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Thermal stability, structural features, and B‐to‐Z transition in DNA tetraloop hairpins as determined by optical spectroscopy in d(CG) 3 T 4 (CG) 3 and d(CG) 3 A 4 (CG) 3 oligodeoxynucleotides
Author(s) -
Hernández Belén,
Baumruk Vladimir,
Gouyette Catherine,
Ghomi Mahmoud
Publication year - 2005
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.20246
Subject(s) - chemistry , raman spectroscopy , crystallography , loop (graph theory) , fourier transform infrared spectroscopy , thermal stability , absorption (acoustics) , stem loop , phase transition , aqueous solution , nucleotide , thermodynamics , materials science , physics , composite material , biochemistry , mathematics , organic chemistry , combinatorics , quantum mechanics , optics , gene
NMR and CD data have previously shown the formation of the T 4 tetraloop hairpin in aqueous solutions, as well as the possibility of the B‐to‐Z transition in its stem in high salt concentration conditions. It has been shown that the stem B‐to‐Z transition in T 4 hairpins leads to S (south)‐ to N (north)‐type conformational changes in the loop sugars, as well as anti to syn orientations in the loop bases. In this article, we have compared by means of UV absorption, CD, Raman, and Fourier transform infrared (FTIR), the thermodynamic and structural properties of the T 4 and A 4 tetraloop hairpins formed in 5′‐d(CGCGCG‐TTTT‐CGCGCG)‐3′ and 5′‐d(CGCGCG‐AAAA‐CGCGCG)‐3′, respectively. In presence of 5 M NaClO 4 , a complete B‐to‐Z transition of the stems is first proved by CD spectra. UV melting profiles are consistent with a higher thermal stability of the T 4 hairpin compared to the A 4 hairpin. Order‐to‐disorder transition of both hairpins has also been analyzed by means of Raman spectra recorded as a function of temperature. A clear Z‐to‐B transition of the stem has been confirmed in the T 4 hairpin, and not in the A 4 hairpin. With a right‐handed stem, Raman and FTIR spectra have confirmed the C2′‐ endo / anti conformation for all the T 4 loop nucleosides. With a left‐handed stem, a part of the T 4 loop sugars adopt a N‐type (C3′‐ endo ) conformation, and the C3′‐ endo / syn conformation seems to be the preferred one for the dA residues involved in the A 4 tetraloop. © 2005 Wiley Periodicals, Inc. Biopolymers 78: 21–34, 2005