Electronic Structure Change in DNA Caused by Base Pair Motions and Its Effect on Charge Transfer in DNA Chains

2016 ◽  
Vol 69 (3) ◽  
pp. 300 ◽  
Author(s):  
Wei Liu ◽  
Jingyao Liu ◽  
Guohui Zheng ◽  
Sanhuang Ke ◽  
Maosheng Miao ◽  
...  
Keyword(s):  
Electronic Structure ◽  
Charge Transfer ◽  
Base Pair ◽  
Collective Motion ◽  
Base Pairs ◽  
Structural Modifications ◽  
Phenyl Rings ◽  
Base Pair Stacking ◽  
Charge Transfer In Dna ◽  
Stack Model

One important aspect of carrier transfer in DNA is its coupling with atomic motions. The collective motion of the base pairs can either improve the charge transfer by enhancing the π stacking between the bases, or trap the carriers due to strong coupling. By utilizing a pseudo-helical base pair stack model, we systematically studied the electronic structure and its dependence to geometry changes that represent the important DNA motions, including the translation, the twist and the torsion of the base pairs. Our calculations reveal that the above motions may significantly change the electron structure and affect their transport properties. In order to improve the transport of carriers in DNA so that it can become a prospective material in future electronics, it is necessary to make large changes to the atomic structure. Our calculations of the electronic structure under large geometry variation, including large base pair stacking deformation and the insertion of phenyl rings in the bases, can provide good guidelines for such structural modifications of DNA.

An electrochemical study based on thymine–Hg–thymine DNA base pair mediated charge transfer processes

RSC Advances ◽  
2015 ◽  
Vol 5 (61) ◽  
pp. 49819-49823 ◽  
Author(s):  
Ensheng Xu ◽  
Yanqin Lv ◽  
Jifeng Liu ◽  
Xiaohong Gu ◽  
Shuqiu Zhang
Keyword(s):  
Charge Transfer ◽  
Base Pair ◽  
Electrochemical Study ◽  
Base Pairs ◽  
Transfer Processes ◽  
Dna Base ◽  
Dna Base Pair

The (TT)n might have more π-overlapping than the corresponding matched base pairs, and the intercalation of Hg(ii) into TT may further increase this overlapping, causing faster CT kinetics.

Fluctuations at the Base Pair Level Effecting Charge Transfer in DNA†

2009 ◽  
Vol 113 (16) ◽  
pp. 3955-3962 ◽  
Author(s):  
Sairam S. Mallajosyula ◽  
Ashutosh Gupta ◽  
Swapan K. Pati
Keyword(s):  
Charge Transfer ◽  
Base Pair ◽  
Charge Transfer In Dna ◽  
Pair Level

TOWARD THE MECHANISM OF LONG-RANGE CHARGE TRANSFER IN DNA: THEORIES AND MODELS

2002 ◽  
Vol 01 (01) ◽  
pp. 225-244 ◽  
Author(s):  
YI JING YAN ◽  
HOUYU ZHANG
Keyword(s):  
Charge Transfer ◽  
Green’S Function ◽  
Long Range ◽  
Green's Function ◽  
Theoretical Development ◽  
Base Pairs ◽  
Hole Charge ◽  
Thymine Adenine ◽  
Recent Theoretical Development ◽  
Charge Transfer In Dna

This article reviews our recent theoretical development toward understanding the interplay of electronic structure and dephasing effects on charge transfer/transport through molecular donor-bridge-acceptor systems. Both the generalized scattering matrix and Green's function formalisms for partially incoherent tunneling processes are summarized. Presented is also an exact mapping between the kinetic rate constants and the electric conductances in evaluation of chemical yields of sequential charge transfer in the presence of competing branching reactions. As an important example, the mechanism of long-range charge transfer in DNA in aqueous solution is investigated with a quantum chemistry implementation of the generalized Green's function formalism. A time scale of about 5 ps is found for the partially incoherent tunneling through a thymine/adenine π-stack in DNA. Numerical results further show that while the carrier oxidative charge does hop sequentially over all guanine sites in a DNA duplex, its tunneling over thymine/adenine bridge base pairs deviates substantially from the superexchange regime. Presented are also evidences for the involvement of both intrastrand and interstrand pathways in the ground state hole charge transfer in DNA.

EFFECTS OF PHASE-BREAKING ON LONG-RANGE CHARGE TRANSFER IN DNA: PARTIALLY-COHERENT-TUNNELING MODEL STUDY

2006 ◽  
Vol 05 (spec01) ◽  
pp. 317-329 ◽  
Author(s):  
PING HAN ◽  
XIN-QI LI ◽  
HOUYU ZHANG ◽  
GUOZHONG HE ◽  
YIJING YAN
Keyword(s):  
Charge Transfer ◽  
Present Theory ◽  
Base Pairs ◽  
Tunneling Model ◽  
Partially Coherent ◽  
Model Study ◽  
Hole Charge ◽  
Microscopic Interpretation ◽  
Charge Transfer In Dna ◽  
Coherent Tunneling

The mechanism of hole charge transfer in DNA of various lengths and sequences is investigated based on a partially coherent tunneling theory (Zhang et al., J Chem Phys117:4578, 2002), where the effects of phase-breaking in adenine–thymine and guanine–cytosine base pairs are treated on equal foot. This work aims at providing a self-consistent microscopic interpretation for rate experiments on various DNA systems. We will also clarify the condition under which the simple superexchange-mediated-hopping picture is valid, and make some comments on the further development of present theory.

scholarly journals Fluctuations at the Base Pair Level Effecting Charge Transfer in DNA

2009 ◽  
Vol 113 (29) ◽  
pp. 8448-8448 ◽  
Author(s):  
Sairam S. Mallajosyula ◽  
Ashutosh Gupta ◽  
Swapan K. Pati
Keyword(s):  
Charge Transfer ◽  
Base Pair ◽  
Charge Transfer In Dna ◽  
Pair Level

Detection of the Glanzmann's Thrombasthenia Mutations in Arab and Iraqi-Jewish Patients by Polymerase Chain Reaction and Restriction Analysis of Blood or Urine Samples

1991 ◽  
Vol 66 (04) ◽  
pp. 500-504 ◽  
Author(s):  
H Peretz ◽  
U Seligsohn ◽  
E Zwang ◽  
B S Coller ◽  
P J Newman
Keyword(s):  
Polymerase Chain Reaction ◽  
Base Pair ◽  
Restriction Analysis ◽  
Urine Samples ◽  
Chain Reaction ◽  
Base Pairs ◽  
Glanzmann’S Thrombasthenia ◽  
Glanzmann's Thrombasthenia ◽  
Base Pair Deletion ◽  
Polymerase Chain

SummarySevere Glanzmann's thrombasthenia is relatively frequent in Iraqi-Jews and Arabs residing in Israel. We have recently described the mutations responsible for the disease in Iraqi-Jews – an 11 base pair deletion in exon 12 of the glycoprotein IIIa gene, and in Arabs – a 13 base pair deletion at the AG acceptor splice site of exon 4 on the glycoprotein IIb gene. In this communication we show that the Iraqi-Jewish mutation can be identified directly by polymerase chain reaction and gel electrophoresis. With specially designed oligonucleotide primers encompassing the mutation site, an 80 base pair segment amplified in healthy controls was clearly distinguished from the 69 base pair segment produced in patients. Patients from 11 unrelated Iraqi-Jewish families had the same mutation. The Arab mutation was identified by first amplifying a DNA segment consisting of 312 base pairs in controls and of 299 base pairs in patients, and then digestion by a restriction enzyme Stu-1, which recognizes a site that is absent in the mutant gene. In controls the 312 bp segment was digested into 235 and 77 bp fragments, while in patients there was no change in the size of the amplified 299 bp segment. The mutation was found in patients from 3 out of 5 unrelated Arab families. Both Iraqi-Jewish and Arab mutations were detectable in DNA extracted from blood and urine samples. The described simple methods of identifying the mutations should be useful for detection of the numerous potential carriers among the affected kindreds and for prenatal diagnosis using DNA extracted from chorionic villi samples.

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