1H-nmr comparative studies of polynucleotides: Conformation and dynamic structure of polyribo(uridylic) and polyribo(cytidylic) acids in neutral solution

✍ Scribed by J. M. Neumann; S. Tran-dinh

• Publisher: Wiley (John Wiley & Sons)
• Year: 1982
• Tongue: English
• Weight: 893 KB
• Volume: 21
• Category: Article
• ISSN: 0006-3525
• DOI: 10.1002/bip.360210211

✦ Synopsis

The conformation and the dynamic structure of single-stranded poly(U) and poly(C) in neutral aqueous solution have been investigated by 'H-nmr at two different frequencies (90 and 250 MHz) and at various temperatures. Measurements of proton chemical shifts, coupling constants JH-H, and proton relaxation times, TI, Tz, versus temperature show a striking difference in conformation and in dynamic structure between the two polynucleotides studied.

The temperature effect on 6 and JH-H is found to be substantial for poly(C) and insignificant for poly(U). The S conformer is favored in poly(U), whereas the N conformer strongly predominates in poly(C) (-go%), similar to the cage for RNAs. These results suggest that single-stranded poly(C) probably possesses a helical or partial helical structure, whereas poly(U) shows a clear preference for the random coil, in agreement with the optical results. The local motions of the ribose and base were studied at various temperatures by measurements on the relaxation times at 90 and 250 MHz. For a given temperature between 22 and 72"C, the ratio T1(90)/T1(250) is practically the same for all poly(U) protons, indicating that in this temperature interval the ribose base unit of poly(U) undergoes an isotropic motion characterized by a single correlation time T ~. Above 52OC, poly(C) exhibits a dynamic structure similar to poly(U). Below this temperature, poly(C) exists in an equilibrium between randomly coiled and single-stranded helix forms. This situation is characterized by a strong cross-relaxation effect and T1 values corresponding to a relatively short apparent correlation time. An activation energy of 4 kcal/mol was determined for the motion of the ribose-base unit in both single-stranded polynucleotides.