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Role of adenine and guanine sites in hole hopping in dna nanowire

Kaur, Inderpreet; Kulkarni, Girish S; Ajore, Ram LU ; Bhardwaj, Richa; kotamarthi, Bhanu Prakash ; Singh , Nirmal and Bharadwaj, Lalit M (2009) In Journal of Theoretical and Computational Chemistry 8(3). p.529-539
Abstract
Transfer integrals for oligos with different bases have been calculated using INDO/Koopman's approximation to unveil the charge transport mechanism in DNA. The sequences, G(A)nG, n = 1, 2, …, 10; G(A)xG(A)yG, x + y = 9; and G(A)xG(A)yG(A)zG, x + y + z = 8, were employed to interpret the Guanine (G) and Adenine(A) hopping. Adenine hopping is found to be faster in G(A)nG sequences with longer Adenine bridges (n ≥ 3). Inserting G-bases in between G(A)10G led to a decrease in the value of transfer integrals. Close analysis has revealed that bridge closer to 3′-end forms a hopping bottleneck; however, the presence of bridge at 5′-end enhances the charge transfer through A-hopping. Further insertion of single G sites in G(A)xG(A)yG (where x + y... (More)
Transfer integrals for oligos with different bases have been calculated using INDO/Koopman's approximation to unveil the charge transport mechanism in DNA. The sequences, G(A)nG, n = 1, 2, …, 10; G(A)xG(A)yG, x + y = 9; and G(A)xG(A)yG(A)zG, x + y + z = 8, were employed to interpret the Guanine (G) and Adenine(A) hopping. Adenine hopping is found to be faster in G(A)nG sequences with longer Adenine bridges (n ≥ 3). Inserting G-bases in between G(A)10G led to a decrease in the value of transfer integrals. Close analysis has revealed that bridge closer to 3′-end forms a hopping bottleneck; however, the presence of bridge at 5′-end enhances the charge transfer through A-hopping. Further insertion of single G sites in G(A)xG(A)yG (where x + y = 9) reduces the transfer integrals, thus explaining the hampering of A-hopping. Hence, sequences of the type G(A)nG, n > 3, are better suited for their application as molecular wire. Finally, studies on the effect of flipping of bases, i.e. flipping G:C to C:G on transfer integrals, have revealed that helical distortions and conformational changes due to sequence variations lead to changes in coupling, which is highly unpredictable.

Role of adenine and guanine sites in hole hopping in dna nanowire (PDF Download Available). Available from: https://www.researchgate.net/publication/250957192_Role_of_adenine_and_guanine_sites_in_hole_hopping_in_dna_nanowire [accessed Jul 25, 2017]. (Less)
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author
publishing date
type
Contribution to journal
publication status
published
in
Journal of Theoretical and Computational Chemistry
volume
8
issue
3
pages
529 - 539
publisher
World Scientific
external identifiers
  • scopus:68049117016
ISSN
0219-6336
DOI
10.1142/S0219633609004873
language
English
LU publication?
no
id
8a6ce823-caf4-48e2-af23-724bb76c96dd
date added to LUP
2017-07-25 11:51:05
date last changed
2017-07-30 05:28:44
@article{8a6ce823-caf4-48e2-af23-724bb76c96dd,
  abstract     = {Transfer integrals for oligos with different bases have been calculated using INDO/Koopman's approximation to unveil the charge transport mechanism in DNA. The sequences, G(A)nG, n = 1, 2, …, 10; G(A)xG(A)yG, x + y = 9; and G(A)xG(A)yG(A)zG, x + y + z = 8, were employed to interpret the Guanine (G) and Adenine(A) hopping. Adenine hopping is found to be faster in G(A)nG sequences with longer Adenine bridges (n ≥ 3). Inserting G-bases in between G(A)10G led to a decrease in the value of transfer integrals. Close analysis has revealed that bridge closer to 3′-end forms a hopping bottleneck; however, the presence of bridge at 5′-end enhances the charge transfer through A-hopping. Further insertion of single G sites in G(A)xG(A)yG (where x + y = 9) reduces the transfer integrals, thus explaining the hampering of A-hopping. Hence, sequences of the type G(A)nG, n &gt; 3, are better suited for their application as molecular wire. Finally, studies on the effect of flipping of bases, i.e. flipping G:C to C:G on transfer integrals, have revealed that helical distortions and conformational changes due to sequence variations lead to changes in coupling, which is highly unpredictable. <br>
<br>
Role of adenine and guanine sites in hole hopping in dna nanowire (PDF Download Available). Available from: https://www.researchgate.net/publication/250957192_Role_of_adenine_and_guanine_sites_in_hole_hopping_in_dna_nanowire [accessed Jul 25, 2017].},
  author       = {Kaur, Inderpreet and Kulkarni, Girish S and Ajore, Ram and Bhardwaj, Richa and kotamarthi, Bhanu Prakash  and Singh , Nirmal  and Bharadwaj, Lalit M},
  issn         = {0219-6336},
  language     = {eng},
  number       = {3},
  pages        = {529--539},
  publisher    = {World Scientific},
  series       = {Journal of Theoretical and Computational Chemistry},
  title        = {Role of adenine and guanine sites in hole hopping in dna nanowire},
  url          = {http://dx.doi.org/10.1142/S0219633609004873},
  volume       = {8},
  year         = {2009},
}