In the current study, the authors quantify the binding activity of particle-immobilized DNA aptamers to their nucleotide and non-nucleotide targets. For the purposes of this work, DNA and vascular endothelial growth factor (VEGF) binding analysis was carried out for VEGF-binding aptamers and compared to that of an ampicillin-binding aptamer as well as a non-aptamer DNA probe. Binding analysis followed incubation of one target type, coincubation of both DNA and VEGF targets, and serial incubations of each target type. Moreover, recovery of aptamer binding activity following displacement of the DNA target from aptamer:DNA duplexes was also explored. Flow cytometry served as the quantitative tool to directly monitor binding events of both the DNA target and protein target to the various aptamer and non-aptamer functionalized particles. The current work demonstrates how processing steps such as annealing and binding history of particle-immobilized aptamers can affect subsequent binding activity. To this end, the authors demonstrate the ability to fully recover DNA target binding activity capabilities and to partially recover protein target binding activity.
References
1.
G.
Tuerk
and L.
Gold
, Science
249
, 505
(1990
).2.
A. D.
Ellington
and J. W.
Szostak
, Nature
346
, 818
(1990
).3.
R.
Stoltenburg
, C.
Reinemann
, and B.
Strehlitz
, Biomol. Eng.
24
, 381
(2007
).4.
J.
Wrzesinski
and S. K.
Jozwiakowski
, FEBS J.
275
, 1651
(2008
).5.
L. C.
Bock
, L. C.
Griffin
, J. A.
Latham
, E. H.
Vermaas
, and J. J.
Toole
, Nature
355
, 564
(1992
).6.
B.
Waybrant
, T. R.
Pearce
, P.
Wang
, S.
Sreevatsan
, and E.
Kokkoli
, Chem. Commun.
48
, 10043
(2012
).7.
M.
Ye
, J.
Hu
, M.
Peng
, J.
Liu
, H.
Liu
, X.
Zhao
, and W.
Tan
, Int. J. Mol. Sci.
13
, 3341
(2012
).8.
W. B.
Shim
, M. J.
Kim
, H.
Mun
, and M. G.
Kim
, Biosens. Bioelectron.
62
, 288
(2014
).9.
A. S. R.
Potty
, K.
Kourentzi
, H.
Fang
, G. W.
Jackson
, X.
Zhang
, G. B.
Legge
, and R. C.
Willson
, Biopolymers
91
, 145
(2009
).10.
H.
Kaur
and L. Y. L.
Yung
, PLoS One
7
, e31196
(2012
).11.
A.
De Rache
, I.
Kejnovska
, M.
Vorlickova
, and C.
Buess-Herman
, Chem. Eur. J.
18
, 4392
(2012
).12.
B.
Waybrant
, T. R.
Pearce
, and E.
Kokkoli
, Langmuir
30
, 7465
(2014
).13.
K.
Hu
, J. W.
Liu
, J.
Chen
, Y.
Huang
, S. L.
Zhao
, J. N.
Tian
, and G. H.
Zhang
, Biosens. Bioelectron.
42
, 598
(2013
).14.
H. X.
Chen
, Y. F.
Hou
, F. J.
Qi
, J. J.
Zhang
, K.
Koh
, Z. M.
Shen
, and G. X.
Li
, Biosens. Bioelectron.
61
, 83
(2014
).15.
B. T.
Houseman
and M.
Mrksich
, Chem. Biol.
9
, 443
(2002
).16.
Z.
Zhang
, S. F.
Chen
, and S. Y.
Jiang
, Biomacromolecules
7
, 3311
(2006
).17.
J. E.
Forman
, I. D.
Walton
, D.
Stern
, R. P.
Rava
, and M. O.
Trulson
Molecular Modeling of Nucleic Acids
, edited by N. B.
Leontis
and J.
SantaLucia
(American Chemical Society
, Washington, DC
, 1998
), pp. 206
–228
.18.
A. W.
Peterson
, L. K.
Wolf
, and R. M.
Georgiadis
, J. Am. Chem. Soc.
124
, 14601
(2002
).19.
H. A.
Ho
, M.
Bera-Aberem
, and M.
Leclerc
, Chem. Eur. J.
11
, 1718
(2005
).20.
R. J.
Mani
, R. G.
Dye
, T. A.
Snider
, S. P.
Wang
, and K. D.
Clinkenbeard
, Biosens. Bioelectron.
26
, 4832
(2011
).21.
M. E.
Craig
, D. M.
Crothers
, and P.
Doty
, J. Mol. Biol.
62
, 383
(1971
).22.
R. D.
Jenison
, S. C.
Gill
, A.
Pardi
, and B.
Polisky
, Science
263
, 1425
(1994
).23.
G.
Orphanides
, T.
Lagrange
, and D.
Reinberg
, Genes Dev.
10
, 2657
(1996
).24.
T. A.
Bickle
and D. H.
Kruger
, Microbiol. Rev.
57
, 434
(1993
).25.
A. K.
Dey
, C.
Griffiths
, S. M.
Lea
, and W.
James
, RNA
11
, 873
(2005
).26.
G.
Gokulrangan
, J. R.
Unruh
, D. F.
Holub
, B.
Ingram
, C. K.
Johnson
, and G. S.
Wilson
, Anal. Chem.
77
, 1963
(2005
).27.
H.
Lago
, A. M.
Parrott
, T.
Moss
, N. J.
Stonehouse
, and P. G.
Stockley
, J. Mol. Biol.
305
, 1131
(2001
).28.
L.
Gold
, N.
Janjić
, T.
Jarvis
, D.
Schneider
, J. J.
Walker
, S. K.
Wilcox
, and D.
Zichi
, Cold Spring Harbor Perspect. Biol.
4
, a003582
(2012
).29.
R. F.
Macaya
, P.
Schultze
, F. W.
Smith
, J. A.
Roe
, and J.
Feignon
, Proc. Natl. Acad. Sci. U. S. A.
90
, 3745
(1993
).30.
K. Y.
Wang
, S.
McCurdy
, R. G.
Shea
, S.
Swaminathan
, and P. H.
Bolton
, Biochemistry
32
, 1899
(1993
).31.
T.
Hermann
and D. J.
Patel
, Science
287
, 820
(2000
).32.
K.
Padmanabhan
, K. P.
Padmanabhan
, J. D.
Ferrara
, J. E.
Sadler
, and A.
Tulinsky
, J. Biol. Chem.
268
, 17651
(1993
).33.
K.
Padmanabhan
and A.
Tulinsky
, Acta Crystallogr., Sect. D
52
, 272
(1996
).34.
J. A.
Kelly
, J.
Feignon
, and T. O.
Yeates
, J. Mol. Biol.
256
, 417
(1996
).35.
L.
Gold
and N.
Janjić
, U.S. patent 5,811,533 (22 September 1998
).36.
D.
Jellinek
, L. S.
Green
, C.
Bell
, and N.
Janjić
, Biochemistry
33
, 10450
(1994
).37.
L. S.
Green
, D.
Jellinek
, C.
Bell
, L. A.
Beebe
, B. D.
Feistner
, S. C.
Gill
, F. M.
Jucker
, and N.
Janjić
, Chem. Biol.
2
, 683
(1995
).38.
J.
Ruckman
, L. S.
Green
, J.
Beeson
, S.
Waugh
, W. L.
Gillette
, D. D.
Henninger
, L.
Claesson-Welsh
, and N.
Janjić
, J. Biol. Chem.
273
, 20556
(1998
).39.
H.
Hasegawa
, K.
Sode
, and K.
Ikebukuro
, Biotechnol. Lett.
30
, 829
(2008
).40.
Y.
Nonaka
, K.
Sode
, and K.
Ikebukuro
, Molecules
15
, 215
(2010
).41.
B. A.
Baker
, G.
Mahmoudabadi
, and V. T.
Milam
, Soft Matter
9
, 11160
(2013
).42.
D. Y.
Zhang
and G.
Seelig
, Nat. Chem.
3
, 103
(2011
).43.
S.
Cheng
, B.
Zheng
, M. Z.
Wang
, M. H. W.
Lam
, and X. W.
Ge
, Anal. Biochem.
446
, 69
(2014
).44.
Y.
Xiao
, B. D.
Piorek
, K. W.
Plaxco
, and A. J.
Heeger
, J. Am. Chem. Soc.
127
, 17990
(2005
).45.
C. P.
Rusconi
, E.
Scardino
, J.
Layzor
, G. A.
Pitoc
, T. L.
Ortei
, D.
Monroe
, and B. A.
Sullenger
, Nature
419
, 90
(2002
).46.
C. P.
Rusconi
, J. D.
Roberts
, G. A.
Pitoc
, S. M.
Nimjee
, R. R.
White
, G.
Quick
, Jr., E.
Scardino
, W. P.
Fay
, and B. A.
Sullenger
, Nat. Biotechnol.
22
, 1423
(2004
).47.
W. U.
Dittmer
, A.
Reuter
, and F. C.
Simmel
, Angew. Chem. Int. Ed.
43
, 3550
(2004
).48.
A.
Reuter
, W. U.
Dittmer
, and F. C.
Simmel
, Eur. Phys. J. E
22
, 33
(2007
).49.
M. R.
Battig
, Y.
Huang
, N.
Chen
, and Y.
Wang
, Biomaterials
35
, 8040
(2014
).50.
B.
Soontornworajit
, J.
Zhou
, M. T.
Shaw
, T.-H.
Fan
, and Y.
Wang
, Chem. Commun.
46
, 1857
(2010
).51.
M. R.
Battig
, B.
Soontornworajit
, and Y.
Wang
, J. Am. Chem. Soc.
134
, 12410
(2012
).52.
M. A. A.
Siddiqui
and G. M.
Keating
, Drugs
65
, 1571
(2005
).53.
C.
Wiesmann
, G.
Fuh
, H. W.
Christinger
, C.
Eigenbrot
, J. A.
Wells
, and A. M.
de Vos
, Cell
91
, 695
(1997
).54.
N.
Ferrara
, Endocr. Rev.
25
, 581
(2004
).55.
K. M.
Song
, E.
Jeong
, W.
Jeon
, M.
Cho
, and C.
Ban
, Anal. Bioanal. Chem.
402
, 2153
(2012
).56.
C. K.
Tison
and V. T.
Milam
, Langmuir
23
, 9728
(2007
).57.
C. K.
Tison
and V. T.
Milam
, Soft Matter
6
, 4446
(2010
).58.
See supplementary material at http://dx.doi.org/10.1116/1.4915107 for schematics of homodimer formation, as well as flow cytometry analysis to evaluate nonspecific and specific binding with various blocking agents, delayed additions of aminated oligonucleotides to EDAC-activated particles, nonspecific binding of VEGF to ampicillin aptamers and specific binding of DNA targets to ampicillin aptamers in the presence of VEGF.
59.
M.
Zuker
, Nucleic Acids Res.
31
, 3406
(2003
).© 2015 American Vacuum Society.
2015
American Vacuum Society
You do not currently have access to this content.
