Circular dichroism of double-helical oligoribonucleotides

543

499

The thermodynamics of double-helix formation in 1 M NaCl have been measured spectrophotometrically for CCGG, CCGGp, CCGGAp, ACCGGp, CCGGUp, and ACCGGUp. The results indicate additional double-helical stability is conferred by the terminal unpaired bases. The 3' A stabilizes the double helix more than the 5' A or the 3' U. The increased stability is due to a more favorable enthalpy change for double-helix formation. Comparison of the thermodynamics for CCGG, ACCGGp, CCGGUp, and ACCGGUp indicates stacking interactions are somewhat more important than pairing interactions in determining the stability of the terminal AU base pairs in ACCGGUp.

mentioning

confidence: 99%

Base-stacking and base-pairing contributions to helix stability: thermodynamics of double-helix formation with CCGG, CCGGp, CCGGAp, ACCGGp, CCGGUp, and ACCGGUp

Petersheim¹,

Turner²

1983

543

499

“…Typically, these structures contain short helical segments which are interrupted by internal loops, mismatches, or bulge nucleotides and terminated by hairpins or dangling ends (Cantor & Schimmel, 1980;Crawford & Stauffer, 1980;Gutell et al, 1985). The contribution of these various structural features to the stability of RNA has been subject to intensive research since the beginning of the seventies (Martin et al, 1971;Borer et al, 1973Borer et al, , 1974Breslauer et al, 1975). By means of improved synthetic techniques more interesting sequences could be realized and became the subject of different studies in the last few years (Petersheim & Turner, 1983;Freier et al, 1983Freier et al, , 1985Freier et al, , 1986aHickey & Turner, 1985;Sugimoto et al, 1987a,b;Turner et al, 1987;Groebe & Uhlenbeck, 1988Longfellow et al, 1990).…”

mentioning

confidence: 99%

Thermodynamics of double- and triple-helical aggregates formed by self-complementary oligoribonucleotides of the type rAxUy

Ohms¹,

Ackermann²

1990

The thermal denaturation of a series of oligoribonucleotides of the form rAxUy (x = 5 or 7 and y = 3-11) has been characterized by means of IR spectroscopy, UV spectroscopy, and DSC. IR spectra proved the occurrence of double- and triple-helical regions at various contents of uracil residues in the nucleotide. From DSC measurements transition enthalpies, entropies, and free enthalpies were derived. The effect of fraying in terminal base pairs of symmetrical nucleotides (x = y) was quantified. Thermodynamic excess parameters due to dangling ends (5'A and 3'U), terminal AU base pairs, and UAU base triplets were obtained by comparing DSC results from different nucleotides. Empirical values for contributions of base stacking and pairing to the stability of terminal AU base pairs have been estimated: for nucleotides under study with a high degree of fraying at the ends of the helix the major stabilization effect comes from base stacking. The size of the cooperative unit lambda in most nucleotides under study is larger than 1; i.e., in these cases intermolecular cooperation takes place. Through deconvolution of DSC data maximum populations of intermediate states FI,max were obtained. On the basis of these results all nucleotides under study were proved to melt in multistate manner. FI,max increases with the number of base pairs, decreases through dangling ends, and shows approximately constant values for triple-helical aggregates of the series rA5Uy as well as rA7Uy.

“…berg et al., 1973;Suck et al, 1973;Camerman et al, 1973), nuclear magnetic resonance (NMR) (Chan and Nelson, 1969;Fang et al, 1971;Barry et al, 1972;Smith et al, 1973;Altona et al, 1974;Evans et al, 1975), and circular dichroism (CD) (Warshaw and Cantor, 1971;Borer et al, 1973) studies and theoretical calculations (Yathindra and Sundaralingam, 1974). At the DNA level, X-ray Arnott and Seising, 1974) and infrared linear dichroism (Brahms et al, : 1973) studies on fibers, as well as wide angle X-ray scattering (Bram, 1973;Bram and Baudy, 1974) in solution, have demonstrated the dependence of DNA structure on counterion, sequence, humidity, and alcohol content of solvent.…”

mentioning

confidence: 99%

Nuclear magnetic resonance investigations of the structure of the self-complementary duplex of d-ApTpGpCpApT in aqueous solution

Patel¹,

Tonelli²

1975

Several features of the structure of the d-ApTpGpCpApT self-complementary duplex in solution are proposed from a nuclear magnetic resonance (NMR) analysis of the proton relaxation times, selective sugar proton coupling constants, and a comparison between the experimental chemical shifts on conversion to strands with those predicted from ring current calculations. The experimental longitudinal proton relaxation times for the various protons in each base pair are consistent with a double helix comprised of antiparallel strands and an anti conformation about the glycosidic bonds for both purine and pyrimidine bases. The molecular rotational correlation time for d-ApTpGpCpApT was calculated to be 1.4 X 10~9 sec at 34°. The sums of the vicinal coupling constants, /hi-h2-+ J , 2"; were found in the range 13-15 Hz, from the spectra of the six sugar Hv triplets of the hexanucleotide between 5.5 and 6.5 ppm. The magnitude of the coupling sum rulesThe structures of nucleic acids in the crystalline state, of fibers, and in solution have been intensely investigated. These include, at the dinucleotide to oligonucleotide level, recent X-ray crystallographic (Sussman et al., 1972; Rosen-