Triple Helical Polynucleotidic Structures: Sugar Conformations Determined by FTIR Spectroscopy

Abstract

Fourier Transform Infrared Spectra of triple stranded polynucleotides containing homopurine dA or rA and homopyrimidine dT or rU strands have been obtained in H2O and D2O solutions as well as in hydrated films at various relative humidities. The spectra are interpreted by comparison with those of double stranded helixes with identical base and sugar composition. The study of the spectral domain corresponding to in-plane double bond stretching vibrations of the bases shows that whatever the initial duplex characterized by a different IR spectrum (A family form poly rA.poly rU, heternomous form poly rA.poly dT, B family form poly dA.poly dT), the triplexes present a similar IR spectrum reflecting similar base interactions. A particular attention is devoted to the 950-800 cm-1 region which contains marker bands of the sugar conformation in the nucleic acids. In solution the existence of only N (C3'endo-A family form) type of sugar pucker is detected in poly rU.poly rA.poly rU and poly dt.poly rA.poly rU. On the contrary absorption bands characteristic of both N (C3'endo-A family form) and S (C2'endo-B family form) type sugars are detected for poly rU.poly rA.poly dT, poly rU.poly dA.poly dT and poly dT.poly rA.poly dT. Finally mainly S (C2'endo-B family form) type sugars are observed in poly dT.poly dA.poly dT.

Triple Helical Polynucleotidic Structures: An FTIR Study Of The C+· G · C Triplet

“…These bands can be unambiguously used for the characterization of unknown sugar geometries. The same marker bands have been discussed for sequences containing only A-T or A-U base pairs and have allowed us to determine the sugar conformations in triple helixes formed by T.A T and U.AU base triplets (33). The FTIR spectra of the triplexes discussed here are presented in Figure Sc,d,e,f.…”

“…Vibrational spectroscopy is a powerful technique to investigate the secondary structures of nucleic acids (28,29). Triple helixes containing T.AT and U.AU base triplets have been studied by Raman spectroscopy (30) and FfiR (31)(32)(33). In particular FfiR spectroscopy allows one to characterize the sugar geometry using unambiguous infrared marker bands of the N and S type conformations.…”

Spectroscopic evidence for an intramolecular RNA triple helix

“…The higher pH value was chosen to ensure that no protonated cytosine residues were likely to be present. An absorption observed at 1,705 cm-' is characteristic of C+ : G: C triplets [20], and disappearance of the adenine absorption around 1,633 cm-' at acidic pH has been shown to indicate the presence of U : A : U triplets [21]. The sugar geometries in nucleic acid dou- ble and triple helices are characterized by IR marker bands in the 1,00&800 cm-' region [22].…”

The Transition from a Neutral-pH Double Helix to a Low-pH Triple Helix Induces a Conformational Switch in the CCCG Tetraloop Closing a Watson-Crick Stem

“…At neutral pH the loop closes the B-type double helix stem of a hairpin. At low pH a triple helix is formed, in which the Watson-Crick double helix is supposed to adopt a conformation somewhere between A and B-type (Liquier et al, 1991;Macaya et al, 1992;Radhakrishnan & Patel, 1994). As is shown in Figure 7, the loop structures are remarkably similar in each situation.…”