The DNA bases interact strongly with gold electrodes, complicating efforts to measure the tunneling conductance through hydrogen-bonded Watson Crick base pairs. When bases are embedded in a self-assembled alkane-thiol monolayer to minimize these interactions, new features appear in the tunneling data. These new features track the predictions of density-functional calculations quite well, suggesting that they reflect tunnel conductance through hydrogen-bonded base pairs.

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3011824PMC
http://dx.doi.org/10.1021/jp104792sDOI Listing

Publication Analysis

Top Keywords

dna bases
8
bases embedded
8
embedded self-assembled
8
conductance hydrogen-bonded
8
base pairs
8
recognition tunneling
4
tunneling measurement
4
measurement conductance
4
conductance dna
4
self-assembled monolayers
4

Similar Publications

Binding of Homeodomain Proteins to DNA with Hoogsteen Base Pair.

J Phys Chem B

January 2025

Department of Physics of Complex Systems, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata 700106, India.

In DNA double helices, Hoogsteen (HG) base pairing is an alternative mode of Watson-Crick (WC) base pairing. HG bp has a different hydrogen bonding pattern than WC bp. We investigate here the binding energy of homeodomain proteins with a HG-DNA duplex, where DNA adopts a HG bp in its sequence.

View Article and Find Full Text PDF

Introduction: Polymerase Chain Reaction (PCR) has been a pivotal scientific technique since the twentieth century, and it is widely applied across various domains. Despite its ubiquity, challenges persist in efficiently amplifying specific DNA templates.

Method: While PCR experimental procedures have garnered significant attention, the analysis of the DNA template, which is the experiment's focal point, has been notably overlooked.

View Article and Find Full Text PDF

NEIL1: the second DNA glycosylase involved in action-at-a-distance mutations induced by 8-oxo-7,8-dihydroguanine.

Free Radic Biol Med

January 2025

Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553, Japan. Electronic address:

8-Oxo-7,8-dihydroguanine (G, 8-hydroxyguanine), an oxidatively damaged base, induces mutations and is involved in cancer initiation. In addition to G:C→T:A transversions at the damaged site, it causes untargeted base substitution (action-at-a-distance) mutations at the G bases of 5'-GpA-3' sites in human cells. Paradoxically, OGG1, a DNA glycosylase involved in the base excision repair (BER) pathway, enhances the action-at-a-distance mutations by G.

View Article and Find Full Text PDF

Alkylated DNA repair by a novel HhH-GPD family protein from Crenarchaea.

Nucleic Acids Res

January 2025

College of Plant Protection, Agricultural University of Hebei, No. 2596 Lekai South Street, Baoding City, Lianchi District, Hebei Province 071001, China.

HhH-GPD (helix-hairpin-helix-glycine/proline/aspartate) family proteins are involved in DNA damage repair. Currently, mechanism of alkylated DNA repair in Crenarchaea has not been fully clarified. The hyperthermophilic model crenarchaeon Saccharolobus islandicus REY15A possesses a novel HhH-GPD family protein (Sis-HhH-GPD), where its Ser152 corresponds to a conserved catalytic Asp in other HhH-GPD homologs.

View Article and Find Full Text PDF

DNA-joining by ligase and polymerase enzymes has provided the foundational tools for generating recombinant DNA and enabled the assembly of gene and genome-sized synthetic products. Xenobiotic nucleic acid (XNA) analogues of DNA and RNA with alternatives to the canonical bases, so-called 'unnatural' nucleobase pairs (UBP-XNAs), represent the next frontier of nucleic acid technologies, with applications as novel therapeutics and in engineering semi-synthetic biological organisms. To realise the full potential of UBP-XNAs, researchers require a suite of compatible enzymes for processing nucleic acids on a par with those already available for manipulating canonical DNA.

View Article and Find Full Text PDF

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!