Biomedical Engineering Reference
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Fig. 8.13 (a) The structure of the designed model DNAmolecule formed by hybridization between
three oligonucleotides. The middle single-stranded segment of poly-T (thymine) has different 12
base long sequences on each end that are complementary to the same number of bases on one end of
other two strands. This facilitates the formation of two double strand regions by Watson-Crick
base-pairing scheme when these single strands are mixed under suitable conditions. The sequence of
the bases in the double-strand regions is shown in the inset. One of the single strands is connected to
a biotin molecule at the free end that is used to attach the complex to a streptavidin-coated
polystyrene bead through biotin-streptavidin binding. (b) The gel electrophoresis pattern obtained
when running the solutions of mixtures containing one, two and three designed single-stranded
DNA molecules under an applied voltage of 25 V (25 min) and then 75 V (200 min) with a 50 bp
DNA ladder reference. Lanes L and A refer to the 50 bp increment DNA ladder and the ssDNA
complex samples. Bands labelled
t
,
d
, and
m
are formed by the monomers, dimers and trimers of the
ssDNA [
31
]. Used with permission. Copyright Nanotechnology 2010
a model DNA system was constructed that consisted of three single-stranded
poly-T (thymine) oligonucleotides: 3
0
-TGTGTGCTGTCG-(T- - -T)
130
-(Biotin)-5
0
;
3
0
-CGACAGCACACA-(T- - -T)
120
-CGGCTATGTTGG-5
0
;3
0
-(T- - -T)
130
--
CCAACATAGCCG-5
0
. The oliogmers were synthesized and PAGE-purified by a
commercial source (Midland Certified Reagent Co, Midland, TX, USA).
The biotin linker at the 5
0
end of the first oliogmer is for attaching a bead, see
Fig.
8.14
. The three single-stranded molecules join by Watson-Crick pairing at
the sticky ends to form a trimer structure with ss-ds-ss-ds-ss segments (see
Fig.
8.13a
). In order for these single-strands to form a trimer complex, the single
strands that form the ends of this complex have only one sticky end whereas
the middle strand has two sticky ends. Each end of the middle molecule is
complementary to the sticky end of only one of the other two strands. In this
design, before base-pairings form, two of the oligonucleotides with one sticky
end are 142 bases long, and the third with two sticky ends is 144 bases long.
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