DNA adopts normal B-form upon incorporation of highly fluorescent DNA base analogue tC: NMR structure and UV-Vis spectroscopy characterization
Journal article, 2004

The influence of the highly fluorescent tricyclic cytosine base analogue (tC) on duplex DNA conformation is investigated. The duplex properties are characterized by absorbance and circular dichroism (CD) for all combinations of neighbouring bases to tC, and an NMR structure is determined for one tC-containing sequence. For the oligonucleotides with one tC incorporated instead of cytosine, the melting temperature is increased on average by 2.7 degrees C above that for the unmodified ones. CD spectra are practically identical for modified and unmodified sequences, indicating an unperturbed B-DNA conformation. The NMR structure determination of the self-complementary sequence 5'-CTC(tC)ACGTGGAG shows a DNA conformation consistent with B-form for the whole duplex. The root-mean-square distance for the nucleotides of the eight central base pairs between the 10 structures with lowest CYANA target functions and a mean structure is 0.45 +/- 0.17 A. The NMR data confirm correct base pairing for tC by the observation of both intrastrand and interstrand imino proton NOEs. Altogether, this suggests that tC works well as a cytosine analogue, i.e. it is situated in the base stack, forming hydrogen bonds with G in the complementary strand, without distorting the DNA backbone conformation. This first example of an artificial, highly fluorescent DNA base that does not perturb the DNA conformation could have valuable applications for the study of the structure and dynamics of nucleic acid systems.

Spectrophotometry

chemistry

Spectrophotometry

chemistry

Nuclear Magnetic Resonance

Fluorescent Dyes

DNA

chemistry

Circular Dichroism

Ultraviolet

Phenothiazines

Temperature

Biomolecular

Nucleic Acid Conformation

Author

Cecilia Engman

University of Gothenburg

Peter Sandin

Chalmers, Department of Chemistry and Bioscience

Sadie Osborne

University of Southampton

Tom Brown

University of Southampton

Martin Billeter

University of Gothenburg

Per Lincoln

Chalmers, Department of Chemistry and Bioscience

Bengt Nordén

Chalmers, Department of Chemistry and Bioscience

Bo Albinsson

Chalmers, Department of Chemistry and Bioscience

Marcus Wilhelmsson

Chalmers, Department of Chemistry and Bioscience

Nucleic Acids Research

0305-1048 (ISSN) 1362-4962 (eISSN)

Vol. 32 17 5087-95

Areas of Advance

Nanoscience and Nanotechnology (2010-2017)

Life Science Engineering (2010-2018)

Subject Categories

Physical Chemistry

Biochemistry and Molecular Biology

DOI

10.1093/nar/gkh844

PubMed

15452275

More information

Latest update

2/28/2018