pairsTable 14.8 New traditional probes (more recent than 1993)Table 14.9 Selected data on fluorescent protein donor–acceptor

interactionsTable 14.10 Quantum dot donor to non quantum dot acceptor tableTable 14.11 Non quantum dot donor to quantum dot acceptor tableTable 14.12 Table of quantum dot–quantum pairsTable 14.13 (andFigure 14.26)

Donor–acceptor pairs with a F€orster distance in a givenrange

j657

FRET – Förster Resonance Energy Transfer: From Theory to Applications, First Edition.Edited by Igor Medintz and Niko Hildebrandt.� 2014 Wiley-VCH Verlag GmbH & Co. KGaA. Published 2014 by Wiley-VCH Verlag GmbH & Co. KGaA.

The tables are either previously published tables with information on traditionalprobes or new tables for traditional probes that are more recent than 1993,fluorescent proteins, and quantum dots. The previously published tables are theSteinberg table (Table 14.1) [1], the Fairclough–Cantor table (Table 14.2) [2], theKawski table (Table 14.3) [3], and the set of tables published by van der Meer, Coker,and Chen (Tables 14.4–14.8) [4]. These tables are presented exactly as they appearedpreviously with minor modifications: tables have been renumbered, distances are

given in nanometers instead of A�ngstr€om, a percent difference column has been

added to Table 14.6, printing errors that created duplicate data, and other similarerrors have been rectified. Moreover, donor–acceptor pair numbers (abbreviated asD:A No.) have been added to all tables about pairs. The sole purpose of this donor–acceptor pair number is to enable convenient cross-referencing. For example, onecan search for a pair by first selecting an acceptor in Table 14.7, followed by findingan appropriate donor in the same table, and then find more detailed information inTable 14.6 by locating the desired pair number. The first 12 tables are more or less inchronological order, but the final table (Table 14.13) contains information fromprevious tables and lists donor–acceptor pairs with F€orster distances in a givenrange, varying from 0–0.49 nm to more than 7 nm. In this table, the D:A pairnumber also plays an essential role. Figure 14.26 shows the frequency distributionof donor–acceptor pairs in a graphical form.

14.1Tables before 1987

The information of the Steinberg table [1] is given in Table 14.1, the table ofFairclough and Cantor [2] is presented in Table 14.2, and the homotransfer datapresented by Kawski [3] are shown in Table 14.3. Kawski has also collected data onthe F€orster distance for homotransfer between chlorophyll a molecules in varioustwo-dimensional solutions (for more recent data see Ref. [20] of Chapter 3). Thisdistance is in the 5.0–9.0 nm range. As already mentioned, these tables are identicalto the original tables except for minor changes and that the distances are in

nanometers (not in A�ngstr€oms) and that a donor–acceptor pair number is listed

for convenience.

14.2Introduction to the Table of Traditional Chromophores

Molecules or compounds that have been widely used as traditional FRETdonors oracceptors are listed in Table 14.5, in which the strongest long-wavelength absorptionpeak (ABS) and the wavelength of maximum fluorescence intensity (EM) are alsoshown. They are organized into 17 families, listed in Table 14.4, on the basis of theirparent molecular structure and are listed according to the order of their ABSs exceptfor the last two families, identified as L and O. Molecules or compounds in each of

658j 14 Data

Table 14.1 The Steinberg R0 table.

D:A No. Donor–acceptor pair R0 [2/3] (nm)

1 Phenol–phenol 1.1–1.72 Indole–indole 1.6–2.33 Phenol–indole 1.5–1.94 Phe–Phe 0.5–0.75 Phe–Tyr 1.2–1.36 Phe–Trp 1.6–1.97 Phe–Tyr� 1.458 Tyr–Phe 0.29 Tyr–Tyr 0.7–0.910 Tyr–Trp 1.3–1.511 Tyr–Tyr� 1.3–1.512 Trp–Tyr 0.2113 Trp–Trp 0.5–0.714 Trp–Tyr� 0.8–1.315 Tyr�–Trp 0.4316 Phe–CO:heme 2.217 Trp–heme 2.518 Phe–CO:heme 3.1–3.719 Trp–heme 2.820 Tyr–ITyr 1.3421 Tyr–I2Tyr 1.4922 Tyr–thyroxine 1.7423 Trp–ITyr 0.7924 Trp–I2Tyr 1.0525 Trp–thyroxine 1.5426 Tyr–DNS 2.027 Trp–DNS 2.128 DNS–DNS 0.929 DNS–heme (Fe3þ) 5.830 DNS–heme (Fe2þ) 6.331 ANS–ANS 2.432 Trp–anthraniloyl 2.033 Trp–PMP 1.6–2.4a)

34 PMP–PMP 0.735 Trp–Cu:transferrin 1.836 Trp–Fe: transferrin 2.137 Trp–Cu:O2 hemocyanin 2.75b)

38 Tyr–NADH 2.539 Trp–NADH 2.5

Data onR0 [2/3], the F€orster distance at k2¼ 2/3, for various donor–acceptor pairs fromRef. [1], in which

details and the original references can be found. D:A No.: donor–acceptor pair number. Phe:phenylalanine, Tyr: tyrosine, Tyr�: ionized tyrosine, ITyr: monoiodotyrosine, I2Tyr: diiodotyrosine,Trp: tryptophan, DNS: 1-dimethyl-aminonaphthalene-5-sulfonate, ANS: 1-anilinonaphthalene-8-sulfo-nate, PMP: pyridoxamine-5-phosphate.a) Range covers four different proteins.b) pH 6.6.

14.2 Introduction to the Table of Traditional Chromophores j659

the first 15 families contain a common chromophoric moiety. In general, thismoiety is responsible for the similar spectral feature of all the family members.However, conjugation with biomolecules or simple modifications may sometimesshift their absorption peak positions quite drastically. The extent of the shiftdepends on the conjugation position of the biomolecule or substituent functionalgroup in relation to the parent and/or on its electron-donating strength. Theabsorption and emission spectra may also be affected significantly by environ-mental factors such as the pH of the aqueous medium, concentrations ofquenching species, and the solvent polarity.In the following discussion, a short description of each of these 17 families is

presented,includingtheirchemicalstructures,mostofwhichweregenerouslyprovidedbyMolecular Probes, Inc., which is nowpart of Invitrogen. Formore detailed optical orchemical reactivity information about a certain dye with which biomolecules can bemodified, see Ref. [182] (see also Refs [133] and [183].

Table 14.2 The Fairclough–Cantor R0 table.

D:A No. Donor QD tD (ns) Acceptor emax x 10 – 4

(M – 1 cm – 1)Jl (OLI) R0 [2/3]

(nm)

21 DNS 0.1–0.2 15–20 FITC 4.2–4.8 7.9–15.9

3.3–4.1

22 DNS 0.1–0.2 15–20 RITC 1.2 3.1 2.8–3.123 Trp 0.10 2 ANS 0.6 — 2.224 AEDANS 0.1–0.5 13–17 FITC 4.2–4.8 7.9–16 3.3–4.825 FITC 0.5 4 RITC 1.2 5.0 4.026 AEDANS 0.1–0.5 13–17 NBD 2.0 4.6 3.0–3.927 AEDANS 0.1–0.5 13–17 pf 3.3 3.9 2.9–3.828 Trp 0.10 2 AEDANS 0.65 0.7 2.229 NBD 0.1–0.5 — RITC 1.2 4.8 3.0–3.9

Data for various donor–acceptor pairs from Ref. [2], in which details can be found.The eight columns have the following information:D:A No. Donor–acceptor pair number, introduced just above Section 14.1Donor DonorQD Donor quantum yield in the absence of transfertD (ns) The lifetime of the donor in the absence of transfer in nanosecondsAcceptor Acceptoremax� 10�4

(M�1 cm�1)The highest value of the molar extinction coefficient of the acceptor in the unitsindicated

Jl (OLI) The overlap integral in wavelength form expressed in OLI units (see Chapter 2and Table 14.6)

R0 [2/3](nm)

F€orster distance at k2¼ 2/3 nm

DNS: 1-dimethylaminonaphthalene-5-sulfonate, Trp: tryptophan, AEDANS: N-((acetylamino)ethyl)-5-naphthylamine-1-sulfonic acid, FITC: fluorescein isothiocyanate, NBD: 7-nitrobenzo-2-oxa-1,3-diazol,RITC: rhodamine isothiocyanate, ANS: 1-anilino-naphthalene-8-sulfonate, pf: proflavine.

660j 14 Data

Table 14.3 The Kawski R0 table.

D:A No. Fluorophore and solvent R0(anisotropy)(nm)

R0(spectra)(nm)

49 Rhodamine B in a cellulose acetate film 5.03� 0.1 4.90� 0.150 Rhodamine B in glycerol–water (740 poise) 5.03 5.0551 Fluorescein in glycerol with 5% water (v/v) 4.18 4.3052 Anthracene in a cellulose acetate film 2.17� 0.05 1.99� 0.153 2-Methylanthracene in a cellulose acetate film 2.04� 0.05 1.97� 0.0554 5-Methyl-2-phenyl-indole in a cellulose acetate film 1.85� 0.05 1.72� 0.05F€orster distances for homotransfer in three-dimensional solutions, from Ref. [3], in whichdetails can be found.

D:A No. Donor–acceptor pair number, introduced just above Section 14.1Fluorophoreand solvent

Fluorophore and solvent

R0

(anisotropy)F€orster distance obtained from anisotropy versus concentration data

R0 (spectra) F€orster distance derived from the equation given inTable 14.6 (see Chapter 2)

Table 14.4 The 17 “families” of traditional dyes (see pages 695–704 for more information aboutthese families).

Identifier Members/description/common chromophore

T Tyrosine, tryptophan, indole, and phenolQ Nucleotide analogues, such as eADP, TNP-AMP, and Y-ATPA ANSI IAEDANSD DNSM Membrane probes: the parinaric acids, DHE, and DPHP PyreneS StilbeneH AnthraceneC CoumarinB BimaneN NBDF FluoresceinE EosinR RhodamineL Lanthanide and transition elementsO Others that do not fit in the preceding categories

These families consist of dyes with a common chromophore or of dyes that are spectroscopically closelyrelated. They are listed in order of absorption wavelength except the last two: from the T-family, wherethe absorption occurs near 280 nm, to the R-family, which absorbs near 540 nm, followed by the L-and0-families. One letter (identifier) stands for the name of the family. A detailed description is given in thetext. This table is adapted from Ref. [4].


Table 14.5 The official names of the dyes given in Table 14.6.

Official name (common name or abbreviation) ABS EM

T: Tryptophan/tyrosine family

Tryptophan (TRP) 270–295 330–344

3-(2-Aminoethyl)indole (3-AI) 272 330

Indole 272 330

Tyrosine 276 288

Q: Nucleotide analogues

1-N(6)-Ethenoadenosine-50-diphosphate (eATP) 300 410

Co(NH3)4 ATP 365 None

20,30-O-(2,4,6-Trinitrophenyl)adenosine-5-diphosphate (TNP-ADP) 408 530–570

20,30-O-(2,4,3-Trinitrophenyl)adenosine monophosphate (TNP-AMP) 408 530–570

20,30-O-(1,4,6-Trinitrocyclohexadienylidine)adenosine-50-triphosphate(TNP-ATP)

408 530–570

CrATP 430 None

6-40-((4-(Dimethylamino)-phenyl)azo)-2-iodoacetanilide-mercaptopurine ribonucleic triphosphate (6-Y-ATP)

465 None

8-40-((4-(Dimethylamino)-phenyl)azo)-2-iodoacetanilide-mercaptopurine ribonucleic triphosphate (8-Y-ATP)

468 None

A: ANS Family

2-(40-Maleimidoanilino)naphthalene-6-sulfonic acid (MIANS) 318 432

2-(4-(Iodoacetamido)anilino)naphthalene-6-sulfonic acid (IAANS) 329 463

N-((Acetylamino)ethyl)-5-naphthylamine-1-sulfonic acid (AEDANS) 337 520

1-Anilinonaphthalene-8-sulfonic acid (1,8-ANS) 370 482

I: IAEDANS family

5-((2-(Iodoacetyl)amino)ethyl)amino)-naphthalene-1-sulfonic acid(1,5-IAEDANS)

337 520

N-(Iodoacetylaminoethyl)-2-aminonaphthalene-6-sulfonic acid(2,6-IAEDANS)

357 412

D: DNS family

N-(2-Dimethylaminonaphthalene-6-sulfonyl)-phosphatidylethanolamine (2,6-DPE)

260 425


270 530


280 480

Dansyl dipalmitoylphosphatidylethanolamine (DDPPE) 333 518

Dansyl dimyristoylphosphatidylethanolamine (DDMPE) 340 520

1-Dimethylamino-5-sulfonylnaphthalene (DASN) 340 578

Dansylaziridine (DNZ) 340 539

Dansyl chloride (DNS-CI) 340 578

662j 14 Data

Dansyl glutamylglycylarginyl (DEGR) 340 530

4-Dimethylaminoazobenzene-4-sulfonyl chloride (Dabsyl chloride) 423 None

M: Membrane probes

cis-Parinaric acid (c -PnA) 318 410

trans-Parinaric acid (t -PnA) 318 410

Dehydroergosterol (DHE) 324 380

1,6-Diphenyl-1,3,5-hexatriene (DPH) 348 426

P: Pyrene family

N-(1-Pyrene)maleimide (1-NPM) 343 376

Pyrenebutyl-methylphosphonofluoridate (PBMPF) 346 376

N-(3-Pyrenyl)maleimide (NPR) 342 376

Dimethyldiazaperopyrenium (DDPP) 342 376

1-Methylpyrenoate (1-MP) 342 378

Pyrenebutylmethylphosphonate (PBMP) 342 378

S: Stilbene family

4,40-Dinitrostilbene-2,20-disulfonate (DNDS) 352 444

2,5-Dimethoxystilbene-40-maleimide (DMSM) 361 420

Dimethylamino-4-maleimidostilbene (DMAMS) 361 420

H: Anthracene family

N-Methylanthraniloyl (NMA) 350 425

Anthraniloyl (ANTHO) 352 442

9-Anthroyloubain (9-AO) 352 442

Anthroylpalmitate (AP) 352 442

16-(9-Anthroyloxy)palmitic acid (16-AP) 359 475

6-(9-Anthroyloxy)stearic acid (6-AS) 359 470






Anthracene (ANTHR) 375 400

9,10-Diphenylanthracene (DPA) 382 415

9-Vinylanthracene (9-VA) 385 425

9-Methylanthroate (9-MA) 386 412

C: Coumarin family

7-Dimethylaminocoumarin-4-acetamide (DACA) 368 459

7-Diethylamino-3-(40-maleimido-phenyl)-4-methylcoumarin (CPM) 385 471

7-Diethylaminocoumaric-4-phenylsuccinimidyl-thioamidinyl(CPM-SH)

385 471

(continued )


B: Bimane family

Monobromotrimethylammoniobimane (qBBr) 378 470

Monobromobimane (mBBr) 396 480

N: NBD family

4-Chloro-7-nitrobenzo-2-oxa-1,3-diazol (NBD chloride) 337 None

4-(N-(Iodoacetoxy)ethyl-N-methylamino)-7-nitrobenz-2,1,3-oxadiazol(IANBD)6-(7-Nitrobenz-2-oxa-1,3-diazol-4-yI)amino-pentyl-methyl-phosphonofluoridate (NBDPF)

485 530

6-(7-Nitrobenz-2-oxa-1,3-diazol-4-yI)amino-hexanoic Add (NBDAH) 488 530

F: Fluorescein family

Acetamidofluorescein (AF) 490 520

Fluorescein-5-maleimide (FM) 490 515

5(6)-Carboxyfluorescein (6CF) 490 515

5-(Iodoacetamido) fluorescein (IAF or 5-IAF) 490 520

Fluorescein thiosemicarbazide (FTC) 492 519

40,50-Dimethoxy-6-carboxy fluorescein (DCF) 492 520

Fluorescein-50-isothiocyanate (FITC) 494 520

Fluorescein mercuric acetate (FMA) 494 520

5(N-Dodecanoylamino) fluorescein (DAF) 495 521

5-(N-Hexadecanoylamino) fluorescein (HAF) 495 521

Fluorescein-6-carboxylic acid (FCA) 495 519

Hexadecylaminofluorescein (HDF) 495 521

Fluorescein thiocarbamyl phosphatidylethanolamine (FTP) 497 521

E: Eosin family

5-(N-Hexadecanoylamino)eosin (HAE) 520 550

5-(Iodoacetamido)eosin (IAE) 520 544

Eosin-5-maleimide (EM) 523 545

Eosin isothiocyanate (EITC) 530 560

N-Eosin-N0-phosphatidylethanolamine (EPE) 530 570

N-Eosin-N0-phosphatidylethanolaminothiourea (EPEU) 530 570

R: Rhodamine family

Tetramethylrhodamine 5(and 6)-maleimide (MTMR) 540 568

Tetramethylrhodamine 5(and 6)-iodoacetamide (ITMR) 547 573

Octadecylrhodamine B chloride (ORB) 556 577

Rhodamine B (RB) 560 579

Table 14.5 (Continued)


664j 14 Data

Rhodamine isothiocyanate (RITC) 560 590

L: Lanthanide and transition elements

Chromium (III) (Cr(III)) 532 687

Europium (III) (Eu (III)) 580

Tris(2,20-bipyridyl)ruthenium(II) (TBPR) 456

Cobalt(II) (Co(II))

Cobalt-EDTA (CoEDTA)

Praseodymium (Pr)

Terbium (III) (Tb(III)) 270 550

O: Other (listed alphabetically by abbreviation)

Acetylcholinesterase (AChE) 290 333

Bilirubin (BILI)

Bacteriorhodopsin (BTR)

Benzoquinonium (BZQ)

cis-Eleostearic acid (cis -ESA)

Chlorine e6 (Cl-e6) 402 670

4-(Dimethyamino)azobenzene-40-maleimide (DABmal) 419 None

4-Dimethylamino-phenylazophenyl-40-maleimide (DABMI) 419 None

2,6-Dichloro-4-aminophenol iloprost (DCHPA)

N-(4-(Dimethylamino)-3,5-dinitrophenyl)-maleimide (DDPM) 442 None

3-(4-(p-N,N-Didecylaminostyryl)-1-pyridinium)-propylsulfonate(Di-10-ASPPS)Dibucaine 365 385

1,10-Dioctadecyl-3,3,30,30-tetramethylindocarbo-cyanine iodide(DiIC18(3))

547 571

1,10-Dioctadecyl-3,3,30,30-tetramethyIindo-dicarbo-cyanine iodide(DiIC18(5))

642 675

3,30-Ditetradecyloxacarbocyanine perchlorate (DiOC(10)-(3)) 490 540

3-N-(2,4-Dinitrophenyl)aminoproprion-amidinyl (aDNP) 475 None

(4-((4-(Dimethylamino)phenyl)azo)phenyl)-iodoacetamide (DPAPIA) 417 None

Erythrosin-50-isothiocyanate (ErlTC) 536 555

Ethidium 526 605

Flavin adenine dinucleotide (FAD) 360 520

1,5-Difluoro-2,4-dinitrobenzene (F(2)DNB) 332 None

4,40-Difiuoro-3,30-dinitrosulfone (F(2)DPS) 370 None

Filipin

Formycin 290 None

Formycin A-50-triphosphate (FTP) 315 350

Hexadecanoylamino acridine (HDA)

Heme A 418 None

(continued )


Heme C 410 None

Heme

Heme (whole b5)

Cytosol hemoglobin (CytHemo)

2-Methylnaphthoate (2-MN)

(2-Methoxy-1-naphthyl)methyl (MNA)

Naphthyl-N-acetyl (NA) 290 350

N-(p-(Benzoxazolyl)phenyl)maleimide (NBPM) 340 380

Naphthylcholinamide (NCA)

N-Naphthyl-23,24-dinor-5-cholen-22-amide-3b-ol (NCAD)

N-Acetyl-p-(p-(dimethylamino)phenyl)azo)-aniline (N-DPAA) 510

N-Cyclohexyl-N0-(4-dimethylamino-1-naphthyl)-carbodiimide (NCD-4)

Octadecyl naphthalene sulfonic acid (ONSA)

Pyridoxamine phosphate (PDAP) 325 395

Pyridoxal-50-phosphate (PDP) 388 None

Porphyrin 404 622

Proflavin

Propidium 493 630

Retinal 560

Rifampican

50-(p-Sulfobenzoyl)-2-aza-1, N(6)-ethenoadenosine (50-SBeA) 395 420

Succinimidyl-3-(2-pyridylthio)-proprionate (SPDP) 260 None

Trinitrobenzene sulfonate (TNBS) 480 None

a-Tocopherol 360 387

The common name or an abbreviation of the dye’s name is given in bold within parentheses, if available.ABS denotes in most cases the wavelength, in nanometers, of the strongest long-wavelength absorptionpeak. EM stands for the wavelength, in nanometers, of maximum fluorescence intensity. The dyes areorganized by “family” (see text). Within the families the dyes with the lowest ABS are listed first exceptin the family of “Other dyes,” which are listed alphabetically by abbreviation. If the quantum yield isnegligible, the EM is given as None. If the ABS and/or EM is not known, no value is given.)



666j 14 Data

Table 14.7 Acceptor–donor pairs with data for the F€orster distance.

D:A No. Acceptor Donor R0 (nm)

55 T: TRP T: TRP 1.213 T: TRP 0.5–0.76 Phe 1.6–1.910 Tyr 1.3–1.515 Tyr� 0.4356 Q: TNP-ATP T: TRP 2.598 A: MIANS 3.2211 P: NPM 3.4230 S: DMSM 3.8272 C: CPM 4.2297 F: FM 3.8308 F: FITC 3.2329 E: EM 2.583 Q: TNP-ADP Q: eADP 5.184 Q: eADP 4.885 Q: eADP 4.38119 I: 1,5-IAEDANS 3.28120 I: 1,5-IAEDANS 3.09121 I: 1,5-IAEDANS 4.03122 I: 1,5-IAEDANS 3.94361 O: ISA 3.4368 O: 50-SBeA 2.2117 Q: TNP-AMP I: 1,5-IAEDANS 4.32118 Q: TNP I: 1,5-IAEDANS 3.05212 Q: Co(NH3)4ATP P: NPM 1.27270 C: CPM 1.52292 N: NBPM 1.32213 Q: CrATP P: NPM 1.25271 C: CPM 1.46293 N: NBPM 1.15123 Q: 6-Y-ATP I: 1,5-IAEDANS 4.1124 Q: 8-Y-ATP I: 1,5-IAEDANS 4.157 A: ANSmal T: TRP 2.9458 T: TRP 2.668 A: ANTHY T: TRP 2.047 A: AEDANS T: TRP 2.259 I: 1,5-1 AEDANS T: TRP 1.8560 T: TRP 2.1361 T: TRP 2.262 D: DNS-Cl T: TRP 2.1194 D: DNS-Cl 3.06377 O: FTP 2.4463 D: DNS T: TRP 2.2373 O: NA 2.08374 O: NA 2.7226 Tyr 2.027 T: TRP 2.1

682j 14 Data

28 D: DNS 0.981 D: DNS-Amide T: Indole 2.4382 T: Indole 2.6186 D: DDPM Q: eADP 2.9287 Q: eADP 3.1188 Q: eADP 2.75114 A: 1,8-ANS 3.3125 I: 1,5-IAEDANS 2.74126 I: 1,5-IAEDANS 2.9193 D: DNS-Cl 2.19214 P: NPM 2.53294 N: NBPM 2.47383 D: DDMPE O: NCAD 2.16179 D: 2,5-DPE D: 2,6-DPE 2.55180 D: 2,6-DPE 2.2864 M: c-PnA T: TRP 2.865 M: DHE T: TRP 2.3366 P: NPM T: TRP 2.799 A: MIANS 1.7215 P: NPM 2.0231 S: DMSM 1.5273 C: CPM 2.0357 P: PI O: AChE 2.19358 P: PBMP O: AChE 2.55359 P: PI & PBMP O: AChE 2.65380 P: 1-MP O: Dimetianiline 2.567 S: DMSM T: TRP 2.8216 S: DMAMS P: NPM 3.8217 S: DNDS P: NPM 2.65236 C: DACA H: NMA 3.38369 O:MNA 3.24375 H: n-AS O: Dibucaine 2.1379 O: a-Tocopherol 1.4206 H: ANTHR M: t-PnA 1.569 C: CPM T: TRP 3.1100 A: MIANS 3.0218 P: NPM 2.32219 P: NPM 3.4226 P: PBMPF 4.0232 S: DMSM 2.5274 C: CPM 3.1298 F: FM 1.4330 E: EM 1.1237 C: CPM-SH H:NMA 4.7489 B: mBBr Q: eADP 2.72290 Q: eADP 3.10493 N: IANBD ester Q: eADP 4.0127 N: IANBD I: 1,5-IAEDANS 5.09128 I: 1,5-IAEDANS 4.62129 I: 1,5-IAEDANS 3.0

(continued )


288 B: mBBr 3.1220 N: NBD P: NPM 3.16221 P: NPM 3.9296 N: NBD 2.845 A: AEDANS 3.0–3.9227 N: NBDPF P: PBMPF 2.97228 N: NBDAH P: PBMPF 3.27275 N: NBD-MANC C: CPM 3.96295 N: NBD-CI N: NBPM 3.13386 O: PDP 1.1370 F: FM T: TRP 2.771 T: TRP 2.5101 A: MIANS 3.4222 P: NPM 3.4233 S: DMSM 4.6279 C: CPM 4.8280 C: CPM 4.8281 C: CPM 4.8299 F: FM 4.9300 F: FM 4.7331 E: EM 3.094 F: 5-IAF Q: eADP 4.5695 Q: eADP 3.751103 A: MIANS 4.15107 A: IAANS 3.45108 A: IAANS 3.11130 I: 1,5-IAEDANS 5.03131 I: 1,5-IAEDANS 4.02132 I: 1,5-IAEDANS 4.05133 I: 1,5-IAEDANS 4.2134 I: 1,5-IAEDANS 4.33–4.98135 I: 1,5-IAEDANS 5.51136 I: 1,5-IAEDANS 4.35137 I: 1,5-IAEDANS 4.8138 I: 1,5-IAEDANS 4.59139 I: 1,5-IAEDANS 4.922140 I: 1,5-IAEDANS 4.5141 I: 1,5-IAEDANS 4.0142 I: 1,5-IAEDANS 4.72143 I: 1,5-IAEDANS 4.4144 I: 1,5-IAEDANS 5.2186 D: DNZ 3.69187 D: DNZ 4.19277 C: CPM 3.8278 C: CPM 4.0102 F: FITC A: MIANS 4.21145 I: 1,5-IAEDANS 4.9



684j 14 Data

146 I: 1,5-IAEDANS 4.44147 I: 1,5-IAEDANS 4.04148 I: 1,5-IAEDANS 4.34149 I: 1,5-IAEDANS 4.81150 I: 1,5-IAEDANS 4.38151 I; 1,5-IAEDANS 4.09152 I; 1,5-IAEDANS 4.9264 H: AO 4.7289 B: mBBr 3.77385 O: NCD-4 3.1240 DNS 3.3–4.143 A: AEDANS 3.3–4.8110 F: AF A: AEDANS 4.3113 F: FIA A: 1,8-ANS 5.08153 F: FTC I: 1,5-IAEDANS 4.4154 I: 1,5-IAEDANS 4.7155 I: 1,5-IAEDANS 4.3156 I: 1,5-IAEDANS 4.2157 I: 1,5-IAEDANS 3.5287 B: qBBr 3.9196 F: HAF D: DNS-CI 3.6276 C: CPM 4.74209 M: c-PnA 2.7203 F: FTP M: DPH 4.5207 F: HDF M: t-PnA 2.84262 H: ANTHR 3.8267 H: AP 4.14382 O: NCA 2.59384 O: ONSA 3.64265 F: FMA H: AO 4.5328 F: FMA 3.74327 F: DCF F: FCA 6.2305 F: 6CF F: 6CF 5.08372 E: EM T: TRP 2.5104 A: MIANS 3.0223 P: NPM 3.0234 S: DMSM 4.6282 C: CPM 4.5283 C: CPM 4.5301 F: FM 5.7302 F: FM 5.7332 E: EM 4.3195 E: EITC D: DNS-Cl 4.6314 F: FITC 5.4158 E: IAE I: 1,5-IAEDANS 5.61188 D: DNZ 4.38189 D: DNZ 4.36190 D: DNZ 4.93181 E: EPE D: 2,6-DPE 3.75182 D: 2,6-DPE 3.91

(continued )


183 D: 1,5-DPE 4.6184 D: 1,5-DPE 4.87337 L: Tb(III) 4.56198 E: HAE D: DEGR 3.84199 D: DEGR 4.37313 F: FITC 5.30324 F: HAF 5.01309 E: C12-Eosin F: FITC 3.58310 F: FITC 4.16311 F: FITC 4.64312 F: FITC 4.51323 F: DAF 5.01191 R: ITMR D: DNZ 4.195192 R: MTMR D: DNZ 4.274235 S: DMSM 4.3284 C: CPM 4.1303 F: FM 5.5304 F: FM 5.5333 E: EM 4.6334 E: EM 4.6200 R: R18 D: DEGR 4.44201 D: DEGR 4.2202 D: DEGR 4.28241 H: 6-AS 4.2244 H: 9-AS 4.3252 H: 12-AS 4.5258 H: 3-AS 3.8320 F: FITC 5.32325 F: HAF 5.43306 R: SRB F: 6CF 5.826315 R: TRITC F: FITC 5.6317 F: FITC 4.07–6.17318 F: FITC 4.0319 F: FITC 5.6316 R: RITC F: FITC 5.644 F: FITC 4.041 DNS 2.8–3.148 NBD 3.0–3.9338 R: RB L: Tb(III) 6.5791 L: Co(II) Q: eADP 1.1492 Q: eADP 0.92159 I: 1,5-IAEDANS 1.40160 L: Pr(III) I: 1,5-IAEDANS 0.93339 L: Tb(III) 0.77340 L: Tb(III) 0.81354 L: Eu(III) 0.85355 L: Eu(III) 0.85



686j 14 Data

341 L: Nd(III) L: Tb(III) 0.93342 L: Tb(III) 0.95352 L: Eu(III) 0.92353 L: Eu(III) 0.89343 L: Ho(III) L: Tb(III) 0.94344 L: Tb(III) 0.97345 L: Er(III) L: Tb(III) 0.81346 L: Tb(III) 0.84370 L: TBPR O: Retinal 3.0573 O: DCHPA T: TRP 1.6674 O: Formycin T: TRP 1.4106 A: MIANS 0.6225 P: NPM 0.975 O: cis-ESA T: TRP 1.676 O: BILI T: TRP 2.8210 M: c-PnA 3.077 O: DABMI T: TRP 2.8115 A: 1,8-ANS 3.49164 I: 1,5-IAEDANS 4.05165 I: 1,5-IAEDANS 3.89166 I: 1,5-IAEDANS 4.11167 I: 1,5-IAEDANS 4.08168 I: 1,5-IAEDANS 4.08169 I: 1,5-IAEDANS 4.15170 I: 1,5-IAEDANS 3.9171 I: 1,5-IAEDANS 4.08–4.15172 I: 1,5-IAEDANS 3.99173 I: 1,5-IAEDANS 4.38197 D: DNS-CI 3.02290 B: mBBr 3.579351 L: Tb(III) 3.2378 O: FTP 2.8278 O: Heme T: TRP 2.93111 A: AEDANS 3.6240 H: 16-AP 3.84243 H: 6-AS 3.77246 H: 9-AS 3.86250 H: 2-AS 3.63251 H: 7-AS 3.82257 H: 12-AS 4.02260 H: 3-AS 3.70261 H: 10-AS 3.9216 Phe-CO 2.217 T: TRP 2.518 Phe-CO 3.1–3.719 T: TRP 2.8174 O: Heme A I: 1,5-IAEDANS 3.6177 I: 2,6-IAEDANS 4.5365 O: Porphyrin 2.05–2.3161 O: Heme C I: 1,5-IAEDANS 3.8

(continued )


178 I: 2,6-IAEDANS 4.879 O: CI T: TRP 5.280 O: b-Napthol T: Tyrosine 1.9896 O: F2DPS Q: eADP 2.8997 O: F2DNB Q: eADP 3.09109 O: DPAPIA A: IAANS 3.22285 C: CPM 3.74105 O: FAD A: MIANS 1.77175 I: 1,5-IAEDANS 1.2224 P: NPM 2.7112 O: N-DPAA A: AEDANS 4.08116 O: CMNP A: 1,8-ANS 2.49162 O: TNBS I: 1,5-IAEDANS 3.1163 O: DiO(C14)3 I: 1,5-IAEDANS 5.7286 O: DiO(C10)3 C: CPM 5.17176 O: Proflavine I: 1,5-IAEDANS 3.8185 O: Di-10-ASPPS D: DDPPE 3.6204 O: Cl e6 M: DPH 3.62205 O: Retinal M: DPH 4.3335 R: R18 5.20–5.629336 R: R18 5.29–5.43356 L: TBPR 4.06366 O: DilC18(5) 4.89–5.58372 O: Retinal 4.90208 O: HDA M: t-PnA 2.11229 O: Ethidium P: DDPP 3.8238 O: aDNP H: NMA 3.29239 O: CytHemo H: 16-AP 3.45242 H: 6-AS 3.46245 H: 9-AS 3.54247 H: 2-AP 3.29249 H: 2-AS 3.34255 H: 12-AS 3.6256 H: 12-AS 4.6268 H: 9-VA 3.79248 O: Di-I-C18(3) H: 2-AS 4.6253 H: 12-AS 5.3269 H: DPA 3.7376 O: Filipin 4.9254 O: Di-I-C18(5) H: 12-AS 2.9259 H: 3-AS 3.1263 O: PERY H: ANTHR 3.35266 O: ErlTC H: AO 4.4307 F: 5-IAF 5.8321 F: FITC 6.2291 O: N-Rho-Pe N: NBD-PC 5.58322 O: eDNP-lys F: FITC 1.7



688j 14 Data

326 O: HHC F: HAF 3.46347 O: Rifampican L: Tb(III) 2.78348 L: Tb(III) 2.35349 O: BTR L: Tb(III) 6.17350 O: NBDA L: Tb(III) 4.46360 O: BZQ O: AChE 2.44362 O: SBeA O: ISA 2.3363 O: PDP O: PDAP 2.62367 O:SPDP O: SPDP 6.8371 O: CoEDTA O: Retinal 1.24381 O: 2-MN O: Dimetianiline 1.11 Phenol Phenol 1.1–1.72 Indole Indole 1.6–2.33 Phenol 1.5–1.94 Phe Phe 0.5–0.78 Tyr 0.25 Tyr Phe 1.2–1.39 Tyr 0.7–0.912 T: TRP 0.217 Tyr� Phe 1.4511 Tyr 1.3–1.514 T: TRP 0.8–1.320 ITyr Tyr 1.3423 T: TRP 0.7921 I2Tyr Tyr 1.4924 T: TRP 1.0522 Thyroxine Tyr 1.7425 T: TRP 1.5429 Heme (Fe3þ) DNS 5.830 Heme (Fe2þ) DNS 6.331 ANS ANS 2.442 T: TRP 2.232 Anthraniloyl T: TRP 2.033 PMP T: TRP 1.6–2.434 PMP 0.735 Cu: transferrin T: TRP 1.836 Fe: transferrin T: TRP 2.137 Cu: O2 hemocyanin T: TRP 2.7538 NADH Tyr 2.539 T: TRP 2.546 pf A: AEDANS 2.9–3.8The information given in this table is contained in Tables 14.1, 14.2, and 14.6, but is rearrangedso that one can easily find a suitable donor for a certain acceptor.

The four columns contain the following information:D:A No. Donor–acceptor pair number, introduced just above Section 14.1Acceptor Acceptor, as Identifier (see Table 14.4): Name (see Table 14.5)Donor Donor, also in the format Identifier: NameR0 (nm) F€orster distance in nanometers


Table 14.8 New traditional probes (more recent than 1993).

D:A No. Donor Acceptor R0 (nm) References

387 1,5-DPE EPE 4.87 [125]388 2,5-DPE EPE 5.12 [125]389 2,6-DPE 2,5-DPE 2.28 [125]390 4,4-Difluoro-4-bora-3a,4a-

diaza-d-indacene (BODIPYFL)

4,4-Difluoro-4-bora-3a,4a-diaza-d-indacene(BODIPY FL)

5.7 [126]

391 5-IAF 5-TMRIA 3.4–4.0 [127]392 5-Methoxyquinazoline-2,4

(1H,3H)-dione-basedemissive uracil analogue

7-Diethyaminocoumarin-3-carboxylic acid

2.7 [128]

393 AEDANS TNP-ATP 4.14 [129]394 FLC 4.72 [129]395 FITC 4.71 [129]396 DABMI 4.00 [129]397 Fluorescein 4.4–4.8 [130]398 Alexa 488 Alexa 568 5.55–6.06 [131]399 Alexa 488 maleimide Alexa 594 maleimide 5.4 [132]400 AlexaFluor 350 QSY 35 4.7 [133]401 AlexaFluor 488 5.0 [134]402 Dabcyl 5.0 [133]403 AlexaFluor 488 QSY 35 4.4 [133]404 Dabcyl 4.9 [133]405 QSY 7 and QSY 9 6.4 [133]406 AlexaFluor 546 6.4 [134]407 AlexaFluor 555 7.0 [134]408 AlexaFluor 568 6.2 [134]409 AlexaFluor 594 6.0 [134]410 AlexaFluor 647 5.6 [134]411 AlexaFluor 546 QSY 35 2.5 [133]412 Dabcyl 2.9 [133]413 QSY 7 and QSY 9 6.7 [133]414 AlexaFluor 568 7.0 [134]415 AlexaFluor 594 7.1 [134]416 AlexaFluor 647 7.4 [134]417 AlexaFluor 555 QSY 7 and QSY 9 4.5 [133]418 AlexaFluor 594 4.7 [134]419 AlexaFluor 647 5.1 [134]420 AlexaFluor 568 QSY 7 and QSY 9 5.6 [133]421 QSY 21 7.5 [133]422 AlexaFluor 647 8.2 [134]423 AlexaFluor 594 QSY 21 7.7 [133]424 AlexaFluor 647 8.5 [134]425 AlexaFluor 647 QSY 21 6.9 [133]426 AMCA Cy3 4.96 [135]427 ANAI IPM 3.0 [136]428 ANN FHS 3.89� 0.02 [137]429 5- or 6-IAF 3.97� 0.03 [137]430 BAP ORANGE-DCF 1.52 [138]431 ODB-2 3.81 [138]

690j 14 Data

432 CVL 2.89 [138]433 RED520 2.19 [138]434 BFP GFP 4.0 [134]435 DsRFP 3.1–3.3 [139]436 BODIPY-FL Rhodamine 5.8 [140]437 BODIPY-FL 5.7 [141]438 BPE CY5 7.2 [142]439 BPE, B-phycoerythrin CY5,

carboxymethylindocyanine7.2 [143]

440 B-Phycoerythrin Cy5 7.2 [139]441 C-460 [Ru(pby)3]

2þ 3.8 [144]442 [Ru(pby)3]

2þ 4.38 [144]443 Carboxyfluorescein

succinimidyl ester (CF)Texas Red 5.1 [139]

444 CC2-DMPE DiSBAC2 4.8 [145]445 CF TR 5.1 [146]446 CFP YFP 5.0 [134]447 GFP 4.8 [134]448 GFP 4.7–4.9 [139]449 CPM Fluorescein 4.7 [147]450 TRS 5.1 [148]451 FM 5.2 [148]452 Cy3 Cy5 5.42 [149]453 Cy5 >5.0 [134]454 Cy5 Cy5.5 >8.0 [139]455 CZ1 ORANGE-DCF 3.56 [138]456 ODB-2 3.77 [138]457 RED520 3.65 [138]458 Dansyl FITC 3.3–4.1 [139]459 Octadecylrhodamine 4.3 [139]460 ODR, octadecylrhodamine 4.3 [143]461 DANZ DABM 3.4 [150]462 DMACA-PLAP NBD-PE 3.96 [151]463 DMSM LY 2.6–3.2 [152]464 DOBIPY BODIPY 5.7 [153]465 DPA PM567 3.28 [154]466 DPA 2.65 [154]467 DPH-PC NBD-PC 3.98–4.05 [155]468 ECFP DPA 4.2 [156]469 EDANS DABCYL 3.3 [141]470 DABCYL 3.3 [126]471 EGFP DPA 3.63 [156]472 EITC ENAI 4.6 [136]473 Eu-DOTA Cy5.5 6.2 [141]474 Eu-DTPA-AMCA Cy5 5.5 [141]475 Eu-DTPA-cs124 Cy5 5.6 [141]476 Eu-TTHA-cs124 Cy5 6.8 [141]477 FITC EM 6.0 [157]478 ETSC 6.1–6.4 [158]479 Eosin thiosemicarbazide 6.1–6.4 [139]480 FITC, fluorescein-5-

isothiocyanateEM, eosin maleimide 6.0 [143]

(continued )


481 Fluorescein TMR 4.9–5.4 [146,148]482 Tetramethylrhodamine 5.5 [141]483 Cy5 4.7 [159]484 Tetramethylrhodamine 5.5 [134]485 QSY 7 and QSY 9 dyes 6.1 [183]486 FNAI EITC 4.5 [136]487 GFP YFP 5.7 [136]488 IAEDANS FITC 4.9 [160]489 IAF TMR 3.7 [161]490 EIA 4.6 [161]491 IANBD DDPM 2.5 [162]492 Indol Dansyamide 2.43 [144]493 IPM FNAI 3.9 [136]494 LY, Lucifer yellow TNP-ADP 3.5 [152]495 EM 5.3 [163]496 TNP-ATP 3.5 [143]497 EM, eosin maleimide 5.3 [143]498 MIANS NBD-Cl 2.35–2.77 [164]499 MNA DACM 3.2 [165]500 NAA DNP 3.3–3.7 [166]501 Naphthalene Dansyl 2.2 [143]502 Dansyl 2.2 [167]503 NBD SRH 4.0–7.4 [168]504 LRH 4.5–7.0 [168]505 NCP CPM 3.4 [168]506 OG488-PLAP C18RhoB 5.65 [151]507 PBFT CPN RB-SL 4.8 [170]508 pCNPhe Trp 1.60� 0.05 [171]509 pENPhe Trp 1.56� 0.03 [171]510 PM567 PM567 4.57 [154]511 Proflavin ETSC 4.6 [158]512 PTSx

a) DiSBAC2 4.1 [145]513 Pyrene Bimane 3.0 [172]514 Coumarin 3.9 [172]515 Rhodamine 6G Malachite green 6.1 [139]516 Tb-DTPA-cs124 TAMRA 6.0 [141]517 TBP ORANGE-DCF 3.39 [138]518 Tetramethylrhodamine Texas Red 5.2 [173]519 Texas Red NBD 5 [153]520 TMR Cy5 5.3 [174]521 TO TO 2.3� 0.7 [175]522 Cy3 3.2� 0.9 [175]523 TAMRA 3.0� 0.8 [175]524 labFQ 2.8� 0.8 [175]525 Cy5 2.6� 0.8 [175]526 labRQ 2.2� 0.8 [175]527 TPB ODB-2 3.46 [138]528 RED520 3.00 [138]

Table 14.8 (Continued )

D:A No. Donor Acceptor R0 (nm) References

692j 14 Data

1) Tryptophan/tyrosine family (T). Two natural amino acids – tryptophan andtyrosine, which can be found inmost proteins or enzymes – are used extensivelyin FRETexperiments. Their chemical structures are shown in Figures 14.1 and14.2. Note that indole and phenol are the respective fluorophoric moieties oftryptophan and tyrosine. Indole, phenol, and their derivatives are also includedin this family. Because of their low ABSs (in the range of 270–295 nm),members of this family are predominantly used as FRET donors for otherfamilies.

2) Nucleotide analogues family (Q). The nucleotide analogues (such as AMP, ADP,and ATP) modified by formation or addition of chromophoric groupings aremembers of this family. The ABS and EM as members of this family dependprimarily on the conjugated groups. Etheno (e) and trinitrophenyl (TNP) appearto be the two most used derivatives in this family. The chemical structures of1,6-ethenoadenosine-50-diphosphate (eADP) and 20- (or 30)-O-(trinitrophenyl)adenosine-50-diphosphate (TNP-ADP) are shown in Figures 14.3 and 14.4. Thee-nucleotides have ABS of 300 nm and EM of 410 nm. The blue fluorescence ofthe etheno derivatives is known to be environmentally insensitive. The ABS and

529 TP-EPS-2 ORANGE-DCF 3.87 [138]530 ODB-2 3.68 [138]531 RED520 3.85 [138]532 Trp Ru(III)(NH3)5 1.2–1.6 [176]533 Nitrobenzoyl 1.6 [177]534 Thionitrobenzoate (TNB) 2.4 [178]535 Tyr-NO2 2.6 [179]536 Nitrobenzenesulfenyl

(NBS)3.0 [177]

537 Dinitrobenzenesulfonyl(DNBS)

3.3 [177]

538 Diphenylhexatriene(DPH)

4.0 [180]

539 eA NBD 3.8 [181]

The five columns contain the following information:D:A No. Donor–acceptor pair number, introduced just above Section 14.1Donor DonorAcceptor AcceptorR0 (nm) F€orster distance in nanometersRef. Reference number

Most of these pairs are from papers after 1993, however, some older pairs that were overlooked inRef. [4] have been added.a) PTSx is a pyrene sulfonic acid.

NH

CH2 C

H

COO–

+NH3

Figure 14.1 Tryptophan.


EM of TNP nucleotides are 408 and 530–570 nm, respectively. Unlike e-nucleo-tides, the free TNP nucleotides are essentially nonfluorescent in water, but arefluorescent when bound to the nucleotide binding site of some proteins. TheTNP nucleotides are used very widely as FRETacceptors for many fluorophores,such as dansyl, coumarin, and fluorescein [21,22].

3) ANS family (A). This family consists of anilinonaphthalene and its derivatives:1-anilinonaphthalene-8-sulfonic acid (1,8-ANS), 2-anilinonaphthalene-6-sul-fonic acid (2,6-ANS), and derivatives of 2,6-ANS, such as maleimido-2,6-ANS (MIANS) and iodoacetamido-2,6-ANS (IAANS). The chemical structuresof 1,8-ANS and 2,6-ANS are shown in Figures 14.5 and 14.6, respectively. TheABS and EM of 1,8-ANS are 370 and 482 nm, respectively. However, the ABSand EM for the 2,6-ANS and its maleimide and iodoacetamide derivativesare significantly blueshifted to about 320–330 and 430–460-nm, respectively.1,8-ANS is a very good environment-sensitive and water-soluble probe. It isessentially nonfluorescent in free water and only weakly fluorescent in boundwater, but it becomes appreciably fluorescent when bound to membranes. Itbecomes even more fluorescent when bound to proteins. The fluorescence ofboth MIANS and IAANS conjugates is quite sensitive to substrate binding, aswell as to protein association and denaturation [9,28]. The quantum yields ofboth MIANS and IAANS are considerably lower (around 0.1 for the most cases)than that of 1,8-ANS (0.25–0.92).

4) IAEDANS family (I). 5-((2-(Iodoacetyl)amino)ethyl)aminonaphthalene-1-sul-fonic acid (1,5-IAEDANS) and N-(iodoacetylamino-ethyl)-2-aminonaphtha-lene-6-sulfonic acid (2,6-IAEDANS) are members of this family. Thechemical structure of (1,5-IAEDANS) is demonstrated in Figure 14.7.

CH2 C

H

COO–

+NH3

HO

Figure 14.2 Tyrosine.

N

N

N

N

N

OH2C

OH OH

OPOP–O

O O

O– O–

Figure 14.3 eADP.

694j 14 Data

IAEDANS features high water solubility and its emission overlaps well with theabsorbance of fluorescein. Therefore, IAEDANS–fluorescein is a very popularFRET donor–acceptor pair despite the large discrepancy between their molarabsorbances at their ABSs [46,51].

5) DNS family (D). The dansyl derivatives and conjugated fatty acids are membersof this family. The dansyl conjugated fatty acids are very sensitive to the solventpolarity. This feature has been utilized for investigating molecular interactionsat membrane surfaces [30]. Dansyl chloride is nonfluorescent until it is reactedwith amines. This feature has been used for quantifying the conjugation ratiowith biomolecules [61]. A wide range of both ABSs and EMs are found in thereferences for this family. The dansyl–eosin pair is a very widely used FRET

N

N N

N

NH2

OH2C

O O

OPOP–O

O O

O– O–

NO2O2N

N–O O–

+

Figure 14.4 TNP-ADP.

NH

HO3S

Figure 14.6 2,6-ANS.

NH SO3H

Figure 14.5 1,8-ANS.


donor–acceptor pair even though the discrepancy between their peak molarabsorbances is quite large. The structures of dansyl chloride (DNS-Cl) and thatof a typical dansyl fatty acid, dansyl dihexadecanoylphosphatidylethanolamine(DDHPE), are shown in Figures 14.8 and 14.9, respectively.

6) Membrane probes family (M). Members of this family include 1,6-diphenyl-1,3,5-hexatriene (DPH), DPH fatty acid, dehydroergosterol (DHE), cis-parinaric acid(c-PNA), and trans-parinaric acid (t-PNA). The chemical structures of DPH,DHE, c-PNA, and t-PNA are shown in Figures 14.10–14.13, respectively. DPHand its derivatized fatty acids exhibit strong fluorescence enhancement uponincorporating the lipid membranes and sensitive fluorescence anisotropyresponses to lipid ordering. The ABS and EM of DPH are 348 and 425 nm,respectively. DHE is a naturally fluorescent sterol. Because its chemicalstructure is almost identical to that of cholesterol, DHE has been usedextensively in membrane studies, especially in the study of lipid–cholesteroland cholesterol–protein interactions in membranes. The ABS and EM of DHE

N(CH3)2

SO2Cl

Figure 14.8 DNS-Cl.

NHCH2CH2NH

SO3H

C CH2l

O

Figure 14.7 1,5-IAEDANS.

N(CH3)2

SO2

OCH2CH2NHP

O

CH2O

O–

CHOCCH3(CH2)14

CH2

O

OCCH3(CH2)14

O

+

Et3NH

Figure 14.9 DDHPE.

696j 14 Data

in aqueous buffer are 324 and 426 nm, respectively. The parinaric acids (both cisand trans) are the closest structural analogues of intrinsic membrane lipidsamong currently available fluorescent probes and can be biosyntheticallyincorporated into cellular membranes [26,104]. Probes for membranes andother macromolecular biological systems have been reviewed in Ref. [184]. TheABS of parinaric acid is about 320 nm and its EM is about 410 nm. The lipid–protein interactions have been extensively studied by the use of FRET betweenparinaric acids and tryptophan [71].

C CH

H

C CH

HCH3CH2

C CH

H

C CH

H

(CH2)7 C OH

O

Figure 14.13 t-PnA.

C CH

H

C CH

H

C CH

H

Figure 14.10 DPH.

HO

Figure 14.11 DHE.

C CCH3CH2

HH

C CH

H

C CH

H

C CH

(CH2)7

H

C OH

O

Figure 14.12 c-PnA.


7) Pyrene family (P). This family consists of all pyrene derivatives. The chemicalstructure of pyrene is shown in Figure 14.14 as an example of this family. TheABS and EM of pyrene are 342 and 377 nm, respectively. When an excitedpyrene collides with a ground-state pyrene, they form an excited-state dimer(excimer) with altered fluorescence emission. A broad excimer band centered at475 nm can be observed in the emission spectrum if the excimer is formed. Thisproperty has been used extensively to study the lateral diffusion rate of lipids inmembranes [70].

8) Stilbene family (S). The stilbene maleimides and stilbene disulfonates aremembers of this family. The ABS and EM of all stilbene derivatives are inthe range of 340–360 and 420–450 nm, respectively. The chemical structures of2,5-dimethyoxystilbene-40-maleimide (DMSM) and 4,40-dinitrostilbene-2,20-disulfonate (DNDS) are shown in Figures 14.15 and 14.16, respectively.

9) Anthracene family (H). This family is formed by some anthracene derivativesand anthroyloxy fatty acids. Members of this family have been used extensivelyas FRET donors. The absorption and emission spectra of the anthroyloxy fattyacids are insensitive to their chemical structure. The ABS and EM of allanthroyloxy fatty acids are about 360 and 470 nm, respectively. Figure 14.17exhibits the chemical structure of anthracene and Figure 14.18 shows thestructure of 2-(9-anthroyloxy) stearic acid (2-AS).

10) Coumarin family (C). This family is formed by all coumarin derivatives. Thestructure of the most popular coumarin derivative, 3-(4-maleimidylphenyl)-7-(diethylamino)-4-methylcoumarin (CPM), is shown in Figure 14.19. Coumarin

CH

OCH3

CH3O

CH N

O

O

Figure 14.15 DMSM.

Figure 14.14 Pyrene.

CH

SO3–

O2N CH NO2

–O3S

Figure 14.16 DNDS.

698j 14 Data

is the most fluorescent UV excitable dye and generally an excellent donor tofluorescein. Its ABS and EM are about 385 and 465 nm, respectively [82,83].

11) Bimane family (B). Two bimane derivatives monobromotrimethyl-ammoniobi-mane (qBBr) and monobromobimane (mBBr) are members of this family.The chemical structure of qBBr is shown in Figure 14.20 and that of mBBr inFigure 14.21.

12) NBD family (N). Nitrobenzyloxadiazole (NBD) derivatives are members of thisfamily. They have spectral features similar to those of fluorescein, but with afluorescence that is strongly quenched by water. The ABS and EM of most NBDderivatives are about 480 and 530nm, respectively. The NBD-labeled fatty acidshave been used to monitor lipid transfer and distribution between vesicles [99].The chemical structure of 6-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)aminohexanoicacid (NBDAH) is shown in Figure 14.22.

C

O

CH C OH

O

O

CH3(CH2)15

Figure 14.18 2-AS.

Figure 14.17 Anthracene.

O

CH3

O(CH3CH2)2N

N

O

O

Figure 14.19 CPM.

N

NH3C

BrH2C

O O

CH2N(CH3)3

CH3

+Br–

Figure 14.20 qBBR.


13) Fluorescein family (F). Fluorescein has very strong absorbance and a highfluorescence quantum yield. This combination of attributes makes fluoresceinan excellent candidate for FRET experiments. The ABS and EM of fluoresceinare 490 and 520 nm, respectively. Fluorescein isothiocyanate (FITC) is by far themost common fluorescent derivatization reagent, especially for immuno-fluorescence. The structure of FITC is shown in Figure 14.23.

14) Eosin family (E). Eosin is less fluorescent than fluorescein. Its ABS and EM are520 and 550 nm, respectively. However, eosin and its derivatives efficientlyabsorb the fluorescence from fluorescein and other fluorophores such as dansyland coumarin, making them good FRET acceptors. The chemical structure ofeosin-5-maleimide (EM) is shown in Figure 14.24.

15) Rhodamine family (R). This family contains all rhodamine derivatives. Thechemical structure of rhodamine B (RB) is shown in Figure 14.25. The ABS andEM of rhodamine derivatives are about 550 and 570 nm, respectively. Thefluorescence quantum yield of rhodamine derivatives is usually about one-fourth of that of fluorescein derivatives. However, because tetramethylrhod-amine is readily excited by the intense mercury line at 546 nm used in mostmicroscopes, it often appears brighter. Moreover, rhodamines are invariablymore stable to photobleaching than fluoresceins, and their absorption and

N

NH3C

BrH2C

O O

CH2Br

CH3

Figure 14.21 mBBR.

NO

N

HN(CH2)5

NO2

C

O

OH

Figure 14.22 NBDAH.

O

N

O

COOH

OH

C S

Figure 14.23 FITC.

700j 14 Data

emission spectra are less sensitive to pH [9]a). “Rigidified” rhodamines aremorephotostable and have higher quantum yields.

16) Lanthanide and transition elements family (L). This family consists of thelanthanide and transition elements that have been utilized as FRET donorsor acceptors. Because the luminescent transitions in the lanthanides are inner-shell electronic transitions, they are shielded from solvent and, as a result, thesefluorophores have a high quantum yield and exhibit sharply spiked emissionsspectra. Good overlap can be obtained with acceptors that absorb in the regionof one of these emission spikes. Since the emission spectra of the lanthanidescontain relatively large dark regions, it is possible to measure sensitizedacceptor emissions without interference from donor fluorescence when usinglanthanides as donors. The lanthanide emission decays as a single exponentialwith an extremely long lifetime. Terbium has a lifetime between 1.5 and 2.2ms,while europium has between 0.6 and 2.3ms [97]. Because of the degeneracy ornear degeneracy of the energy levels for the lanthanide ions, the emissionis expected to be of low polarization and the uncertainty in k2 is relatively small(k2 is near 2/3) (see Chapter 3) [185]. A disadvantage of using lanthanides is theirextremely weak absorption. Hence, it is necessary to covalently attach a sensitizerto them [97,109]. Chelates of terbium are excellent energy donors to the retinalchromophores of purple membrane, having a maximum F€orster distance of6.2 nm [108]. Distances between calcium binding sites in proteins have beenmeasured extensively by theuse of FRETbetweenprotein-bound lanthanide ions.

OO

COOH

OH

Br

Br Br

N OO

Br

Figure 14.24 EM.

O

C

N(CH2CH3)2

O(CH2)5CH3

O

(CH3CH2)2N Cl–+

Figure 14.25 RB.

a) Prieto, M. (1991) Personal communication.


17) Others (O). This family includes some other more recent FRET donors andacceptors that are not covered by the preceding families. In particular, weinclude fluorescent proteins and semiconductor quantum dots:Fluorescent protein family (FP). Although this family can be quite diverse in

terms of structure and emission, the vast majority consists of b-barrelprotein structures that surround the central chromophore. The seminalwork of Roger Tsien with green fluorescent protein (GFP) highlighted thepotential of these fluorophores that can be expressed in vivo in both cells andanimals independently or as FRET fusions with other FPs. The latterconfiguration allows FRET-based sensing by judicious placement of asensing element that responds and transduces signal by altering theFRET efficiency. Many variants are available and are usually designatedby their particular emission color or a fruit color, that is, red fluorescentprotein or mTangerine (m designating monomeric structure). These pro-teins are undergoing continuous engineering to improve their long-termphotostability, pH/ionic sensitivity, quantum yield, robustness, and theirspectral range. They can, however, behindered by theneed toundergo in vivomaturation processes that form the active chromophore from key residues.Another commonly utilized FP is the b-phycoerythrin light harvestingcomplex that consists of a supramacromolecular protein complex displayingmore than 30 phycobilin chromophores in one protein structure. Thecumulative effect of all these chromophores is to endow the protein complexwith an extinction coefficient approach 2.5� 106 M�1 cm�1 and a quantumyield �98%. Overall, as these are protein-based fluorophores, they aresusceptible to environments that deteriorate biological molecules.

Semiconductor quantum dot family (QD). For these purposes, these nano-crystals consist almost exclusively of binary combinations of semi-conductor materials in either a core-only or a core–shell structure.The latter consists of a shell of wider bandgap material that is usedto both passivate and protect the core, especially for biological or aqueousapplications. The photoluminescence of these materials arises fromcontrolling their energy levels by the size of the crystal and forcingthem to be in a quantum confined regime that is smaller than the Bohrradius of the corresponding bulk material. For FRET-based applications,QDs offer many advantages that are not cumulatively available to organicdyes or fluorescent proteins [186]. These include (i) high quantum yieldsand absorption spectra that continuously increase toward the UVcoupled to remarkably strong photostability; (ii) the ability to size-tune the QDs photoluminescence that allows matching spectral overlapwith a particular acceptor; (iii) the ability to be excited at almost anywavelength short of their emission due to their large effective Stokesshift – this allows minimal direct excitation of an acceptor; (iv) some ofthe highest multiphoton action cross sections known that allows accessto multiphoton FRET configurations; and (v) the ability to array multipleacceptors (or donors) around the QD that can proportionally increase the

702j 14 Data

FRET acc eptor cross sec tion a nd all ow control over FRET effi ciency in agiven c ons truct [186]. These combined p rope rties have driven a stronginte rest in de ve loping QDs for FRET purp oses; howe ve r, their specifi cbiological ap plication, espe cially in biosens ing, continues t o be hind ere dby di ffi culties in c ont rollably a ttaching biomo l ecules to t heir surfac esuc h that they can engage in optimal i nteract ions with a t arget.

14.3F €orster Distances and Other FRET Data before 1994

Table 14.5 lists the official names and, if available, abbreviated names of thechromophores considered in Ref. [4]. Table 14.6 lists a large number of donor –acceptor pairs with data on the donor quantum yield in the absence of FRET, theoverlap integral, and the F €orster distance of the pairs. This table allows one to searchfor an appropriate pair by donor. The data gathered by Dos Remedios et al. [191] havebeen completely incorporated in Table 14.6.Table 14.7 is useful if one has a particular acceptor in mind and would like to

identify suitable donors for it. When a donor for the acceptor has been found, thecomplete information on the pair should be obtained from Table 14.6.

14.4F €orster Distances for Traditional Probes More Recent Than 1993

An extensive search of sources produced after the publication of Ref. [4] resulted inTable 14.8. This table contains FRET data on traditional probes more recent than1993 and on traditional probes before 1993 that were overlooked in Ref. [4]. Inpapers published after 1994, values for kappa-squared, the quantum yield of thedonor in the absence of transfer, and the overlap integral are often not reported.Accordingly, Table 14.8 lists only the donor– acceptor pairs with the pair number, theF€orster distance R0, and the reference number.

14.5FRET Data on Fluorescent Proteins

Many genetically encoded FRET probes that employ fluorescent proteins have beendeveloped and are widely used (see Chapters 9 and 10). Table 14.9 presentsinformation on FRET using fluorescent proteins. Wherever appropriate, shortdescriptions of applications and comments have been included in the table.Table 14.9 consists of five parts: 14.9a with blue fluorescent proteins as donors,14.9b with cyan fluorescent proteins as donors, 14.9c with green fluorescentproteins as donors, 14.9d with yellow fluorescent proteins as donors, and 14.9ein which quantum dots are donors and fluorescent proteins are acceptors. Addi-tional information is available in http://www.microscopyu.com/tutorials/java/fluorescence/fpfret/index.htm.

14.5 FRET Data on Fluorescent Proteins j703

http://www.microscopyu.com/tutorials/java/.uorescence/fpfret/index.htm

http://www.microscopyu.com/tutorials/java/.uorescence/fpfret/index.htm

Table 14.13 Donor–acceptor pairs with a F€orster distance in a given range.

R0 range (nm) D:A No.

>7.00 415, 416, 421, 422, 423, 424, 438, 439, 440, 454, 503, 834, 868, 901, 925,937, 938, 943, 954, 955, 966, 967, 969, 972, 979, 980, 981, 982, 995, 997,999, 1011, 1015, 1020, 1021, 1027, 1029, 1030, 1034, 1036

6.50–7.00 338, 367, 407, 413, 414, 425, 476, 503, 504, 621, 660, 704, 750, 760, 762,778, 820, 821, 848, 850, 859, 860, 870, 882, 897, 900, 926, 954, 1006,1022

6.00–6.49 30, 317, 321, 327, 349, 398, 405, 406, 408, 409, 473, 477, 478, 479, 480,485, 503, 504, 515, 516, 559, 583, 588, 596, 602, 603, 609, 687, 688, 706,727, 735, 746, 760, 788, 817, 874, 897, 905, 908, 909, 915, 922, 941, 950,954, 975, 1010, 1014

5.50–5.99 29, 135, 158, 163, 291, 301, 302, 303, 304, 306, 307, 315, 316, 317, 319,335, 366, 390, 398, 410, 420, 436, 437, 464, 474, 475, 482, 484, 487, 503,504, 506, 563, 565, 572, 578, 584, 648, 667, 674, 698, 699, 723, 760, 766,772, 777, 780, 790, 793, 803, 815, 855, 873, 906, 907, 911, 912, 917, 918,954, 956, 965, 1019, 1028

5.00–5.49 49, 50, 79, 83, 113, 127, 130, 144, 253, 286, 305, 313, 314, 317, 320, 323,324, 325, 335, 336, 366, 388, 399, 401, 402, 419, 443, 445, 446, 450, 451,452, 453, 481, 495, 497, 503, 504, 518, 519, 520, 546, 547, 552, 558, 561,562, 566, 568, 569, 570, 575, 583, 586, 594, 595, 597, 654, 659, 662, 664,690, 691, 701, 724, 726, 729, 731, 733, 740, 745, 753, 760, 773, 774, 789,816, 840, 841, 886, 910, 916, 1009

4.50–4.99 43, 49, 84, 94, 128, 134, 137, 138, 139, 140, 142, 145, 149, 152, 154, 177,178, 183, 184, 190, 195, 203, 233, 234, 237, 248, 252, 256, 264, 265, 276,279, 280, 281, 282, 283, 299, 300, 311, 312, 317, 333, 334, 337, 366, 372,376, 387, 394, 395, 397, 400, 404, 417, 418, 426, 444, 447, 448, 449, 472,481, 483, 486, 488, 490, 503, 504, 507, 510, 511, 542, 551, 552, 554, 567,571, 573, 574, 582, 583, 600, 604, 605, 607, 637, 647, 649, 678, 683, 689,692, 693, 694, 695, 712, 713, 722, 731, 739, 741, 758, 767, 781, 792, 927,928, 1017

4.00–4.49 40, 43, 44, 51, 85, 93, 102, 103, 110, 117, 121, 123, 124, 131, 132, 133,134, 136, 141, 143, 146, 147, 148, 150, 151, 153, 155, 156, 164, 166, 167,168, 169, 171, 173, 187, 188, 189, 191, 192, 199, 200, 201, 202, 205, 226,235, 241, 244, 257, 266, 267, 272, 284, 310, 317, 318, 332, 350, 356, 361,391, 393, 397, 403, 429, 434, 442, 458, 459, 460, 467, 468, 503, 512, 522,538, 542, 553, 554, 593, 598, 599, 601, 606, 638, 639, 640, 652, 657, 658,663, 697, 700, 702, 722, 731, 734, 748, 763, 764, 801, 823, 825, 831, 838,894, 902, 977, 996

3.50–3.99 18, 40, 43, 45, 46, 48, 95, 111, 122, 157, 161, 165, 170, 172, 174, 176,181, 182, 185, 186, 196, 198, 204, 216, 221, 229, 230, 240, 243, 245, 246,250, 251, 255, 258, 260, 261, 262, 268, 269, 275, 277, 285, 287, 289, 290,297, 328, 384, 391, 428, 429, 431, 441, 455, 456, 457, 458, 462, 467, 471,489, 493, 494, 496, 500, 514, 522, 523, 524, 529, 530, 531, 539, 541, 543,555, 577, 591, 592, 611, 614, 634, 641, 650, 676, 677, 696, 714, 824, 826,828, 875, 889, 892, 971, 1015

(continued )

14.5 FRET Data on Fluorescent Proteins j741

14.6FRET Data on Quantum Dots

Quantum dots have been used very frequently since the mid-1990s in FRET.Tables 14.10–14.12 list FRET data involving quantum dots. In Table 14.10, thedonors are quantum dots, but the acceptors are not. In Table 14.11, the acceptors arequantum dots, but the donors are not. Table 14.12 shows FRETdata for which bothdonors and acceptors are quantum dots.

14.7Donor–Acceptor Pairs with a F€orster Distance in a Given Range

Often researchers have an approximate F€orster distance in mind and would like todetermine donor–acceptor pairs with a R0 near this distance. They can find thesepairs in Table 14.13, which lists all the pairs of Tables 14.1–14.3, 14.6, and 14.8–14.12

3.00–3.49 18, 40, 41, 43, 45, 46, 48, 69, 87, 90, 97, 98, 100, 101, 104, 107, 109, 114,115, 118, 119, 120, 129, 162, 194, 197, 210, 211, 219, 220, 222, 223, 228,236, 238, 239, 242, 247, 249, 259, 263, 274, 288, 295, 308, 326, 331, 351,364, 369, 370, 385, 391, 427, 435, 458, 461, 463, 465, 469, 470, 499, 500,505, 513, 517, 521, 522, 523, 524, 525, 526, 527, 528, 536, 537, 544, 545,550, 577, 613, 624, 650, 674, 675, 676, 685, 747, 754, 756, 757, 769, 806,828, 829, 887, 889, 892, 936, 962, 971

2.50–2.99 17, 19, 37, 38, 39, 41, 46, 56, 57, 58, 64, 66, 67, 70, 71, 72, 76, 77, 78, 82,86, 88, 89, 96, 125, 126, 179, 207, 209, 214, 217, 224, 227, 232, 254, 296,329, 347, 358, 359, 363, 374, 378, 380, 382, 392, 411, 412, 432, 463, 466,491, 498, 521, 522, 523, 524, 525, 526, 535, 540, 675, 679, 680, 684, 685,686, 755, 828, 829, 843, 888, 889, 892, 970

2.00–2.49 2, 16, 26, 27, 31, 32, 33, 36, 42, 47, 52, 53, 60, 61, 62, 63, 65, 68, 81, 116,180, 193, 208, 215, 218, 273, 294, 348, 357, 360, 362, 365, 368, 373, 375,377, 383, 389, 433, 492, 498, 501, 502, 521, 522, 523, 524, 525, 526, 534,625, 675, 685, 715, 888

1.50–1.99 1, 2, 3, 6, 10, 11, 22, 25, 33, 35, 52, 53, 54, 59, 73, 75, 80, 99, 105, 206,231, 270, 322, 430, 508, 509, 521, 525, 526, 532, 533, 832

1.00–1.49 1, 5, 7, 10, 11, 14, 20, 21, 24, 55, 74, 91, 159, 175, 212, 213, 271, 292,293, 298, 330, 371, 379, 381, 386, 526, 532, 792

0.50–0.99 4, 9, 13, 14, 23, 28, 34,, 92, 106, 160, 225, 339, 340, 341, 342, 343, 344,345, 346, 352, 353, 354, 355

0–0.49 8, 12, 15

R0 is the F€orster distance in the range indicated in nanometers, summarizing data fromTables 14.1–14.12except Tables 14.4 and 14.5. D:A No. is the donor–acceptor pair number.

Table 14.13 (Continued )

R0 range (nm) D:A No.

742j 14 Data

rearranged by the range of the F€orster distance for the pairs. Note that R0 values ofabout 900 pairs listed here are distributed as follows:

Numberof pairs

Range innanometer

Numberof pairs

Range innanometer

Numberof pairs

Range innanometer

3 0–0.49 75 2.50–2.99 108 5.00–5.4923 0.50–0.99 101 3.00–3.49 65 5.50–5.9928 1.00–1.49 97 3.50–3.99 49 6.00–6.4932 1.50–1.99 110 4.00–4.49 30 6.50–7.0055 2.00–2.49 110 4.50–4.99 40 >7.00

Figure 14.26 shows the frequency distribution of donor–acceptor pairs in agraphical form. Note that of the 40 pairs with F€orster distances larger than about7 nm, 29 pairs involve quantum dots (pairs containing quantum dots start at pairnumber 609). Pairs with a relatively large uncertainty in the F€orster distance appearmore than once in Figure 14.26 and in Table 14.13. For example, pair number 1 hasan R0 of 1.1–1.7 nm [1]. As a result, it is listed four times in Figure 14.26 in intervals:1.0 nm < R0� 1.2 nm, 1.2 nm < R0� 1.4 nm, 1.4 nm < R0� 1.6 nm, and 1.6 nm< R0� 1.8 nm; this pair is listed twice in Table 14.13: in the 1.00–1.49 nm range andin the 1.50–1.99 nm range.

14.8Table–Reference Directory

Most of the references refer to specific tables as indicated below:

Table Reference

Table 14.1 [1]Table 14.2 [2]Table 14.3 [3]Table 14.6 [5–124,184,185,187]a),b)

Table 14.8 [125–181,183]Table 14.9 [188–235]Table 14.10 [186,236–439]Table 14.11 [440–482]Table 14.12 [483–517]

a) Griep, M.A. (1991) Personal communication.b) Sklar, L.A. (1992) Personal communication.

744j 14 Data

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