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DNA Base Pairing

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Erwin Chargaff’s rules on DNA equivalence paved the way for the discovery of base pairing in DNA. Chargaff’s rules state that in a double-stranded DNA molecule,

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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...

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Mismatch Repair

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Electronic coupling mediated by stacked [Thymine-Hg-Thymine] base pairs.

Alexander A Voityuk¹

¹Institució Catalana de Recerca i Estudis Avançats, Institute of Computational Chemistry, Universitat de Girona, 17071 Girona, Spain. alexander.voityuk@icrea.es

The Journal of Physical Chemistry. B

|October 20, 2006

Summary

Stable metal-mediated base pairs containing mercury (Hg) can form in DNA. Quantum calculations show these Hg-DNA base pairs enhance charge transfer efficiency in DNA duplexes, particularly for electron transfer.

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Area of Science:

Biophysics
Quantum Chemistry
Molecular Biology

Background:

Stable metal-mediated base pairs, specifically Thymine-Mercury-Thymine, have recently been synthesized.
Understanding charge transfer in DNA is crucial for developing novel electronic devices and understanding biological processes.

Purpose of the Study:

To investigate the impact of metal-mediated base pairs on charge transfer efficiency in DNA.
To compare charge transfer in DNA duplexes containing mercury base pairs with those containing canonical base pairs.

Main Methods:

Quantum mechanical calculations were performed on double-stranded DNA pi-stacks.
Calculations focused on sequences with varying numbers of mercury-mediated base pairs (X = [Thymine-Hg-Thymine]) and canonical base pairs (GT(n)G).

Main Results:

Charge transfer efficiency in short DNA duplexes with one mercury base pair (GXG) was similar to canonical pairs (GTG).
DNA duplexes with multiple mercury base pairs (GXXG, GXXXG) exhibited 2.5-3.0 times stronger donor-acceptor coupling compared to canonical analogs.
Mercury's valence orbitals were found to be less involved in hole transfer but potentially important for excess electron transfer.

Conclusions:

Metal-mediated base pairs can significantly enhance charge transfer properties in DNA.
The presence of mercury base pairs offers a tunable mechanism for modulating electronic coupling in DNA, with implications for DNA electronics.
Mercury's role in charge transfer differs for hole versus electron transfer, suggesting specific applications for each.