PMID- 2549508
OWN - NLM
STAT- MEDLINE
DCOM- 19890929
LR  - 20190501
IS  - 0305-1048 (Print)
IS  - 1362-4962 (Electronic)
IS  - 0305-1048 (Linking)
VI  - 17
IP  - 15
DP  - 1989 Aug 11
TI  - Thermodynamic stability and statistical significance of potential stem-loop 
      structures situated at the frameshift sites of retroviruses.
PG  - 6143-52
AB  - RNA stem-loop structures situated just 3' to the frameshift sites of the 
      retroviral gag-pol or gag-pro and pro-pol regions may make important 
      contributions to frame-shifting in retroviruses. In this study, the thermodynamic 
      stability and statistical significance of such secondary structural features 
      relative to others in the sequence have been assessed using a newly developed 
      method that combines calculations of the lowest free energy of formation of RNA 
      secondary structures and the Monte Carlo simulations. Our results show that 
      stem-loop structures situated just 3' to the frameshift sites are both highly 
      stable and statistically significant relative to others in the gag-pol or gag-pro 
      and pro-pol junction domains (both 300 nucleotides upstream and downstream from 
      the possible frameshift sites are included) of Rous sarcoma virus (RSV), human 
      immunodeficiency virus (HIV-1), bovine leukemia virus (BLV), human T-cell 
      leukemia virus type II (HTLV-II), and mouse mammary tumor virus (MMTV). No other 
      more stable, or significant folding regions are predicted in these domains.
FAU - Le, S Y
AU  - Le SY
AD  - Laboratory of Mathematical Biology, National Cancer Institute, Frederick, MD 
      21701.
FAU - Chen, J H
AU  - Chen JH
FAU - Maizel, J V
AU  - Maizel JV
LA  - eng
GR  - N01-CO-74102/CO/NCI NIH HHS/United States
PT  - Journal Article
PT  - Research Support, U.S. Gov't, P.H.S.
PL  - England
TA  - Nucleic Acids Res
JT  - Nucleic acids research
JID - 0411011
RN  - 0 (Gene Products, gag)
RN  - 0 (RNA, Viral)
RN  - 0 (Retroviridae Proteins)
SB  - IM
MH  - Avian Sarcoma Viruses/genetics
MH  - Base Sequence
MH  - Drug Stability
MH  - Gene Products, gag
MH  - HIV-1/genetics
MH  - Human T-lymphotropic virus 2/genetics
MH  - Leukemia Virus, Bovine/genetics
MH  - Mammary Tumor Virus, Mouse/genetics
MH  - Molecular Sequence Data
MH  - *Nucleic Acid Conformation
MH  - Protein Biosynthesis
MH  - *RNA, Viral
MH  - Retroviridae/*genetics
MH  - Retroviridae Proteins/*genetics
MH  - Thermodynamics
PMC - PMC318267
EDAT- 1989/08/11 00:00
MHDA- 1989/08/11 00:01
CRDT- 1989/08/11 00:00
PHST- 1989/08/11 00:00 [pubmed]
PHST- 1989/08/11 00:01 [medline]
PHST- 1989/08/11 00:00 [entrez]
AID - 10.1093/nar/17.15.6143 [doi]
PST - ppublish
SO  - Nucleic Acids Res. 1989 Aug 11;17(15):6143-52. doi: 10.1093/nar/17.15.6143.