Abstract
Structural features of pyrimidine · pyrimidine mismatches in the interior of oligonucleotide duplexes have been investigated by high resolution two-dimensional proton nuclear magnetic resonance (n.m.r.) spectroscopy. These studies were conducted on the self-complementary d( C-G-C- T A-G-C-T- T -G-C-G ) duplex (designated T · T 12-mer) and the self-complementary d( C-G-C- C -A-G-C-T- C -G-C-G ) duplex (designated C · C 12-mer) containing T · T and C · C pairs located at identical positions four base-pairs from either end of the duplex. Proton n.m.r. studies on the T · T 12-mer duplex were undertaken in the neutral pH range, while studies on the C · C 12-mer duplex were recorded at acidic pH. The proton spectra narrowed considerably on lowering the pH below neutrality for the C · C 12-mer duplex. Two-dimensional nuclear Overhauser enhancement spectroscopy (NOESY) data sets have been recorded on the T · T 12-mer and C · C 12-mer duplexes in high salt H 2O and D 2O solution. The magnitude of the NOE crosspeaks and the directionality of the NOE connectivities demonstrate that both duplexes are right-handed with all bases, including those at the mismatch site, adopting an anti configuration about the glycosidic bond. The observed base and sugar proton chemical shifts suggest structural similarities for the trinucleotide segments centered about the T · T and C · C mismatches. A NOE is detected between the resolved imino protons of T4 and T9 at the mismatch site, consistent with formation of a stacked “wobble” T4( anti) · T9( anti) pair in the T · T 12-mer duplex. A comparison of the imino proton chemical shift and NOE data suggests that the imino-carbonyl hydrogen bonds in the wobble T · T mismatch are weaker than the corresponding imino-carbonyl hydrogen bonds in the wobble G · T mismatch. The 4-amino protons of C4 and C9 at the mismatch site in the C · C 12-mer duplex do not exhibit the pattern of hydrogen-bonded and exposed protons separated by approximately 1·5 parts per million characteristic of cytidine amino protons involved in Watson-Crick G · C pairing. The experimental data are insufficient to differentiate between wobble C( anti) · C + ( anti) and other pairing possibilities for the mismatch in the C · C 12-mer duplex at acidic pH.
Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
