PMID- 10744025
OWN - NLM
STAT- MEDLINE
DCOM- 20000421
LR  - 20190607
IS  - 1355-8382 (Print)
IS  - 1469-9001 (Electronic)
IS  - 1355-8382 (Linking)
VI  - 6
IP  - 3
DP  - 2000 Mar
TI  - Contribution of the intercalated adenosine at the helical junction to the 
      stability of the gag-pro frameshifting pseudoknot from mouse mammary tumor virus.
PG  - 409-21
AB  - The mouse mammary tumor virus (MMTV) gag-pro frameshifting pseudoknot is an 
      H-type RNA pseudoknot that contains an unpaired adenosine (A14) at the junction 
      of the two helical stems required for efficient frameshifting activity. The 
      thermodynamics of folding of the MMTV vpk pseudoknot have been compared with a 
      structurally homologous mutant RNA containing a G x U to G-C substitution at the 
      helical junction (U13C RNA), and an A14 deletion mutation in that context 
      (U13CdeltaA14 RNA). Dual wavelength optical melting and differential scanning 
      calorimetry reveal that the unpaired adenosine contributes 0.7 (+/-0.2) kcal 
      mol(-1) at low salt and 1.4 (+/-0.2) kcal mol(-1) to the stability (deltaG(0)37) 
      at 1 M NaCl. This stability increment derives from a favorable enthalpy 
      contribution to the stability deltadeltaH = 6.6 (+/-2.1) kcal mol(-1) with 
      deltadeltaG(0)37 comparable to that predicted for the stacking of a dangling 3' 
      unpaired adenosine on a G-C or G x U base pair. Group 1A monovalent ions, NH4+, 
      Mg2+, and Co(NH3)6(3+) ions stabilize the A14 and deltaA14 pseudoknots to largely 
      identical extents, revealing that the observed differences in stability in these 
      molecules do not derive from a differential or specific accumulation of ions in 
      the A14 versus deltaA14 pseudoknots. Knowledge of this free energy contribution 
      may facilitate the prediction of RNA pseudoknot formation from primary nucleotide 
      sequence (Gultyaev et al., 1999, RNA 5:609-617).
FAU - Theimer, C A
AU  - Theimer CA
AD  - Department of Biochemistry and Biophysics, Center for Macromolecular Design, 
      Texas A&M University, College Station 77843-2128, USA.
FAU - Giedroc, D P
AU  - Giedroc DP
LA  - eng
GR  - AI40187/AI/NIAID NIH HHS/United States
GR  - GM42569/GM/NIGMS NIH HHS/United States
PT  - Comparative Study
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PT  - Research Support, U.S. Gov't, P.H.S.
PL  - United States
TA  - RNA
JT  - RNA (New York, N.Y.)
JID - 9509184
RN  - 0 (Cations)
RN  - 0 (Cations, Divalent)
RN  - 0 (Intercalating Agents)
RN  - 0 (Metals)
RN  - 0 (RNA, Viral)
RN  - K72T3FS567 (Adenosine)
SB  - IM
MH  - Adenosine/metabolism/*physiology
MH  - Animals
MH  - Base Sequence
MH  - Calorimetry, Differential Scanning
MH  - Cations/pharmacology
MH  - Cations, Divalent/pharmacology
MH  - *Frameshifting, Ribosomal
MH  - Genes, gag/*genetics
MH  - Genes, pol/*genetics
MH  - Hot Temperature
MH  - Intercalating Agents/metabolism
MH  - Mammary Tumor Virus, Mouse/*physiology
MH  - Metals/pharmacology
MH  - Mice
MH  - Molecular Sequence Data
MH  - *Nucleic Acid Conformation
MH  - Nucleic Acid Denaturation
MH  - RNA Stability/*physiology
MH  - RNA, Viral/chemistry/metabolism/physiology
MH  - Retroviridae Infections/metabolism
MH  - Tumor Virus Infections/metabolism
PMC - PMC1369923
EDAT- 2000/04/01 09:00
MHDA- 2000/04/29 09:00
PMCR- 2000/03/01
CRDT- 2000/04/01 09:00
PHST- 2000/04/01 09:00 [pubmed]
PHST- 2000/04/29 09:00 [medline]
PHST- 2000/04/01 09:00 [entrez]
PHST- 2000/03/01 00:00 [pmc-release]
AID - 10.1017/s1355838200992057 [doi]
PST - ppublish
SO  - RNA. 2000 Mar;6(3):409-21. doi: 10.1017/s1355838200992057.