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Proofreading

Proofreading

Synthesis of new DNA molecules starts when DNA polymerase links nucleotides together in a sequence that is complementary to the template DNA strand. DNA polymerase has a higher affinity for the correct base to ensure fidelity in DNA replication. The DNA polymerase furthermore proofreads during replication, using an exonuclease domain that cuts off incorrect nucleotides from the nascent DNA strand.Errors during Replication Are Corrected by the DNA Polymerase EnzymeGenomic DNA is synthesized in...

Proofreading

Proofreading

Synthesis of new DNA molecules is carried out by the enzyme DNA polymerase, which adds nucleotides on the daughter strand complementary to the template DNA strand. DNA polymerase has a higher affinity to add the correct base and ensures fidelity during DNA replication. Furthermore, it exhibits proofreading activity during replication, using an exonuclease domain that cuts off incorrect nucleotides from the nascent DNA strand.
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Mismatch Repair

Mismatch Repair

Organisms are capable of detecting and fixing nucleotide mismatches that occur during DNA replication. This sophisticated process requires identifying the new strand and replacing the erroneous bases with correct nucleotides. Mismatch repair is coordinated by many proteins in both prokaryotes and eukaryotes.
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During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA. Marilyn Kozak discovered that the sequence RCCAUGG (where R stands for...

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Determining 3'-Termini and Sequences of Nascent Single-Stranded Viral DNA Molecules during HIV-1 Reverse Transcription in Infected Cells

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Rapid long-distance hole transfer through consecutive adenine sequence.

Tadao Takada¹, Kiyohiko Kawai, Mamoru Fujitsuka

¹The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka, Japan.

Journal of the American Chemical Society

|August 24, 2006

Summary

Long-distance hole transfer in DNA occurs efficiently through adenine (A) sequences via a multistep mechanism. This process, known as A-hopping, was confirmed using modified DNA molecules and time-resolved absorption measurements.

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Area of Science:

Molecular Biology
Biophysics
Organic Chemistry

Background:

Long-distance charge transfer is crucial for biological processes.
Adenine (A) sequences in DNA can mediate charge transport.
Understanding DNA charge transfer mechanisms is vital for molecular electronics and therapeutics.

Purpose of the Study:

To investigate the mechanism of long-distance hole transfer through consecutive adenine (A) sequences in DNA.
To determine the efficiency and distance dependence of hole transfer via A-hopping.
To elucidate the role of DNA in mediating charge transport over extended lengths.

Main Methods:

Synthesis of DNA molecules modified with naphthalimide (NI) and phenothiazine (PTZ) chromophores separated by A-tracts.
Time-resolved transient absorption spectroscopy to monitor charge transfer dynamics.
Analysis of spectral changes to identify radical intermediates and assess transfer efficiency.

Main Results:

Efficient hole transfer was observed over long adenine (A) sequences, even up to A30.
Formation of naphthalimide (NI) radical anion and phenothiazine (PTZ) radical cation confirmed hole transfer.
Hole transfer efficiency showed weak distance dependence, suggesting a multistep hopping mechanism.

Conclusions:

Hole transfer via A-hopping in DNA is an efficient and rapid process.
Consecutive adenine sequences facilitate long-distance charge transport through a multistep mechanism.
This study provides fundamental insights into DNA-mediated charge transfer.