Polarity of annealing and structural analysis of the RNase H resistant alpha-5'-d(TACACA). beta-5'-r(AUGUGU) hybrid determined by high-field sup 1 H, sup 13 C, and sup 31 P NMR analysis

Journal Article · Tue Nov 13 00:00:00 EST 1990 · Biochemistry; (USA)

DOI:https://doi.org/10.1021/bi00497a007· OSTI ID:6152388

Gmeiner, W H; Rao, K E; Rayner, B; Vasseur, J J; Morvan, F; Imbach, J L; Lown, J W ^[1]

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1. Univ. of Alberta, Edmonton (Canada)

The novel hybrid duplex alpha-5'-d(TACACA)-3'.beta-5'-r(AUGUGU)-3' was analyzed extensively by 1D and 2D NMR methods. Two forms of the duplex exist in about an 80:20 ratio. Analysis of the exchangeable imino protons of the major component revealed that three AU and one AT base pair are present in addition to two GC base pairs, confirming that the duplex anneals in parallel orientation. The presence of the AT base pair, which can only be accounted for by a parallel duplex, was confirmed by a selective INEPT experiment, which correlated the thymidine imino proton to its C5 carbon. The lesser antiparallel form could be detected by exchangeable and nonexchangeable proton resonances in both strands. An exchange peak was observed in the NOESY spectrum for the thymidine methyl group resonance in both the predominant and lesser conformations, indicating the lifetime of the individual structures was on the millisecond time scale. The nonexchangeable protons of the predominant duplex were assigned by standard methods. The sugar pucker of the ribonucleosides was determined to be of the S type by a pseudorotation analysis according to Altona, with the J-couplings measured from the multiplet components of the phase-sensitive COSY experiment. The NOE pattern observed for the alpha-deoxynucleosides also suggested an S-type sugar pucker. The adoption of an S-type sugar pucker for both strands indicates that, in contrast to RNA.DNA duplexes formed exclusively from beta-nucleotides, the alpha-DNA.beta-RNA duplex may form a B-type helix. The 31P resonances of the alpha and beta strands have very different chemical shifts in the hybrid duplex and the difference persists above the helix melting temperature, indicating an intrinsic difference in 31P chemical shift for nucleotides differing only in the configuration about the glycosidic bond.

• OSTI ID: 6152388
• Journal Information: Biochemistry; (USA), Vol. 29:45; ISSN 0006-2960
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
NUCLEOSIDES
MOLECULAR STRUCTURE
CARBON 13
CHEMICAL SHIFT
COMPUTERIZED SIMULATION
DEUTERIUM
DNA HYBRIDIZATION
HELICAL CONFIGURATION
NMR SPECTRA
NUCLEAR MAGNETIC RESONANCE
NUCLEIC ACIDS
PHOSPHORUS 31
PROTONS
TRACER TECHNIQUES
BARYONS
CARBON ISOTOPES
CONFIGURATION
ELEMENTARY PARTICLES
EVEN-ODD NUCLEI
FERMIONS
HADRONS
HYBRIDIZATION
HYDROGEN ISOTOPES
ISOTOPE APPLICATIONS
ISOTOPES
LIGHT NUCLEI
MAGNETIC RESONANCE
NUCLEI
NUCLEONS
NUCLEOTIDES
ODD-EVEN NUCLEI
ODD-ODD NUCLEI
ORGANIC COMPOUNDS
PHOSPHORUS ISOTOPES
RESONANCE
RIBOSIDES
SIMULATION
SPECTRA
STABLE ISOTOPES
550201* - Biochemistry- Tracer Techniques