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Exploring the mechanisms of DNA hybridization on a surface
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10.1063/1.4775480
/content/aip/journal/jcp/138/3/10.1063/1.4775480
http://aip.metastore.ingenta.com/content/aip/journal/jcp/138/3/10.1063/1.4775480

Figures

Image of FIG. 1.
FIG. 1.

Different bonding motifs for probe-target complexes of unequal length: (a) matching sequence on target strand is at the 5 (“bottom”) end of the molecule, (b) matching sequence on the target strand is at the 3 end (“top”) of the molecule, and (c) matching sequence on the target strand is in the “middle” of the molecule.

Image of FIG. 2.
FIG. 2.

Order parameters used as reaction coordinates for projections of the free energy landscape of hybridization.

Image of FIG. 3.
FIG. 3.

Free energy of hybridization of 2JYK hybridizing in bulk as a function of strand separation distance (ξ) and angle (θ).

Image of FIG. 4.
FIG. 4.

Free energy of hybridization of 2JYK hybridizing on the surface as a function of strand separation distance (ξ) and angle (θ).

Image of FIG. 5.
FIG. 5.

Potential of mean force (Φ) of DNA hybridization of unevenly lengthed strands in the bulk and on the surface as a function of the distance between the strands (ξ). Panel (a) “top,” Panel (b) “middle,” Panel (c) “bottom.”

Image of FIG. 6.
FIG. 6.

Potential of mean force (Φ) of DNA hybridization of unevenly lengthed strands on the surface as a function of distance between the strands (ξ) and angle made by the strands (θ). Panel (a) “top,” Panel (b) “middle,” Panel (c) “bottom.”

Image of FIG. 7.
FIG. 7.

Representative snapshots for configurations of the system for the “top” and “bottom” unevenly lengthed strands corresponding to low-energy minima in Figure 6 .

Tables

Generic image for table
Table I.

Human insulin sequences (listed 5 to 3) used to study the effect of probe/target duplexes of uneven length. The probe strand is found in the first line and is complimentary to the portion of each target sequence found in bold font. Target 1 is designed so that the complimentary bases are found at the “top” of the duplex when properly hybridized to the surface-bound probe. Similarly, Targets 2 and 3 are designed so that the complimentary bases are found in the “middle” and “bottom” of the duplex respectively (see Figure 1 ).

Generic image for table
Table II.

Changes in free energy for the hybridization process of 2JYK in the bulk and on the surface.

Generic image for table
Table III.

Changes in free energy for the hybridization of various insulin probe/target pairs in the bulk and on the surface.

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/content/aip/journal/jcp/138/3/10.1063/1.4775480
2013-01-16
2014-04-19
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Exploring the mechanisms of DNA hybridization on a surface
http://aip.metastore.ingenta.com/content/aip/journal/jcp/138/3/10.1063/1.4775480
10.1063/1.4775480
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