75
US006264825B1 (12) United States Patent Blackburn et al. (10) Patent N0.: (45) Date of Patent: US 6,264,825 B1 *Jul. 24, 2001 (54) (75) (73) (*) (21) (22) (63) (60) (51) (52) (58) BINDING ACCELERATION TECHNIQUES FOR THE DETECTION OF ANALYTES Inventors: Gary Blackburn, Glendora, CA (US); Stephen E. Creager, Central, SC (US); Scott Fraser, La Canada, CA (US); Bruce D. Irvine, Glendora, CA (US); Thomas J. Meade, Altadena, CA (US); Stephen D. O’Connor, Pasadena, CA (US); Robert H. Terbrueggen, Manhattan Beach, CA (US); J 0st G. Vielmetter; Thomas W. Welch, both of Pasadena, CA (US) Assignee: Clinical Micro Sensors, Inc., Pasadena, CA (US) Notice: Subject to any disclaimer, the term of this patent is extended or adjusted under 35 U.S.C. 154(b) by 0 days. This patent is subject to a terminal dis claimer. Appl. No.: Filed: 09/338,726 Jun. 23, 1999 Related U.S. Application Data Continuation of application No. 09/134,058, ?led on Aug. 14, 1998. Provisional application No. 60/090,389, ?led on Jun. 23, 1998. Int. Cl.7 ................................................... .. G01N 27/26 U.S. Cl. ..................... .. 205/777.5; 204/403; 204/450; 204/452; 204/409; 204/600; 204/603 Field of Search ................................... .. 204/403, 415, 204/409, 451, 456, 601, 606, 452, 602, 290 R; 205/7775, 775; 422/681; 435/6, 183 ELECTROPHORESIS ELECTRODE (56) References Cited U.S. PATENT DOCUMENTS 4,707,352 11/1987 Stavrianopoulos. 4,707,440 11/1987 Stavrianopoulos ..................... .. 435/6 4,711,955 12/1987 Ward et a1. . 4,755,458 7/1988 Rabbani et al. . 4,787,963 11/1988 MacConnell. 4,840,893 6/1989 Hill et a1. ............................... .. 435/6 (List continued on neXt page.) FOREIGN PATENT DOCUMENTS 2090904 9/1993 (CA) . 0 063 879 11/1982 (EP) . 0 234 93s 2/1987 (EP) . (List continued on neXt page.) OTHER PUBLICATIONS DerWent Publications abstract XP—002124777 (J P9288080), Nov. 1997.* Albers et al. (“Design of novel molecular Wires for realizing long—distance electron transfer”, Bioelectrochemistry and Bioenergetics, 42 (1997), 25—33), 1997.* AiZaWa et al. (“Integrated molecular systems for Biosen sors”, Sensors and Actuators b, 24—25 (1995) 1—5), 1995* (List continued on neXt page.) Primary Examiner—T. Tung Assistant Examiner—A1eX Noguerola (74) Attorney, Agent, or Firm—Flehr Hohabch Test Albritton & Herbert LLP; Richard F. Trecartin, Esq.; Robin M. Silva, Esq. (57) ABSTRACT The invention relates to compositions and methods useful in the acceleration of binding of target analytes to capture ligands on surfaces. Detection proceeds through the use of an electron transfer moiety (ETM) that is associated With the target analyte, either directly or indirectly, to alloW elec tronic detection of the ETM. 29 Claims, 22 Drawing Sheets E: DETECTION SQEAOPVK-F __-> 41 Er ELECTRODE ELECTROPHORESIS ELECTRODE

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Page 1: SQEAOPVK-F __-> 41 Er ELECTRODE

US006264825B1

(12) United States Patent Blackburn et al.

(10) Patent N0.: (45) Date of Patent:

US 6,264,825 B1 *Jul. 24, 2001

(54)

(75)

(73)

(*)

(21) (22)

(63)

(60)

(51)

(52)

(58)

BINDING ACCELERATION TECHNIQUES FOR THE DETECTION OF ANALYTES

Inventors: Gary Blackburn, Glendora, CA (US); Stephen E. Creager, Central, SC (US); Scott Fraser, La Canada, CA (US); Bruce D. Irvine, Glendora, CA (US); Thomas J. Meade, Altadena, CA (US); Stephen D. O’Connor, Pasadena, CA (US); Robert H. Terbrueggen, Manhattan Beach, CA (US); J 0st G. Vielmetter; Thomas W. Welch, both of Pasadena, CA (US)

Assignee: Clinical Micro Sensors, Inc., Pasadena, CA (US)

Notice: Subject to any disclaimer, the term of this patent is extended or adjusted under 35 U.S.C. 154(b) by 0 days.

This patent is subject to a terminal dis claimer.

Appl. No.:

Filed:

09/338,726 Jun. 23, 1999

Related U.S. Application Data

Continuation of application No. 09/134,058, ?led on Aug. 14, 1998. Provisional application No. 60/090,389, ?led on Jun. 23, 1998.

Int. Cl.7 ................................................... .. G01N 27/26

U.S. Cl. ..................... .. 205/777.5; 204/403; 204/450;

204/452; 204/409; 204/600; 204/603

Field of Search ................................... .. 204/403, 415,

204/409, 451, 456, 601, 606, 452, 602, 290 R; 205/7775, 775; 422/681; 435/6,

183

ELECTROPHORESIS ELECTRODE

(56) References Cited

U.S. PATENT DOCUMENTS

4,707,352 11/1987 Stavrianopoulos. 4,707,440 11/1987 Stavrianopoulos ..................... .. 435/6

4,711,955 12/1987 Ward et a1. . 4,755,458 7/1988 Rabbani et al. . 4,787,963 11/1988 MacConnell. 4,840,893 6/1989 Hill et a1. ............................... .. 435/6

(List continued on neXt page.)

FOREIGN PATENT DOCUMENTS

2090904 9/1993 (CA) . 0 063 879 11/1982 (EP) . 0 234 93s 2/1987 (EP) .

(List continued on neXt page.)

OTHER PUBLICATIONS

DerWent Publications abstract XP—002124777 (J P9288080), Nov. 1997.* Albers et al. (“Design of novel molecular Wires for realizing long—distance electron transfer”, Bioelectrochemistry and Bioenergetics, 42 (1997), 25—33), 1997.* AiZaWa et al. (“Integrated molecular systems for Biosen sors”, Sensors and Actuators b, 24—25 (1995) 1—5), 1995*

(List continued on neXt page.)

Primary Examiner—T. Tung Assistant Examiner—A1eX Noguerola (74) Attorney, Agent, or Firm—Flehr Hohabch Test Albritton & Herbert LLP; Richard F. Trecartin, Esq.; Robin M. Silva, Esq.

(57) ABSTRACT

The invention relates to compositions and methods useful in the acceleration of binding of target analytes to capture ligands on surfaces. Detection proceeds through the use of an electron transfer moiety (ETM) that is associated With the target analyte, either directly or indirectly, to alloW elec tronic detection of the ETM.

29 Claims, 22 Drawing Sheets

E:

— DETECTION

SQEAOPVK-F __-> 41 Er ELECTRODE

ELECTROPHORESIS ELECTRODE

Page 2: SQEAOPVK-F __-> 41 Er ELECTRODE

US 6,264,825 B1 Page 2

US. PATENT DOCUMENTS OTHER PUBLICATIONS

4,849,513 7/1989 Smith et al. ......................... .. 536/27 Lincoln et al, (Short—Circuiting the Molecular Wire: Coop 4,868,103 9/1989 Stavrianopoulos et al. . erative Binding of A—[Ru(phen)2dppZ]2+ and 4,894,325 1/1990 Englehardt et al. . A—[Rh(phi)2bipy]3+ to DNA, J. Am. Chem. SOC. 1997, 119, 4,943,523 7/1990 Stavrianopoulos . 1454—1455), 1997.* 4,952,685 8/1990 Stavrianopoulos. Reimers et al. (“Towards efr?cient molecular Wires and 4,994,373 2/1991 stavrianopolllos - switches: the Brooker ions”)Biosystems 35 (1995).* 5,002,885 3/1991 stavfianopoulos - Allerman, K.S., et al., “Electrochemical Reciti?cation at a 5,013,831 5/1991 Stavrianopoulos - Monolayer—Modi?ed Electrode,” J. Phys. Chem, 100:(42) 5,015,569 * 5/1991 Pontius ............................. .. 435/681 17050_17058(1996)_

5’O82’83O 1/1992 Bfakel et a1" Arkin, M., et al., “Evidence for Photoelectron Transfer 5,156,810 10/1992 Ribi : ................................ .. 422/8201 Through DNA Intercalation,” J‘ Inorganic Biochem~ 5’175’269 12/1992 stavnanopoulos' Abstracts 6th International Conference on Bioinor ' , gan1c 5,194,133 * 3/1993 Clark etal. ........................ .. 204/608 Chemistr 51(1) & (2)526 (1993) 5,241,060 8/1993 Englehardt et al.. _ _ y’ “ ' _ ' 1,

5,278,043 1/1994 Bannwarth et al. .............. .. 536/23.1 Bans“, 5“ a1~> Conductmg Polymer Sensors’ TRIR 5,312,527 5/1994 Mikkelsen et al. ........... .. 204/153.12 4(9)1307—311 (1996) 5’328’824 7/1994 Ward et a1_ _ Baum, R. M., “VieWs on Biological, Long—Range Electron 5,403,451 4/1995 Riviello et al. ................. .. 204/153.1 Transfer Stir Debate,” C&E1\C PP 20—23 (1993) 5,449,767 9/1995 Ward etal.. Bechtold, R., et al., “Ruthenium—Modi?ed Horse Heart 5,472,881 12/1995 Beebe et al. ......................... .. 436/94 Cytochrome c: Effect of pH and Ligation on the Rate of 5,476,928 12/1995 Ward etal.. Intramolecular Electron Transfer betWeen Ruthenium(II)

5,491,097 2/1996 61 al. .......................... .. and Heme(HI),” Chen/L) 575057321 * 4/1996 Caron ct a1~ 216/20 Bidan, “Electroconducting conjugated polymers: neW sen

5’532’128 * 7/1996 Eggers etal' " 435/6 sitive matrices to build up chemical or electrochemical 5,565,552 10/1996 Magda et al. ........................ .. 534/11 Sensors A Review,” Sensors and Actuators) B64556 5,571,568 11/1996 Ribietal. .......................... .. 427/487 (1992)

5,573,906 11/1996 Bannwarth et al. ................... .. 435/6 Biotechnology and Genetics: Genetic Screening Integrated 5’582’984 12/1996 Blemarz et al' ' Circuit The Economist (Feb 25—Mar 3 1995) 5,591,578 1/1997 Meade et al. .......................... .. 435/6 ’ “ '_ _ ' ’ ' _

5,595,908 1/1997 Fawcett 6t ill. ...................... .. 534/11 BPguslavsky> L'_et al» APPhCamnS of redOX Polymers 1“ 576017982 2/1997 Sargent et aL _ _____ __ 435/6 biosensors,” Solid State Ionics, 60:189—197 (1993). 5,605,662 2/1997 Heller et a1_ __ 422/681 BoWler, B. E., et al., “Long—Range Electron Transfer in 5,620,850 4/1997 Bamdad et a1_ 530/300 Donor (Spacer) Acceptor Molecules and Proteins,” Progress 5,632,957 5/1997 Heller et a1, __ 422/681 in Inorganic Chemistry: Bioinorganic Chemistry, 5,694,932 * 12/1997 Michel ......... .. 600/345 38Z259—322 (1990).

5,705,346 1/1998 Okamoto et al. ...................... .. 435/6 Brun, A, M,’ et al,, “Photochemistry of Intercalated Quater 5,705,348 1/1998 Meade 61 al. .......................... .. 435/6 nary Diazaaroma?c Salts,” SOC” 5,727,548 * 3/1998 Hill et al. 600/372 113;8153_8159 (1991)_ 577287532 * 3/1998 Ackley ~~~~~ ~~ 435/6 Bumm, et al., “Are Single Molecular Wires Conducting?,”

5,770,369 6/1998 Meade 61 al. .. Science 5’776’672 7/1998 Hashlmoto et a1‘ 435/6 Cantor, C.R. et al., “Report on the Sequencing by Hybrid 5,780,234 7/1998 Meade et al. .......................... .. 435/6 . . ,, . _

578437767 12/1998 Beanie ' 1Zat1on Workshop, Genomics, 13.13~78—1383 (1992). 579457286 * 8/1999 Krihak et a1‘ n 435/6 Carr, J.D., et al., Novel Electrochemical Sensors for neutral 5,968,745 * 10/1999 Thorp etal. ........................... .. 435/6 M°1eCu1eS> Chem Commune 16494550 (1997)

FOREIGN PATENT DOCUMENTS

0 229 442 0 229 943 0 599 337 0515615 238166

90/05732 92/10757 93/10267 93/23425 94/22889 95/11755 95/15971 96/40712 97/01646 98/04740 98/20162 98/35232 99/14596

7/1987 7/1987 1/1994 9/1996 of 1988 5/1990 6/1992 5/1993 11/1993 10/1994 5/1995 6/1995 12/1996 1/1997 2/1998 5/1998 8/1998 3/1999

(EP) .

(EP) .

(EP) .

(GB) .

(JP) .

(W0) .

(W0) .

(W0) .

(W0) .

(W0) .

(W0) .

(W0) .

(W0) .

(W0) .

(W0) .

(W0) .

(W0) .

(W0) .

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Telser, J ., et al., “DNA Oligomers and Duplexes Containing a Covalently Attached Derivative of Tris(2,2‘—bipyridine)ru thenium(II): Synthesis and Characterization by Thermody namic and Optical Spectroscopic Measurements,” J. Am. Chem. Soc, 111:7221—7226 (1989). Thara, T., et al., “Gene Sensor using Ferrocenyl Oligonucle otide,” Chem. Commun., 1609—1610 (1997). Tour, “Conjugated Macromolecules of Precise Length and Constitution. Organic Synthesis for the Construction of Nanoarchitectures,” Chem. Rev., 96:537—553 (1996). Tour, et al., “Self—Assembled Monolayers and Multilayers of Conjugated Thiols, ot—u)—Dithiols, and Thioacetyl—Con taining Adsorbates. Understanding Attachments betWeen Potential Molecular Wires and Gold Surfaces,” J. Am. Chem. Soc, 117:9529—9534 (1995). Tullius, TD. and BA. Dombroski, “Iron(II) EDTA Used to Measure the Helical TWist Along Any DNA Molecule,” Science, 230:679—681 (1985). Turro, N., et al. “Ph0t0electr0n Transfer Between Molecules Adsorbed in Restricted Spaces, ” Ph0t0chem. Convers. Stor age Sol. Energy, Proc. Int. Conf., 8th, pp. 121—139 (1990). Turro, N.J., et al., “Molecular Recognition and Chemistry in Restriceted Reaction Spaces. Photophysics and Photoin duced Electron Transfer on the Surfaces of Micelles, Den drimers, and DNA,” Acc. Chem. Res., 24:332—340 (1991). Uosake, K., et al., “A Self—Assembled Monolayer of Fer rocenylalkane Thiols on Gold as an Electron Mediator for the Reduction of Fe (III)—EDTA in Solution,” Electro chemica Acta., 36(11/12):1799—1801 (1991). Van Ness, J ., et al., “A Versatile Solid Support System for OligodeoXynucleotide Probe—Based Hybridization Assays,” Nucleic Acids Research, 19(12):3345—3349 (1991). Weber, et al., “Voltammetry of RedoX—Active Groups Irre versibly Adsorbed onto Electrodes. Treatment Using the Marcus Relation betWeen Rate and Overpotential,” Anal. Chem., 66:3164—3172 (1994). Williams, et al., “Studies of oligonucleotide interactions by hybridisation to arrays: the in?uence of dangling ends or dupleX yield,” Nucleic Acids Research, 22(8):1365—1367 (1994). Winkler, J .R., et al., “Electron Transfer in Ruthenium—Modi ?ed Proteins,” Chem. Rev., 92:369—379 (1992). Xu, et al., “Immobilization of DNA on an Aluminum (III) alkaneobisphosphonate Thin Film With Electrogenerated Chemiluminescent Detection,” J. Am. Chem. Soc, 116:8386—8387 (1994). Xu, et al., “Immobilization and Hybridization of DNA on an A1uminum(III) Alkanebisphosphonate Thin Film With Elec trogenerated Chemiluminescent Detection,” J. Am. Chem. Soc, 117:2627—2631 (1995). Yang, et al., “GroWth and Characterization of Metal(II) Alkaneobisphosphonate Multilayer Thin Film on Gold Sur faces,” J. Am. Chem. Soc, 115:11855—11862 (1993). Zhou, et al., “Fluorescent Chemosensors Based on Energy Migration in Conjugated Polymers: The Molecular Wire Approach to Increased Sensitivity,” J. Am. Chem. Soc, 117:12593—12602 (1995). Pontius, et al., “Rapid Renaturation of Complementary DNA Strands Mediated by Cationic Detergents: A Role for High—Probability Binding Domains in Enhancing the Kinet ics of Molecular Assembly Processes,” Proc. Natl. Acad. Sci. USA, 88:8237—8241 (Sep. 1991).

Pontius, et al., “Renaturation of Complementary DNA Strands Mediated gby Puri?ed Mammalian Heterogeneous Nuclear Ribonucleoprotein A1 Protein: Implications for a Mechanism for Rapid Molecular Assembly,” Proc. Natl. Acad. Sci. USA., 87:8403—8407 (Nov. 1990).

Gineitis, et al., “Dissociation and Isolation of Chromatin Proteins in Salt Solutions by an Aqueous TWo—Phase Sys tem,” Analytical Biochemistry, 139:400—403 (1984). Kohne, et al., “Room Temperature Method for Increasing the Rate of DNS Reassociation by Many Thousandfold: The Phenol Emulsion Reassociation Technique,” Biochemistry, 16(24):5329—5341 (1977). Caruana, et al., “Enzyme—Ampli?ed Amerometric Detection of Hybridization and of a Single Base Pair Mutation in an 18—Base Oligonucleotide on a 7—um—Diameter Microelec trode,” J. Am. Chem. Soc., 121:769—774 (1999).

Albertsson, P. “Partition Studies on Nucleic Acids I. In?u ence of Electrolytes, Polymer Concentration and Nucleic Acid Conformation on the Partition in the DeXtran—Poly ethylene Glycol System,” Biochim. Biophys. Acta., 103:1—12 (1965).

Miiller, et al., “DNA Fractionation by TWo—Phase Partition With Aid of a Base—Speci?c Macroligand,” Analytical Bio chemistry, 118:269—277 (1981). Miiller, W. “Partitioning of Nucleic Acids,” Partitioning In Aqueous TWo—Phase Systems, 227—266 (1985).

Gingeras, et al., “Hybridization Properites of Immobilized Nucleic Acids,” Nucleic Acids Research, 15(13):5373—5390 (1987). Wetmur, J. “Acceleration of DNA Renaturation Rates,” Biopolymers, 14:2517—2524 (1975). Amasino, R. “Acceleration of Nucleic Acid Hybridization Rate by Polyethylene Glycol,” Analytical Biochemistry, 152:304—307 (1986).

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* cited by examiner

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U.S. Patent Jul. 24, 2001 Sheet 1 0f 22 US 6,264,825 B1

40

30

20 20 [25 f 10

I30

FIG._ 10

i0 l_L|60 40 f

A; 30 FIG._1D

FIG._ 1E

50 re

20 21 22 23 10 _ FQ If I FQ (‘-11 I ‘Q ¢12 / 13

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U.S. Patent Jul. 24, 2001 Sheet 2 0f 22 US 6,264,825 B1

FIG._2

535

?g 500 510

FIG._ 12

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U.S. Patent Jul. 24, 2001 Sheet 3 0f 22 US 6,264,825 B1

120 If

///////// FIG"'3A K105

K120

>n / / / K105

FIG._3B

1 00

06

110 111

112

1

/////v

( FIG._3C

7 0

0 n w |/ k1 m / fw1|||_|/ ??kzé/ |/

1 6 W m l/ M |/ m /

K 105

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U.S. Patent Jul. 24, 2001 Sheet 4 0f 22 US 6,264,825 B1

FIG._

r120

FIG._4B

/////// K105 k108 FIG._4C

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U.S. Patent Jul. 24, 2001 Sheet 5 0f 22 US 6,264,825 B1

140 106

, |W ///////// k105

FIG._4D

PEAK CURRENT VERSUS LOCATION

350

300—

250

200 Ip (nA)

150

100

50

0 \\ DNA1 MDNAZW DNA3 DNA4

DNA SAMPLE

FIG._ 14

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U.S. Patent Jul. 24, 2001 Sheet 7 0f 22 US 6,264,825 B1

*-135 135 $135

*- *-135 120

100 K /[\'*-15’5 100’ 106 ‘ ' ' ' ' 106

n

108

/////////// 105

| 1‘ . ‘\ | 100 152 120/ *-135‘

111 151 110 150 *-135

112 145 141 *-135 142 *‘135

106

1111/1110 111108 /// /L/ U 105 107

FIG._5E

\ / Fr \ /

100 161

160

162

n

106 n

11 1011111111118 // ///// // k105 107

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U.S. Patent Jul. 24, 2001 Sheet 8 0122 US 6,264,825 B1

/ I I

F1 160 w 110 111 - 161

162

K 112\ 150 151

\ 153

\100

1110611111 111111114!‘ //////////L/ / / k 1 7

"’5 FIG._5G 0

I 1 |

m 120/ 110 5

172 00 142 145 141 142 *435

[ /*-135*_135 106 \ \l ' ' ’ 'I

/

14 141

1

H1 {735 *-135 108

/ / / k105

4-1351 1 / / / /(/

FIG._5H '07

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U.S. Patent Jul. 24, 2001 Sheet 9 0f 22 US 6,264,825 B1

*-135

7%??? *-135 106 220 107

F'a-“RlHlHlWHVHWw / / / / / / / / / / / / / K105

220

230 232 * - 135 <9 ,

WWW H508 ////

240 *-135*_135 *-135

106 ?ggih 107 FIG._6D i H

/ / //// ///k/

106

FIG._ 6C / /

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U.S. Patent Jul. 24, 2001 Sheet 10 0f 22 US 6,264,825 B1

<> <> 299 *-135 *-1f:5135

106 220 M35 106

F's-~65 I l H l H l H k W” ////k/105/////k%7/

,

FIG._6F < i /

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U.S. Patent Jul. 24, 2001 Sheet 11 0f 22 US 6,264,825 B1

3 Hat

\ m2 m2 m2 m2

\\J\\\J\\\\ \\\\J \\ QEHZFAZ :_ EH‘ :

m2 E5525 _ _ _ _.

w 63% - am A 8m x

8w

5;. m2; mm: mm:

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U.S. Patent Jul. 24, 2001 Sheet 12 0f 22 US 6,264,825 B1

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U.S. Patent Jul. 24, 2001 Sheet 13 0f 22 US 6,264,825 B1

= FIRST HYBRIDIZABLE PORTION OF LABEL PROBE

'\./\/\/\., : RECRUITMENT LINKER

(ETM) (ETM) " " (ETM)n

(ETM)n (NUCLEIC ACID)

a":1/,’",/""l/"'ol/"'oI) A/\/B/\/C/\/ D/\/E/\/\/\F'\/\/\/\/ l l g

ETM ETM ETM METALLOCENE

(METALLOCENE)n

A = NUCLEOSIDE REPLACEMENT E = METALLOCENE POLYMER, ATTACHED B = ATTACHMENT TO A BASE TO A RIBOSE, PHOSPHATE, OR BASE C = ATTACHEMENT TO A RIBOSE F = DENDRIMER STRUCTURE, A‘I'I'ACHED D = ATTACHMENT TO A PHOSPHATE vIAA RIBOSE, PHOSPHATE OR BASE

E J

FIG Y7A

6%» (NUCLEIC ACID)

A G = ATTACHMENT VIAA “BRANCHING

§ STRUCTURE”, THROUGH RIBOSE, B W ETM PHOSPHATE OR BASE

C W ETM

D W ETM

EW (METALLOCENE)n ; (ETM)n F (ETM)n g (ETM)n

(ETM)r1 \ J

FIG. T75

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