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Kinetics of charge transfer in DNA containing a mismatch.

Osakada Y, Kawai K, Fujitsuka M, Majima T - Nucleic Acids Res. (2008)

Bottom Line: While the single-base mismatch would significantly affect the CT in DNA, the kinetic basis for the drastic decrease in the CT efficiency through DNA containing mismatches still remains unclear.We assumed that further elucidating of the kinetics in mismatched sequences can lead to the discrimination of the DNA single-base mismatch based on the kinetics.In this study, we investigated the detailed kinetics of the CT through DNA containing mismatches and tried to discriminate a mismatch sequence based on the kinetics of the CT in DNA containing a mismatch.

View Article: PubMed Central - PubMed

Affiliation: The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki Osaka 567-0047, Japan.

ABSTRACT
Charge transfer (CT) in DNA offers a unique approach for the detection of a single-base mismatch in a DNA molecule. While the single-base mismatch would significantly affect the CT in DNA, the kinetic basis for the drastic decrease in the CT efficiency through DNA containing mismatches still remains unclear. Recently, we determined the rate constants of the CT through the fully matched DNA, and we can now estimate the CT rate constant for a certain fully matched sequence. We assumed that further elucidating of the kinetics in mismatched sequences can lead to the discrimination of the DNA single-base mismatch based on the kinetics. In this study, we investigated the detailed kinetics of the CT through DNA containing mismatches and tried to discriminate a mismatch sequence based on the kinetics of the CT in DNA containing a mismatch.

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CT in DNA containing a mismatch. (a) Kinetic scheme for charge injection via CT between adenines (As) and subsequent CT between Gs. NI was attached to the A6 sequence at one end of the duplex in order to inject a charge on guanine (G) nearest to NI within the laser duration of 10 ns via CT between As. Following the CT from the G (nearest to NI) to G-containing mismatch (CT through bridge DNA), charge migrates through GC repeat and finally trapped by PTZ to monitor the CT through the DNA by the formation of PTZ radical cation (PTZ•+). The rate constants for CT from the G (nearest to NI) to G-containing mismatch (kht) were determined by the kinetic modeling based on the kinetics of rapid CT between GC repeat as previously reported (23). (b) Sequences of NI- and PTZ-modified DNA used in this study. Assembly-1 (GC-1, GT-1, GA-1, GT-4, AA-1, TT-1 and AC-1) was based on the GAC/CTG sequence (GC-1), substituted by a G mismatch (GT-1, GA-1, GT-4) or A/A, T/T or A/C mismatch (AA-1, TT-1 and AC-1). Assembly-2 (GC-2, GT-2, GA-2 and GT-5) was based on the GTC/CAG sequence (GC-2), substituted by a G mismatch (GC-2, GT-2, GA-2 and GT-5). Assembly-3 (GC-3, GT-3, GA-3, AA-3 and TT-3) was based on the GAAG/CTTC sequence (GC-3), substituted by a G mismatch (GT-3, GA-3) and A/A or T/T mismatch (AA-3 and TT-3), respectively.
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Figure 1: CT in DNA containing a mismatch. (a) Kinetic scheme for charge injection via CT between adenines (As) and subsequent CT between Gs. NI was attached to the A6 sequence at one end of the duplex in order to inject a charge on guanine (G) nearest to NI within the laser duration of 10 ns via CT between As. Following the CT from the G (nearest to NI) to G-containing mismatch (CT through bridge DNA), charge migrates through GC repeat and finally trapped by PTZ to monitor the CT through the DNA by the formation of PTZ radical cation (PTZ•+). The rate constants for CT from the G (nearest to NI) to G-containing mismatch (kht) were determined by the kinetic modeling based on the kinetics of rapid CT between GC repeat as previously reported (23). (b) Sequences of NI- and PTZ-modified DNA used in this study. Assembly-1 (GC-1, GT-1, GA-1, GT-4, AA-1, TT-1 and AC-1) was based on the GAC/CTG sequence (GC-1), substituted by a G mismatch (GT-1, GA-1, GT-4) or A/A, T/T or A/C mismatch (AA-1, TT-1 and AC-1). Assembly-2 (GC-2, GT-2, GA-2 and GT-5) was based on the GTC/CAG sequence (GC-2), substituted by a G mismatch (GC-2, GT-2, GA-2 and GT-5). Assembly-3 (GC-3, GT-3, GA-3, AA-3 and TT-3) was based on the GAAG/CTTC sequence (GC-3), substituted by a G mismatch (GT-3, GA-3) and A/A or T/T mismatch (AA-3 and TT-3), respectively.

Mentions: The rate constants of the single-step CT between G bases (kht) were determined from kinetic modeling. Analysis of time profiles based on the multistep hopping mechanism was performed with numerical analysis by using Matlab software (23). Kinetic model of multistep CT process is shown in Figure 3. Charge recombination process can be ignored because the charge separated state persists over hundred microseconds when NI and the nearest G are separated by six or five A–T base pairs (Figures S2, S3 and S4). According to Figure 3, example simultaneous differential equations for DNAs described in Figure 1a are shown as Equation (1).1where [Gi] (i = 1 ∼ n) and [PTZ] correspond to the charge population at G and PTZ sites, respectively, ks is the CT rate constant between Gs except for k1 which is the rate constants for the CT from G5 to PTZ (23).Figure 1.


Kinetics of charge transfer in DNA containing a mismatch.

Osakada Y, Kawai K, Fujitsuka M, Majima T - Nucleic Acids Res. (2008)

CT in DNA containing a mismatch. (a) Kinetic scheme for charge injection via CT between adenines (As) and subsequent CT between Gs. NI was attached to the A6 sequence at one end of the duplex in order to inject a charge on guanine (G) nearest to NI within the laser duration of 10 ns via CT between As. Following the CT from the G (nearest to NI) to G-containing mismatch (CT through bridge DNA), charge migrates through GC repeat and finally trapped by PTZ to monitor the CT through the DNA by the formation of PTZ radical cation (PTZ•+). The rate constants for CT from the G (nearest to NI) to G-containing mismatch (kht) were determined by the kinetic modeling based on the kinetics of rapid CT between GC repeat as previously reported (23). (b) Sequences of NI- and PTZ-modified DNA used in this study. Assembly-1 (GC-1, GT-1, GA-1, GT-4, AA-1, TT-1 and AC-1) was based on the GAC/CTG sequence (GC-1), substituted by a G mismatch (GT-1, GA-1, GT-4) or A/A, T/T or A/C mismatch (AA-1, TT-1 and AC-1). Assembly-2 (GC-2, GT-2, GA-2 and GT-5) was based on the GTC/CAG sequence (GC-2), substituted by a G mismatch (GC-2, GT-2, GA-2 and GT-5). Assembly-3 (GC-3, GT-3, GA-3, AA-3 and TT-3) was based on the GAAG/CTTC sequence (GC-3), substituted by a G mismatch (GT-3, GA-3) and A/A or T/T mismatch (AA-3 and TT-3), respectively.
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Related In: Results  -  Collection

License
Show All Figures
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Figure 1: CT in DNA containing a mismatch. (a) Kinetic scheme for charge injection via CT between adenines (As) and subsequent CT between Gs. NI was attached to the A6 sequence at one end of the duplex in order to inject a charge on guanine (G) nearest to NI within the laser duration of 10 ns via CT between As. Following the CT from the G (nearest to NI) to G-containing mismatch (CT through bridge DNA), charge migrates through GC repeat and finally trapped by PTZ to monitor the CT through the DNA by the formation of PTZ radical cation (PTZ•+). The rate constants for CT from the G (nearest to NI) to G-containing mismatch (kht) were determined by the kinetic modeling based on the kinetics of rapid CT between GC repeat as previously reported (23). (b) Sequences of NI- and PTZ-modified DNA used in this study. Assembly-1 (GC-1, GT-1, GA-1, GT-4, AA-1, TT-1 and AC-1) was based on the GAC/CTG sequence (GC-1), substituted by a G mismatch (GT-1, GA-1, GT-4) or A/A, T/T or A/C mismatch (AA-1, TT-1 and AC-1). Assembly-2 (GC-2, GT-2, GA-2 and GT-5) was based on the GTC/CAG sequence (GC-2), substituted by a G mismatch (GC-2, GT-2, GA-2 and GT-5). Assembly-3 (GC-3, GT-3, GA-3, AA-3 and TT-3) was based on the GAAG/CTTC sequence (GC-3), substituted by a G mismatch (GT-3, GA-3) and A/A or T/T mismatch (AA-3 and TT-3), respectively.
Mentions: The rate constants of the single-step CT between G bases (kht) were determined from kinetic modeling. Analysis of time profiles based on the multistep hopping mechanism was performed with numerical analysis by using Matlab software (23). Kinetic model of multistep CT process is shown in Figure 3. Charge recombination process can be ignored because the charge separated state persists over hundred microseconds when NI and the nearest G are separated by six or five A–T base pairs (Figures S2, S3 and S4). According to Figure 3, example simultaneous differential equations for DNAs described in Figure 1a are shown as Equation (1).1where [Gi] (i = 1 ∼ n) and [PTZ] correspond to the charge population at G and PTZ sites, respectively, ks is the CT rate constant between Gs except for k1 which is the rate constants for the CT from G5 to PTZ (23).Figure 1.

Bottom Line: While the single-base mismatch would significantly affect the CT in DNA, the kinetic basis for the drastic decrease in the CT efficiency through DNA containing mismatches still remains unclear.We assumed that further elucidating of the kinetics in mismatched sequences can lead to the discrimination of the DNA single-base mismatch based on the kinetics.In this study, we investigated the detailed kinetics of the CT through DNA containing mismatches and tried to discriminate a mismatch sequence based on the kinetics of the CT in DNA containing a mismatch.

View Article: PubMed Central - PubMed

Affiliation: The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki Osaka 567-0047, Japan.

ABSTRACT
Charge transfer (CT) in DNA offers a unique approach for the detection of a single-base mismatch in a DNA molecule. While the single-base mismatch would significantly affect the CT in DNA, the kinetic basis for the drastic decrease in the CT efficiency through DNA containing mismatches still remains unclear. Recently, we determined the rate constants of the CT through the fully matched DNA, and we can now estimate the CT rate constant for a certain fully matched sequence. We assumed that further elucidating of the kinetics in mismatched sequences can lead to the discrimination of the DNA single-base mismatch based on the kinetics. In this study, we investigated the detailed kinetics of the CT through DNA containing mismatches and tried to discriminate a mismatch sequence based on the kinetics of the CT in DNA containing a mismatch.

Show MeSH