Abstract
In order to understand the structure of DNAs and their interactions when on microarray surfaces, we performed the first all-atom molecular dynamics simulation of DNA tethered to a surface. On the surface, the binding of the DNA was enhanced, and its average equilibrium conformation was the B form. The DNA duplex spontaneously tilted towards its nearest neighbor and settled in a leaning position with a interaxial distance of 2.2 nm. This close packing of the DNAs, which affects both in situ synthesis and deposition of probes on microarray surfaces, can thus be explained by salted-induced colloidlike DNA-DNA attractions.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 233-235 |
| Number of pages | 3 |
| Journal | Theoretical Chemistry Accounts |
| Volume | 106 |
| Issue number | 3 |
| DOIs | |
| State | Published - Jul 2001 |
| Externally published | Yes |
Fingerprint
ASJC Scopus subject areas
- Physical and Theoretical Chemistry
Cite this
A study of DNA tethered to a surface by an all-atom molecular dynamics simulation. / Wong, Ka Yiu; Pettitt, Bernard.
In: Theoretical Chemistry Accounts, Vol. 106, No. 3, 07.2001, p. 233-235.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - A study of DNA tethered to a surface by an all-atom molecular dynamics simulation
AU - Wong, Ka Yiu
AU - Pettitt, Bernard
PY - 2001/7
Y1 - 2001/7
N2 - In order to understand the structure of DNAs and their interactions when on microarray surfaces, we performed the first all-atom molecular dynamics simulation of DNA tethered to a surface. On the surface, the binding of the DNA was enhanced, and its average equilibrium conformation was the B form. The DNA duplex spontaneously tilted towards its nearest neighbor and settled in a leaning position with a interaxial distance of 2.2 nm. This close packing of the DNAs, which affects both in situ synthesis and deposition of probes on microarray surfaces, can thus be explained by salted-induced colloidlike DNA-DNA attractions.
AB - In order to understand the structure of DNAs and their interactions when on microarray surfaces, we performed the first all-atom molecular dynamics simulation of DNA tethered to a surface. On the surface, the binding of the DNA was enhanced, and its average equilibrium conformation was the B form. The DNA duplex spontaneously tilted towards its nearest neighbor and settled in a leaning position with a interaxial distance of 2.2 nm. This close packing of the DNAs, which affects both in situ synthesis and deposition of probes on microarray surfaces, can thus be explained by salted-induced colloidlike DNA-DNA attractions.
UR - http://www.scopus.com/inward/record.url?scp=0035588097&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=0035588097&partnerID=8YFLogxK
U2 - 10.1007/s002140100269
DO - 10.1007/s002140100269
M3 - Article
AN - SCOPUS:0035588097
VL - 106
SP - 233
EP - 235
JO - Theoretical Chemistry Accounts
JF - Theoretical Chemistry Accounts
SN - 1432-881X
IS - 3
ER -