Abstract
DNA orientation near surfaces determines many properties related to hybridization efficiency. We performed a 40-ns molecular dynamics simulation to study the structure and orientation of a 12-base-pair DNA duplex tethered to a neutral, epoxide-coated silica surface. Starting with a canonical B-form tethered in an up-right position, normal to the surface, the DNA tilted to over 55° and back. The time scale was a few nanoseconds for tilting events. The linker between the DNA and the surface went from standing upright to tilted, and finally collapsed on the surface. Although the DNA conformation fluctuated, it remained closed to B-form for the entire 40 ns. Calculations of helical parameters of the DNA show that the tethered end of the DNA changed its conformation noticeably when attracted to the surface.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 570-578 |
| Number of pages | 9 |
| Journal | Biopolymers |
| Volume | 73 |
| Issue number | 5 |
| DOIs | |
| State | Published - Apr 5 2004 |
| Externally published | Yes |
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Keywords
- DNA chip
- DNA orientation
- Hybridization
- Molecular dynamics
ASJC Scopus subject areas
- Biochemistry, Genetics and Molecular Biology(all)
- Biochemistry
- Biophysics
Cite this
Orientation of DNA on a Surface from Simulation. / Wong, Ka Yiu; Pettitt, Bernard.
In: Biopolymers, Vol. 73, No. 5, 05.04.2004, p. 570-578.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Orientation of DNA on a Surface from Simulation
AU - Wong, Ka Yiu
AU - Pettitt, Bernard
PY - 2004/4/5
Y1 - 2004/4/5
N2 - DNA orientation near surfaces determines many properties related to hybridization efficiency. We performed a 40-ns molecular dynamics simulation to study the structure and orientation of a 12-base-pair DNA duplex tethered to a neutral, epoxide-coated silica surface. Starting with a canonical B-form tethered in an up-right position, normal to the surface, the DNA tilted to over 55° and back. The time scale was a few nanoseconds for tilting events. The linker between the DNA and the surface went from standing upright to tilted, and finally collapsed on the surface. Although the DNA conformation fluctuated, it remained closed to B-form for the entire 40 ns. Calculations of helical parameters of the DNA show that the tethered end of the DNA changed its conformation noticeably when attracted to the surface.
AB - DNA orientation near surfaces determines many properties related to hybridization efficiency. We performed a 40-ns molecular dynamics simulation to study the structure and orientation of a 12-base-pair DNA duplex tethered to a neutral, epoxide-coated silica surface. Starting with a canonical B-form tethered in an up-right position, normal to the surface, the DNA tilted to over 55° and back. The time scale was a few nanoseconds for tilting events. The linker between the DNA and the surface went from standing upright to tilted, and finally collapsed on the surface. Although the DNA conformation fluctuated, it remained closed to B-form for the entire 40 ns. Calculations of helical parameters of the DNA show that the tethered end of the DNA changed its conformation noticeably when attracted to the surface.
KW - DNA chip
KW - DNA orientation
KW - Hybridization
KW - Molecular dynamics
UR - http://www.scopus.com/inward/record.url?scp=1842632558&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=1842632558&partnerID=8YFLogxK
U2 - 10.1002/bip.20004
DO - 10.1002/bip.20004
M3 - Article
C2 - 15048781
AN - SCOPUS:1842632558
VL - 73
SP - 570
EP - 578
JO - Biopolymers
JF - Biopolymers
SN - 0006-3525
IS - 5
ER -