Solution conformation of an RNA hairpin loop

Journal Article · Tue May 01 00:00:00 EDT 1990 · Biochemistry; (USA)

DOI:https://doi.org/10.1021/bi00469a026· OSTI ID:6169836

Puglisi, J D; Wyatt, J R; Tinoco, I Jr ^[1]

---

1. Univ. of California, Berkeley (USA)

The hairpin conformation adopted by the RNA sequence {sup 5{prime}}GCGAUUUCUGACCGCC{sup 3{prime}} has been studied by one-and two-dimensional NMR spectroscopy. Exchangeable imino spectra in 60 mM Na{sup +} indicate that the hairpin has a stem of six base pairs (indicated by boldface type) and a loop of three nucleotides. NOESY spectra of nonexchangeable protons confirm the formation of the stem region. The duplex has an A-conformation and contains an A{center dot}C apposition; a G{center dot}U base pair closes the loop region. The stem nucleotides have C3{prime}-endo sugar conformations, as expected of an A-form duplex, whereas the three loop nucleotides adopt C2{prime}-endo sugar puckers. Stacking within the loop, C{sub 8} upon the sugar of U{sub 7}, stabilizes the structure. The pH dependence of both the exchangeable and nonexchangeable NMR spectra is consistent with the formation of an A{sup +}{center dot}C base pair, protonated at the N1 position of adenine. The stability of the hairpin was probed by using absorbance melting curves. The hairpin structure with the A{sup +}{center dot}C base pair is about +2 kcal/mol less stable in free energy at 37{degree}C than the hairpin formed with an A{center dot}U pair replacing the A{sup +}{center dot}C pair.

• OSTI ID: 6169836
• Journal Information: Biochemistry; (USA), Vol. 29:17; ISSN 0006-2960
• Country of Publication: United States
• Language: English

Related Subjects

62 RADIOLOGY AND NUCLEAR MEDICINE
RNA
NUCLEAR MAGNETIC RESONANCE
AQUEOUS SOLUTIONS
CHEMICAL SHIFT
FREE ENERGY
MOLECULAR STRUCTURE
NMR SPECTRA
PH VALUE
TEMPERATURE DEPENDENCE
DISPERSIONS
ENERGY
MAGNETIC RESONANCE
MIXTURES
NUCLEIC ACIDS
ORGANIC COMPOUNDS
PHYSICAL PROPERTIES
RESONANCE
SOLUTIONS
SPECTRA
THERMODYNAMIC PROPERTIES
550601* - Medicine- Unsealed Radionuclides in Diagnostics