Solution conformation of an oligonucleotide containing a G.G mismatch determined by nuclear magnetic resonance and molecular mechanics

• Published in: Nucleic acids research Vol. 19; no. 24; pp. 6771 - 6779
• Main Authors: COGNET, J. A. H, GABARRO-ARPA, J, LE BRET, M, VAN DER MAREL, G. A, VAN BOOM, J. H, FAZAKERLEY, G. V
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press 25.12.1991
• Subjects: Analytical, structural and metabolic biochemistry; Bacteriophage lambda - genetics; Base Sequence; Biological and medical sciences; DNA Repair - genetics; Dna, deoxyribonucleoproteins; Fundamental and applied biological sciences. Psychology; Guanosine - chemistry; Magnetic Resonance Spectroscopy; Models, Molecular; Molecular Sequence Data; Nucleic Acid Conformation; Nucleic Acid Heteroduplexes - chemistry; Nucleic Acid Heteroduplexes - genetics; Nucleic acids; Oligodeoxyribonucleotides - chemistry; Oligodeoxyribonucleotides - genetics; Base mismatching; Molecular structure; DNA; Oligonucleotide; NMR spectrometry; Mutation; Oligodeoxyribonucleotide; Conformation
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/19.24.6771

We have determined by two-dimensional nuclear magnetic resonance studies and molecular mechanics calculations the three dimensional solution structure of the non-selfcomplementary oligonucleotide, d(GAGGAGGCACG). d(CGTGCGTCCTC) in which the central base pair is G.G. This is the first structural determination of a G.G mismatch in a oligonucleotide. Two dimensional nuclear magnetic resonance spectra show that the bases of the mismatched pair are stacked into the helix and that the helix adopts a classical B-DNA form. Spectra of the exchangeable protons show that the two guanosines are base paired via their imino protons. For the non-exchangeable protons and for some of the exchangeable protons nuclear Overhauser enhancement build up curves at short mixing times have been measured. These give 84 proton-proton distances which are sensitive to the helix conformation. One of the guanosines adopts a normal anti conformation while the other is syn or close to syn. All non-terminal sugars are C2' endo. These data sets were incorporated into the refinement of the oligonucleotide structure by molecular mechanics calculations. The G.G mismatch shows a symmetrical base pairing structure. Although the mismatch is very bulky many of its features are close to that of normal B-DNA. The mismatch induces a small lateral shift in the helix axis and the sum of the helical twist above and below the mismatch is close to that of B-DNA.