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

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

Engman, Cecilia, 1974 (author): Gothenburg University,Göteborgs universitet,Institutionen för kemi,Department of Chemistry,University of Gothenburg

Sandin, Peter, 1977 (author): Chalmers tekniska högskola,Chalmers University of Technology

Osborne, Sadie (author): University of Southampton

Brown, Tom (author): University of Southampton

Billeter, Martin, 1955 (author): Gothenburg University,Göteborgs universitet,Institutionen för kemi,Department of Chemistry,University of Gothenburg

Lincoln, Per, 1958 (author): Chalmers tekniska högskola,Chalmers University of Technology

Nordén, Bengt, 1945 (author): Chalmers tekniska högskola,Chalmers University of Technology

Albinsson, Bo, 1963 (author): Chalmers tekniska högskola,Chalmers University of Technology

Wilhelmsson, Marcus, 1974 (author): Chalmers tekniska högskola,Chalmers University of Technology

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Oxford University Press (OUP), 2004
2004
English.
In: Nucleic Acids Research. - : Oxford University Press (OUP). - 1362-4962 .- 0305-1048. ; 32:17, s. 5087-95

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Journal article (peer-reviewed)

Abstract Subject headings

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.

Subject headings

NATURVETENSKAP -- Kemi -- Fysikalisk kemi (hsv//swe)
NATURAL SCIENCES -- Chemical Sciences -- Physical Chemistry (hsv//eng)
NATURVETENSKAP -- Biologi -- Biokemi och molekylärbiologi (hsv//swe)
NATURAL SCIENCES -- Biological Sciences -- Biochemistry and Molecular Biology (hsv//eng)

Keyword

Circular Dichroism
DNA
chemistry
Fluorescent Dyes
chemistry
Nuclear Magnetic Resonance
Biomolecular
Nucleic Acid Conformation
Phenothiazines
chemistry
Spectrophotometry
Spectrophotometry
Ultraviolet
Temperature
Spectrophotometry

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NATURAL SCIENCES: NATURAL SCIENCES; and Chemical Science ...; and Physical Chemist ...

NATURAL SCIENCES: NATURAL SCIENCES; and Biological Scien ...; and Biochemistry and ...

Articles in the publication: Nucleic Acids Re ...

By the university: University of Gothenburg; Chalmers University of Technology

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