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From the Functional and structural inter-relationships of RNA and
proteins in the execution and control of biological processes such as
RNA processing, RNA splicing, and translation are increasingly
apparent. In this minireview, I present an RNA chaperone hypothesis,
which fosters the view that constraints imposed by fundamental problems
in the folding of RNA have profoundly influenced the nature of
RNA/protein interactions in biology. The origin of this view is
outlined as follows. RNA has two fundamental folding problems: a
tendency to fold into and become kinetically trapped in
alternative conformations and a difficulty in specifying a single
tertiary structure that is thermodynamically strongly favored
over competing structures. RNA-binding proteins can help solve both RNA
folding problems. Nonspecific RNA-binding proteins ( ``RNA chaperone'' refers to proteins that aid in
RNA folding and is not meant to refer to chaperones made of RNA. ( There are no established
examples of RNA chaperones that act in vivo. This hypothesis
is presented because the in vitro data reviewed herein provide
support for the hypothesis and this view provides a conceptual
framework for RNA folding and RNA/protein interactions. The kinetic
problem in RNA folding is emphasized, while space constraints have
greatly limited discussion of the thermodynamic problem.
The Two Fundamental Folding Problems of RNA Many of the examples of RNA misfolding in vitro suggest that the inactive or alternative conformer is kinetically
trapped such that it does not revert to the active conformation even
after long periods of time. Early work showed that several tRNAs were
isolated in two conformations, only one of which could be charged by
the cognate aminoacyl-tRNA
synthetase(11, 12, 13, 14) . An
inactive tRNA Larger RNAs provide much additional evidence for a kinetic folding
problem. For example, in vitro self-splicing reactions of
group I introns, which are >200 nucleotides, typically do not
proceed to completion. This suggests the presence of kinetically
trapped, alternatively folded conformers (see also (20, 21, 22, 23, 24, 25, 26) ). The RNA folding problems observed in vitro could be
relevant to the in vivo behavior of RNA or could instead arise
as an artifact of in vitro handling of RNA, as RNA is
typically purified under denaturing conditions and then renatured. A
comparison of the primary, secondary, and tertiary structure of RNA and
proteins, based in part on an insightful analysis of tRNA
structure(27) , suggests that the kinetic folding problems
described above and additional thermodynamic folding problems are
intrinsic to RNA (summarized in Fig. 1and Table 1).
Figure 1:
RNA folding and the
effect of RNA chaperones. A, schematic free energy profiles
for folding of RNA in the absence (solid line) and presence (dashed line) of an RNA chaperone. Species with only secondary
structure are shown to emphasize the stability of RNA secondary
structure and the tendency to be trapped in incorrect secondary
structures, even though such species may not exist as discrete
intermediates. Only one alternative RNA secondary structure and only
one tertiary structure are shown for simplicity. The barrier for going
from unfolded to the correct secondary structure with and without
chaperone is shown as the same, although binding of a chaperone could
slow correct folding, as observed with protein chaperones. A protein
that lowers this barrier to speed the folding process can be referred
to as a ``guide.'' Chaperones work by decreasing the barrier
for escaping from the incorrectly folded structure. B, one of
several physical models of how an RNA chaperone could facilitate
refolding of misfolded RNAs. Imperfect charge complementarity between
the protein surface and RNA secondary structure (prot
The potential for alternative folds
appears to be a common property of RNAs. Even random RNAs are predicted
to have structures with about half of the residues base-paired,
consistent with the estimated helical content of randomly associated
RNAs(35, 36) .
Solutions to the RNA Folding Problems:
RNA Chaperones and Specific RNA-binding Proteins
This idea was apparently suggested for RNA over 20 years
ago(38, 39) . It was shown that the protein UP1, a
fragment of hnRNP ( Several recent
experiments strongly support such an in vitro RNA chaperone
activity of RNA-binding proteins. Slow physical steps in the reaction
of a hammerhead ribozyme limit turnover and specificity (43) so
this system provides an intermolecular model for the kinetic problems
in RNA folding, i.e. dissociation of intermolecular duplexes
is crucial for turnover and for discrimination against incorrect
(mispaired) RNA substrates(44) . This can be likened to the
unraveling of RNAs that have adopted incorrect secondary structures
during folding. Proteins such as the NC protein from HIV-1 and the
hnRNP A1 protein were shown to facilitate these physical steps and
thereby enhance the ribozyme reaction. In addition, the NC protein
resolved a kinetically trapped misfolded complex with
HH16(4, 6, 46, 47) . As mentioned
above, the self-splicing of group I introns in vitro is often
slow and inefficient, whereas splicing in vivo appears to be
fast and efficient(48) . In some cases, proteins facilitate
splicing in vivo by binding specifically to and stabilizing
the catalytically active conformation of the intron (49, 50, 51) . In contrast, the E. coli S12 ribosomal protein facilitates proper folding of group I
introns by nonspecific binding, suggesting a second mechanism for
aiding group I intron splicing in vivo(5) .
Characterization of the S12 protein facilitation further strengthened
the analogy between RNA chaperones and protein chaperones. (i) The S12
protein shows no preferential binding to group I introns over exons or
other RNAs, suggesting that S12 does not act by specifically stabilize
the intron's catalytic conformation. (ii) The S12 protein is also
able to facilitate a hammerhead ribozyme reaction, analogous to the NC
and hnRNP A1 proteins, further suggesting a nonspecific rather than
specific mode of action. (iii) The S12 protein promotes splicing of a
population of kinetically trapped, unreactive precursor RNA, suggesting
an ability to resolve misfolded RNAs. (iv) Protein chaperones function
solely during a folding step and are not present in the final active
species. The same stimulatory effect on group I self-splicing was
observed whether or not S12 was removed by proteolysis prior to
initiation of the self-splicing reaction. Thus, the S12 protein is
required solely for folding and can act as a true chaperone.
Figure 2:
Preassociation binding pathway in which a
specific RNA-binding protein also has RNA chaperone activity, using
nonspecific interactions to facilitate proper folding of its cognate
RNA. The nonspecific and specific interactions are represented
schematically by the absence and presence, respectively, of charge and
shape complementarity within the complexes.
Protein chaperones appear to be a distinct class of molecules
designed to facilitate protein folding. In contrast, the significant
extent of nonspecific binding by RNA-binding proteins suggests that
many RNA-binding proteins may exhibit RNA chaperone activity in
vitro. Protein chaperones
facilitate folding but do not remain bound to the final folded protein
product, whereas RNA chaperones may facilitate the folding process and
subsequently remain bound because of high levels of nonspecific binding
affinity. This may represent a basic difference in the primary
recognition element for the two classes of chaperones. Protein
chaperones appear to recognize unfolded proteins because of exposed
hydrophobic residues; when the protein folds and these residues are
buried, the chaperone no longer binds strongly(52) . In
contrast, the charged phosphodiester backbone and their bases are
likely to be at least partially exposed in unfolded or misfolded RNA,
allowing nonspecific binding, especially via electrostatic
interactions. Mechanistic studies of protein chaperones have
suggested that they prevent misfolding by sequestering unfolded forms
so that they cannot aggregate(52, 55, 56) .
RNA chaperones may act similarly by binding to regions of an RNA and
preventing or slowing formation of certain intramolecular structures.
The RNA chaperones have also been shown to resolve RNAs that have
already misfolded (see above), whereas the protein chaperones that have
been best characterized can bind and sequester unfolded proteins but
appear unable to bind efficiently to and resolve protein aggregates.
The high nonspecific binding activity of RNA-binding proteins may
account for this difference by allowing RNA chaperones to bind and
subsequently to resolve misfolded RNA conformers (Fig. 1B). However, recent in vivo characterization of the Hsp104 protein has suggested that it
actively resolubilizes protein aggregates(57, 58) , although the molecular basis
for this is not known. There are proteins other than the chaperones
referred to above that aid proper protein folding such as prolyl
isomerases and protein disulfide-isomerases(55) . Specific
RNA-binding proteins can exhibit RNA chaperone activity by helping to
prevent and resolve misfolding of both cognate and noncognate RNA (Fig. 2). Specific RNA-binding proteins could also aid the
process of folding for the cognate RNA by acting as
``guides'' in the folding process, i.e. by trapping
correctly folded domains or subdomains to help bias the RNA to follow
along the folding path toward the final correctly folded structure. In
addition, protein/protein interactions can bring together two RNAs (or
two regions of one RNA), thereby increasing the probability of duplex
formation or other interactions(2, 59, 60) .
Proteins that do this might be referred to as matchmakers, rather than
chaperones(7) . Such proteins may be involved in spliceosome
assembly. There is evidence that the hnRNP A1 protein can act as both a
chaperone and matchmaker (2, 6, 7) . RNA
chaperones, matchmakers, and guides each can increase the observed rate
of RNA/RNA assembly, so that it often may be difficult to distinguish
these mechanistically. RNAs could also act as RNA chaperones to
assist in the folding of other RNAs. ``Facilitators'' are
RNAs that base-pair to a ribozyme adjacent to the
substrate(61) ; they presumably prevent the ribozyme from
folding up upon itself, thereby increasing access for base-pairing to
the substrate. This is analogous to the facilitation of duplex
formation by single-strand binding proteins. There are several examples
of intramolecular changes that either introduce or resolve problems in
folding of an RNA (e.g.(62) and (63) ). This
might be likened to the role of the prosequence in reducing a kinetic
barrier in the folding of certain bacterial proteases(32) .
The use of energy by Rd-ATPases could also allow RNA folding
and unfolding steps to be integrated and regulated within complex
biological phenomena. For example, an Rd-ATPase may be used to
dissociate the U4-U6 snRNP complex at just the right time in
spliceosomal assembly, facilitating assembly of a catalytically active
spliceosome and/or preventing inappropriate or premature
splicing(68) . U4 may act as an RNA chaperone made of RNA that
prevents misfolding of U6.) Rd-ATPases could also help select between
alternative splice sites and prevent inaccurate splicing via a
proofreading function that limits the time allotted for individual
assembly and catalytic steps(69) . Rd-ATPases have also been
implicated in ribosomal assembly and translational initiation. The above ideas can be placed within a unifying but
speculative evolutionary context in which an early step in the
transition from the RNA world to the RNA/protein world was the
emergence of nonspecific RNA-binding peptides with chaperone-type
activities. These peptides could have provided a selective advantage in
a primitive RNA-dominated world by rescuing RNAs from kinetic traps,
aiding in the structural transition of a postreplicative duplex to a
folded, functional single-stranded RNA, and helping RNAs more broadly
explore structural alternatives. The appearance of a functional
nonspecific RNA-binding peptide is expected to be more probable than
the appearance of a specific RNA binder because there are more
solutions to the problem of nonspecific binding and because a
nonspecific binder would have many potential functional targets. Later in evolution, the problems in folding RNA could have
been parlayed into new opportunities for biological systems
via cooperation between RNA and proteins, with nonspecific RNA-binding
proteins with RNA chaperone functions developing binding preferences
and ATP-dependent activities for use in control and regulation. For
example, the hnRNP A1 protein has RNA chaperone activity (6, 7, 46) and also appears to be involved in
splice site selection(70) , and the NC protein from HIV has
chaperone activity and appears to bind viral RNA specifically during
packaging(4) .
Orchestration of RNA Chaperone Activity in Vivo The nonspecific RNA-binding proteins that enhance RNA
function can also shut down RNA function at higher concentrations, so
that there is a limited ``window of opportunity'' for each
protein to be functional (1, 6, 7) . How then
can a cell orchestrate the function of a large number of such proteins
amidst a pool of near-random RNA without merely binding to and
obscuring the function of a large subset of the RNAs? How are the
chaperones removed to allow the RNA to function? How does a specific
RNA-binding protein find its cognate RNA? The answers to these
questions are not known. Although the concentrations of the various RNA
and protein components and their affinities can be regulated to
influence RNA processing and function (e.g. Refs. 31, 33, 71,
72), it is not clear that affinities can be tuned and concentrations
regulated precisely enough to fully avoid problems of inappropriate
RNA/protein pairings and proteins obscuring RNA function. Higher order
temporal and spatial cellular organization could be used to avoid these
problems and to integrate RNA/protein interactions into other cellular
processes. RNA could be ``handed off'' from one protein to
another, with hnRNP proteins binding pre-mRNA as it is transcribed,
perhaps being selectively replaced by proteins to set the stage for
spliceosomal assembly and splicing(9, 34) . After
splicing, the mRNA may be escorted to the cytoplasm by a subset of the
hnRNPs and by other proteins (10) and then delivered to the
ribosome for translation. Evidence for hand offs of proteins from one
chaperone to another during folding (29, 56) provides
a conceptual precedent for analogous action by RNA chaperones. The
replacement of one protein by another could be spatially or temporally
regulated by spatial segregation of specific RNAs and specific
RNA-binding proteins within the nucleus (as for ribosomal assembly
within the nucleolus) or by fast initial binding of more weakly bound
proteins followed by slower binding of more strongly bound proteins and
complexes. A general advantage of keeping RNA molecules
protein-bound is that proteins can dissociate faster than some RNA
self-structures unravel on their own, allowing the RNA to change
partners in a timely fashion throughout its processing odyssey.
However, in some instances, the kinetic stability of RNA structures has
been co-opted for cellular function; the classical example is
attenuation of the trp and other bacterial operons that are
regulated via a choice between alternative RNA secondary
structures(45) . It will be fascinating over the coming
years to learn how RNA folding is controlled within the organization of
RNA processing and RNA function. On the molecular level, it will be
fascinating to unravel the mechanisms of RNA folding and RNA chaperone
activity.
Volume 270,
Number 36,
Issue of September 08, pp. 20871-20874, 1995
©1995 by The American Society for Biochemistry and Molecular Biology, Inc.
INTRODUCTION
The Two Fundamental Folding Problems of RNA
Solutions to the RNA Folding Problems:
RNA Chaperones and Specific RNA-binding Proteins
An Evolutionary Perspective
Orchestration of RNA Chaperone Activity in Vivo
FOOTNOTES
REFERENCES
)solve
the kinetic folding problem in vivo by acting as RNA
chaperones that prevent RNA misfolding and resolve misfolded RNAs,
thereby ensuring that RNA is accessible for its biological function. In
addition, specific RNA-binding proteins can solve the thermodynamic
folding problem by stabilizing a specific tertiary structure. The
emergence of nonspecific RNA-binding peptides with chaperone-type
activities may have been an early step in the transition from the RNA
world to the RNA/protein world. Specific RNA-binding proteins may also
have RNA chaperone activities that help prevent misfolding of their
cognate RNAs. RNA-dependent ATPases may act as RNA chaperones that
spatially and temporally control RNA conformational rearrangements. 
)For clarity, the classical chaperones that aid protein
folding are referred to as ``protein chaperones.'' In keeping
with the accepted definition of protein chaperones, RNA chaperones are
defined as proteins that aid in the process of RNA folding by
preventing misfolding or by resolving misfolded species. This is in
contrast to proteins that help protein or RNA folding by catalyzing
steps along the folding pathway or by stabilizing the final folded
protein or RNA structure.
was stable on the hour time scale in the
presence or absence of Mg
, but was converted to an
active conformation upon heating in the presence of
Mg
(12) . These inactive tRNAs apparently
adopt stable alternative secondary
structures(15, 16, 17, 18, 19) .
RNA). The protein speeds unfolding by favoring
conformational excursions that increase charge complementarity. The
protein binds more strongly to the unfolded RNA (prot
RNA) relative to the folded RNA
because the unfolded RNA is free to rearrange to give charge
complementarity with the protein. Refolding can occur from this state
to either the correct or incorrect secondary structure and is driven by
the stabilization from base pair formation, which counters the
destabilization from loss of charge
complementarity.
Primary Structure
RNA has a paucity of primary structure
diversity compared with proteins, with just 4 side chains instead of
20. Furthermore, the 4 RNA side chains are more similar to one another
than the protein side chains. The RNA side chains come in only two
``sizes,'' purine and pyrimidine, and each is a planar group
decorated with hydrogen bond donors and acceptors, whereas the protein
side chains comprise hydrophobic, hydrophilic, and charged groups of
varying sizes and shapes. The dearth of primary structure diversity, or
low ``information content,'' of an RNA polymer (relative to a
protein polymer) would be expected to render it more difficult for an
RNA sequence to specify a unique tertiary structure.Secondary Structure
The high thermodynamic
stability of RNA duplexes is expected to result in kinetic folding
problems. The most stable protein 
-helices dissociate on the
sub-microsecond time scale(28) . In contrast, an RNA duplex of
10 base pairs has a half-time for dissociation of 30 min, and
G/C-rich duplexes of 10 base pairs have dissociation half-times up to
100 years at 30 °C(30) . Thus, RNA can get stuck in
the wrong conformation (Fig. 1). This kinetic problem could
prevent a structured RNA from adopting the correct conformation, could
prevent access to mRNA, and could even prevent turnover of an RNA
subsequent to correct folding.
Tertiary Structure
The problem of stable
alternative secondary folds is exacerbated by fortuitous tertiary
interactions with 2`-hydroxyls, phosphoryl groups, and metal ions and
by the formation of nonstandard base/base interactions that can further
stabilize incorrect RNA conformers. Even after RNA adopts the correct
secondary structure, it is not yet ``out of the woods.'' The
low information content of RNA primary structure is further decreased
by sequestering the base-pairing faces of residues in the interior of
duplexed regions, while the side chains of proteins face outward in
-helices and 
-sheets. Each RNA secondary structure element
thus has a strong resemblance to others, so that RNA can have a
difficult time specifying a unique tertiary structure. For example, a
duplex of the Tetrahymena group I ribozyme docks into tertiary
interactions incorrectly approximately 1/1000 of the time, and
mutations increase this misdocking to about one-half (37) . (
)Thus, although there may be difficulty in ensuring that
the correct tertiary structure of an RNA is formed, this problem is not
insurmountable; a free energy preference of only 2 kcal/mol is
sufficient to ensure >95% correct folding. (
)
RNA Chaperones
The underlying basis
for the idea of RNA chaperones is simple. RNA has a fundamental folding
problem, a tendency to be kinetically trapped in misfolded forms (Fig. 1). Nonspecific RNA-binding proteins can overcome this
problem in vitro. It is therefore suggested that RNA-binding
proteins act as RNA chaperones to solve this RNA folding problem in
vivo.
)A1 protein, could renature 5 S and tRNAs
that were kinetically trapped in alternative conformations and
suggested that such activities would be necessary in biology. DNA
annealing experiments appear to have provided the intellectual roots
for these ideas(40) . Long single strands of RNA or DNA
reassociate orders of magnitude slower than short oligonucleotides, in
part because the longer nucleic acids form intramolecular structures
that limit access by the complementary strand. Catalysis of
polynucleotide annealing by single-strand nucleic acid-binding
proteins, such as T4 gene 32 protein and Escherichia coli SSB,
would then arise from a disruption of intramolecular structure that
enhances access for intermolecular
base-pairing(40, 41) . The RNA chaperone proposal
brings molecular chaperones full circle, as early speculation about the
involvement of chaperones in protein folding, which is now
well established, was framed by analogy to the ability of single-strand
nucleic acid-binding proteins to catalyze nucleic acid duplex
formation: both facilitate correct folding by preventing
misfolding(42) . The energetics of RNA chaperone action are
depicted schematically in Fig. 1A, and one physical
model is portrayed in Fig. 1B.Why a Specific RNA-binding Protein Would Also Act As an
RNA Chaperone: a ``Preassociation'' Binding
Mechanism
Even if a specific RNA-binding protein solves
RNA's thermodynamic folding problem by stabilizing the correct
RNA conformation, kinetic problems of attaining that conformation
remain, as depicted in the bottom pathway of Fig. 2. (i) The RNA
can be kinetically trapped in misfolded conformations (k), and (ii) the correctly folded RNA may
lack the thermodynamic stability to exist long enough to be
trapped efficiently by its cognate protein (k
versus k
). The ability of the S12
ribosomal protein to act as an RNA chaperone in the folding of group I
introns (5) raises the intriguing possibility that this
chaperone activity also solves these kinetic folding problems. Both
problems could be avoided by following a preassociation binding
mechanism (Fig. 2, top pathway), in which the protein
initially uses nonspecific interactions and/or a subset of specific
interactions to bind the unfolded RNA and prevent misfolding. The high
levels of nonspecific binding exhibited by many specific RNA-binding
proteins could allow this chaperone activity. Subsequently, the RNA
might undergo conformational rearrangements within the complex (or via
multiple partial or complete dissociations and reassociations, not
shown) until the correct conformation is attained and trapped by
specific interactions with the protein. Proteins that act via the top
pathway of Fig. 2can be referred to as specific RNA-binding
proteins that exhibit RNA chaperone ``activity.''
The Analogy between Protein and RNA
Chaperones
Protein chaperones have suggested that they
facilitate the process of protein folding by preventing
misfolding(52, 53) . As described above, proteins also
appear to facilitate RNA folding by preventing misfolding. The
following comparisons between RNA and protein chaperones may help
elucidate properties that are unique to RNA chaperones as well as
concepts that are fundamental to both RNA and protein chaperones. Over 20 different proteins from E. coli extracts were able to facilitate group I intron splicing in
vitro(5) , but it is not known which proteins, if any, act
as cellular RNA chaperones. The hnRNP proteins, which coat pre-mRNA as
it is transcribed, represent the most obvious candidate class for
cellular RNA chaperones (see also (54) ).Extending the RNA/Protein Folding Analogy to
RNA-dependent ATPases
Most or all of the known protein
chaperones use ATP(52) , in contrast to the RNA chaperones
discussed above. The RNA-dependent ATPases (Rd-ATPases), which
constitute a large family of proteins (64) , (
)may
be more akin to the protein chaperones as they use the energy of ATP
hydrolysis to facilitate structural transitions. However, despite this
gross similarity, there appear to be mechanistic distinctions. The
GroEL/GroES chaperonin appears to use ATP to strike a balance between
allowing the unfolded protein the opportunity to fold in solution versus sequestering it to prevent aggregation with other
unfolded proteins (65, 53, 66) . In contrast,
Rd-ATPases are presumably more akin to helicases, using ATP to disrupt
duplex and other structured regions in a stepwise fashion(67) .
It is not known to what extent ATP-independent and ATP-dependent
proteins are employed in vivo in the folding and unfolding of
RNA.
))))))
©1995 by The American Society for Biochemistry and Molecular Biology, Inc.
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V. Arluison, S. Hohng, R. Roy, O. Pellegrini, P. Regnier, and T. Ha Spectroscopic observation of RNA chaperone activities of Hfq in post-transcriptional regulation by a small non-coding RNA Nucleic Acids Res., February 16, 2007; 35(3): 999 - 1006. [Abstract] [Full Text] [PDF]
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A. Barkan, L. Klipcan, O. Ostersetzer, T. Kawamura, Y. Asakura, and K. P. Watkins The CRM domain: An RNA binding module derived from an ancient ribosome-associated protein RNA, January 1, 2007; 13(1): 55 - 64. [Abstract] [Full Text] [PDF]
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P. Tijerina, H. Bhaskaran, and R. Russell Nonspecific binding to structured RNA and preferential unwinding of an exposed helix by the CYT-19 protein, a DEAD-box RNA chaperone PNAS, November 7, 2006; 103(45): 16698 - 16703. [Abstract] [Full Text] [PDF]
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 I. Karakasiliotis, Y. Chaudhry, L. O. Roberts, and I. G. Goodfellow Feline calicivirus replication: requirement for polypyrimidine tract-binding protein is temperature-dependent. J. Gen. Virol., November 1, 2006; 87(Pt 11): 3339 - 3347. [Abstract] [Full Text] [PDF]
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I. Iost and M. Dreyfus DEAD-box RNA helicases in Escherichia coli Nucleic Acids Res., September 10, 2006; 34(15): 4189 - 4197. [Abstract] [Full Text] [PDF]
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R. J. W. Schoemaker and A. P. Gultyaev Computer simulation of chaperone effects of Archaeal C/D box sRNA binding on rRNA folding Nucleic Acids Res., April 13, 2006; 34(7): 2015 - 2026. [Abstract] [Full Text] [PDF]
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V. R. Tadigotla, D. O Maoileidigh, A. M. Sengupta, V. Epshtein, R. H. Ebright, E. Nudler, and A. E. Ruckenstein Thermodynamic and kinetic modeling of transcriptional pausing PNAS, March 21, 2006; 103(12): 4439 - 4444. [Abstract] [Full Text] [PDF]
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S. Mohr, M. Matsuura, P. S. Perlman, and A. M. Lambowitz A DEAD-box protein alone promotes group II intron splicing and reverse splicing by acting as an RNA chaperone PNAS, March 7, 2006; 103(10): 3569 - 3574. [Abstract] [Full Text] [PDF]
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J. J. DeStefano and O. Titilope Poliovirus Protein 3AB Displays Nucleic Acid Chaperone and Helix-Destabilizing Activities J. Virol., February 15, 2006; 80(4): 1662 - 1671. [Abstract] [Full Text] [PDF]
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M. Helm Post-transcriptional nucleotide modification and alternative folding of RNA Nucleic Acids Res., February 1, 2006; 34(2): 721 - 733. [Abstract] [Full Text] [PDF]
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M. A. MIR and A. T. PANGANIBAN The bunyavirus nucleocapsid protein is an RNA chaperone: Possible roles in viral RNA panhandle formation and genome replication RNA, February 1, 2006; 12(2): 272 - 282. [Abstract] [Full Text] [PDF]
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 K. Hunger, C. L. Beckering, F. Wiegeshoff, P. L. Graumann, and M. A. Marahiel Cold-Induced Putative DEAD Box RNA Helicases CshA and CshB Are Essential for Cold Adaptation and Interact with Cold Shock Protein B in Bacillus subtilis J. Bacteriol., January 1, 2006; 188(1): 240 - 248. [Abstract] [Full Text] [PDF]
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 S.L. WOLIN and E.J. WURTMANN Molecular Chaperones and Quality Control in Noncoding RNA Biogenesis Cold Spring Harb Symp Quant Biol, January 1, 2006; 71(0): 505 - 511. [Abstract] [PDF]
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R. Ivanyi-Nagy, I. Kanevsky, C. Gabus, J.-P. Lavergne, D. Ficheux, F. Penin, P. Fosse, and J.-L. Darlix Analysis of hepatitis C virus RNA dimerization and core-RNA interactions. Nucleic Acids Res., January 1, 2006; 34(9): 2618 - 2633. [Abstract] [Full Text] [PDF]
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P. Favaretto, A. Bhutkar, and T. F. Smith Constraining ribosomal RNA conformational space Nucleic Acids Res., September 9, 2005; 33(16): 5106 - 5111. [Abstract] [Full Text] [PDF]
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J. S. Bois, S. Venkataraman, H. M. T. Choi, A. J. Spakowitz, Z.-G. Wang, and N. A. Pierce Topological constraints in nucleic acid hybridization kinetics Nucleic Acids Res., July 25, 2005; 33(13): 4090 - 4095. [Abstract] [Full Text] [PDF]
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T. H. Johnson, P. Tijerina, A. B. Chadee, D. Herschlag, and R. Russell Structural specificity conferred by a group I RNA peripheral element PNAS, July 19, 2005; 102(29): 10176 - 10181. [Abstract] [Full Text] [PDF]
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A. BELISOVA, K. SEMRAD, O. MAYER, G. KOCIAN, E. WAIGMANN, R. SCHROEDER, and G. STEINER RNA chaperone activity of protein components of human Ro RNPs RNA, July 1, 2005; 11(7): 1084 - 1094. [Abstract] [Full Text] [PDF]
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E. J. Fialcowitz, B. Y. Brewer, B. P. Keenan, and G. M. Wilson A Hairpin-like Structure within an AU-rich mRNA-destabilizing Element Regulates trans-Factor Binding Selectivity and mRNA Decay Kinetics J. Biol. Chem., June 10, 2005; 280(23): 22406 - 22417. [Abstract] [Full Text] [PDF]
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S. S. KWAN and D. A. BROW The N- and C-terminal RNA recognition motifs of splicing factor Prp24 have distinct functions in U6 RNA binding RNA, May 1, 2005; 11(5): 808 - 820. [Abstract] [Full Text] [PDF]
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R. Grossberger, O. Mayer, C. Waldsich, K. Semrad, S. Urschitz, and R. Schroeder Influence of RNA structural stability on the RNA chaperone activity of the Escherichia coli protein StpA Nucleic Acids Res., April 22, 2005; 33(7): 2280 - 2289. [Abstract] [Full Text] [PDF]
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Z. Li and Y. Zhang Predicting the secondary structures and tertiary interactions of 211 group I introns in IE subgroup Nucleic Acids Res., April 20, 2005; 33(7): 2118 - 2128. [Abstract] [Full Text] [PDF]
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K. SEMRAD, R. GREEN, and R. SCHROEDER RNA chaperone activity of large ribosomal subunit proteins from Escherichia coli RNA, December 1, 2004; 10(12): 1855 - 1860. [Abstract] [Full Text] [PDF]
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K. Kahlina, I. Goren, J. Pfeilschifter, and S. Frank p68 DEAD Box RNA Helicase Expression in Keratinocytes: REGULATION, NUCLEOLAR LOCALIZATION, AND FUNCTIONAL CONNECTION TO PROLIFERATION AND VASCULAR ENDOTHELIAL GROWTH FACTOR GENE EXPRESSION J. Biol. Chem., October 22, 2004; 279(43): 44872 - 44882. [Abstract] [Full Text] [PDF]
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S. L. Heilman-Miller, T. Wu, and J. G. Levin Alteration of Nucleic Acid Structure and Stability Modulates the Efficiency of Minus-Strand Transfer Mediated by the HIV-1 Nucleocapsid Protein J. Biol. Chem., October 15, 2004; 279(42): 44154 - 44165. [Abstract] [Full Text] [PDF]
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S.-W. Park, R. Vepachedu, R. A. Owens, and J. M. Vivanco The N-Glycosidase Activity of the Ribosome-inactivating Protein ME1 Targets Single-stranded Regions of Nucleic Acids Independent of Sequence or Structural Motifs J. Biol. Chem., August 13, 2004; 279(33): 34165 - 34174. [Abstract] [Full Text] [PDF]
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 P. TOMPA and P. CSERMELY The role of structural disorder in the function of RNA and protein chaperones FASEB J, August 1, 2004; 18(11): 1169 - 1175. [Abstract] [Full Text] [PDF]
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G. Cristofari, R. Ivanyi-Nagy, C. Gabus, S. Boulant, J.-P. Lavergne, F. Penin, and J.-L. Darlix The hepatitis C virus Core protein is a potent nucleic acid chaperone that directs dimerization of the viral (+) strand RNA in vitro Nucleic Acids Res., May 11, 2004; 32(8): 2623 - 2631. [Abstract] [Full Text] [PDF]
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C. Gabus, R. Mazroui, S. Tremblay, E. W. Khandjian, and J.-L. Darlix The fragile X mental retardation protein has nucleic acid chaperone properties Nucleic Acids Res., April 19, 2004; 32(7): 2129 - 2137. [Abstract] [Full Text] [PDF]
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 M. Belfort Two for the price of one: a bifunctional intron-encoded DNA endonuclease-RNA maturase Genes & Dev., December 1, 2003; 17(23): 2860 - 2863. [Full Text] [PDF]
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C.-C. Wang, T.-C. Chang, C.-W. Lin, H.-L. Tsui, P. B. C. Chu, B.-S. Chen, Z.-S. Huang, and H.-N. Wu Nucleic acid binding properties of the nucleic acid chaperone domain of hepatitis delta antigen Nucleic Acids Res., November 15, 2003; 31(22): 6481 - 6492. [Abstract] [Full Text] [PDF]
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S. Lyonnais, R. J. Gorelick, J.-L. Mergny, E. Le Cam, and G. Mirambeau G-quartets direct assembly of HIV-1 nucleocapsid protein along single-stranded DNA Nucleic Acids Res., October 1, 2003; 31(19): 5754 - 5763. [Abstract] [Full Text] [PDF]
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G. Krishnamoorthy, B. Roques, J.-L. Darlix, and Y. Mely DNA condensation by the nucleocapsid protein of HIV-1: a mechanism ensuring DNA protection Nucleic Acids Res., September 15, 2003; 31(18): 5425 - 5432. [Abstract] [Full Text] [PDF]
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R. H. Roda, M. Balakrishnan, M. N. Hanson, B. M. Wohrl, S. F. J. Le Grice, B. P. Roques, R. J. Gorelick, and R. A. Bambara Role of the Reverse Transcriptase, Nucleocapsid Protein, and Template Structure in the Two-step Transfer Mechanism in Retroviral Recombination J. Biol. Chem., August 22, 2003; 278(34): 31536 - 31546. [Abstract] [Full Text] [PDF]
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N. Lee, R. J. Gorelick, and K. Musier-Forsyth Zinc finger-dependent HIV-1 nucleocapsid protein-TAR RNA interactions Nucleic Acids Res., August 15, 2003; 31(16): 4847 - 4855. [Abstract] [Full Text] [PDF]
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M. J. Heath, S. S. Derebail, R. J. Gorelick, and J. J. DeStefano Differing Roles of the N- and C-terminal Zinc Fingers in Human Immunodeficiency Virus Nucleocapsid Protein-enhanced Nucleic Acid Annealing J. Biol. Chem., August 15, 2003; 278(33): 30755 - 30763. [Abstract] [Full Text] [PDF]
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 Y. Ikawa, K. Sasaki, H. Tominaga, and T. Inoue The P5 Activator of a Group IC Ribozyme Can Replace the P7.1/7.2 Activator of a Group IA Ribozyme J. Biochem., May 1, 2003; 133(5): 665 - 670. [Abstract] [Full Text] [PDF]
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S. S. Derebail, M. J. Heath, and J. J. DeStefano Evidence for the Differential Effects of Nucleocapsid Protein on Strand Transfer in Various Regions of the HIV Genome J. Biol. Chem., April 25, 2003; 278(18): 15702 - 15712. [Abstract] [Full Text] [PDF]
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Y. Iwatani, A. E. Rosen, J. Guo, K. Musier-Forsyth, and J. G. Levin Efficient Initiation of HIV-1 Reverse Transcription in Vitro. REQUIREMENT FOR RNA SEQUENCES DOWNSTREAM OF THE PRIMER BINDING SITE ABROGATED BY NUCLEOCAPSID PROTEIN-DEPENDENT PRIMER-TEMPLATE INTERACTIONS J. Biol. Chem., April 11, 2003; 278(16): 14185 - 14195. [Abstract] [Full Text] [PDF]
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O. Boussadia, M. Niepmann, L. Creancier, A.-C. Prats, F. Dautry, and H. Jacquemin-Sablon Unr Is Required In Vivo for Efficient Initiation of Translation from the Internal Ribosome Entry Sites of both Rhinovirus and Poliovirus J. Virol., March 15, 2003; 77(6): 3353 - 3359. [Abstract] [Full Text] [PDF]
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Y. Ikawa, K. Tsuda, S. Matsumura, S. Atsumi, and T. Inoue Putative intermediary stages for the molecular evolution from a ribozyme to a catalytic RNP Nucleic Acids Res., March 1, 2003; 31(5): 1488 - 1496. [Abstract] [Full Text] [PDF]
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Z.-S. Huang, W.-H. Su, J.-L. Wang, and H.-N. Wu Selective Strand Annealing and Selective Strand Exchange Promoted by the N-terminal Domain of Hepatitis Delta Antigen J. Biol. Chem., February 14, 2003; 278(8): 5685 - 5693. [Abstract] [Full Text] [PDF]
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R. H. Roda, M. Balakrishnan, J. K. Kim, B. P. Roques, P. J. Fay, and R. A. Bambara Strand Transfer Occurs in Retroviruses by a Pause-initiated Two-step Mechanism J. Biol. Chem., November 27, 2002; 277(49): 46900 - 46911. [Abstract] [Full Text] [PDF]
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 P. Bjork, G. Bauren, S. Jin, Y.-G. Tong, T. R. Burglin, U. Hellman, and L. Wieslander A Novel Conserved RNA-binding Domain Protein, RBD-1, Is Essential For Ribosome Biogenesis Mol. Biol. Cell, October 1, 2002; 13(10): 3683 - 3695. [Abstract] [Full Text] [PDF]
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C. Waldsich, R. Grossberger, and R. Schroeder RNA chaperone StpA loosens interactions of the tertiary structure in the td group I intron in vivo Genes & Dev., September 1, 2002; 16(17): 2300 - 2312. [Abstract] [Full Text] [PDF]
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 J. Kufel, C. Allmang, L. Verdone, J. D. Beggs, and D. Tollervey Lsm Proteins Are Required for Normal Processing of Pre-tRNAs and Their Efficient Association with La-Homologous Protein Lhp1p Mol. Cell. Biol., July 15, 2002; 22(14): 5248 - 5256. [Abstract] [Full Text] [PDF]
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J. H. A. Nagel, A. P. Gultyaev, K. J. Oistamo, K. Gerdes, and C. W. A. Pleij A pH-jump approach for investigating secondary structure refolding kinetics in RNA Nucleic Acids Res., July 1, 2002; 30(13): e63 - e63. [Abstract] [Full Text] [PDF]
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W.-h. Zhang, C. K. Hwang, W.-S. Hu, R. J. Gorelick, and V. K. Pathak Zinc Finger Domain of Murine Leukemia Virus Nucleocapsid Protein Enhances the Rate of Viral DNA Synthesis in Vivo J. Virol., June 27, 2002; 76(15): 7473 - 7484. [Abstract] [Full Text] [PDF]
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S.-B. Jin, J. Zhao, P. Bjork, K. Schmekel, Per. O. Ljungdahl, and L. Wieslander Mrd1p Is Required for Processing of Pre-rRNA and for Maintenance of Steady-state Levels of 40 S Ribosomal Subunits in Yeast J. Biol. Chem., May 17, 2002; 277(21): 18431 - 18439. [Abstract] [Full Text] [PDF]
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A. V. Pisarev, M. A. Skabkin, A. A. Thomas, W. C. Merrick, L. P. Ovchinnikov, and I. N. Shatsky Positive and Negative Effects of the Major Mammalian Messenger Ribonucleoprotein p50 on Binding of 40 S Ribosomal Subunits to the Initiation Codon of beta -Globin mRNA J. Biol. Chem., May 3, 2002; 277(18): 15445 - 15451. [Abstract] [Full Text] [PDF]
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R. Russell, I. S. Millett, M. W. Tate, L. W. Kwok, B. Nakatani, S. M. Gruner, S. G. J. Mochrie, V. Pande, S. Doniach, D. Herschlag, et al. Rapid compaction during RNA folding PNAS, April 2, 2002; 99(7): 4266 - 4271. [Abstract] [Full Text] [PDF]
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J. Guo, T. Wu, B. F. Kane, D. G. Johnson, L. E. Henderson, R. J. Gorelick, and J. G. Levin Subtle Alterations of the Native Zinc Finger Structures Have Dramatic Effects on the Nucleic Acid Chaperone Activity of Human Immunodeficiency Virus Type 1 Nucleocapsid Protein J. Virol., March 27, 2002; 76(9): 4370 - 4378. [Abstract] [Full Text] [PDF]
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U. F. Muller and H. U. Goringer Mechanism of the gBP21-mediated RNA/RNA annealing reaction: matchmaking and charge reduction Nucleic Acids Res., January 15, 2002; 30(2): 447 - 455. [Abstract] [Full Text] [PDF]
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R. Russell, X. Zhuang, H. P. Babcock, I. S. Millett, S. Doniach, S. Chu, and D. Herschlag Exploring the folding landscape of a structured RNA PNAS, December 21, 2001; (2001) 221593598. [Abstract] [Full Text] [PDF]
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L. Rong, C. Liang, M. Hsu, X. Guo, B. P. Roques, and M. A. Wainberg HIV-1 Nucleocapsid Protein and the Secondary Structure of the Binary Complex Formed between tRNALys.3 and Viral RNA Template Play Different Roles during Initiation of (-) Strand DNA Reverse Transcription J. Biol. Chem., December 7, 2001; 276(50): 47725 - 47732. [Abstract] [Full Text] [PDF]
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G. M. Wilson, K. Sutphen, M. Moutafis, S. Sinha, and G. Brewer Structural Remodeling of an A + U-rich RNA Element by Cation or AUF1 Binding J. Biol. Chem., October 12, 2001; 276(42): 38400 - 38409. [Abstract] [Full Text] [PDF]
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O. G. Rossler, A. Straka, and H. Stahl Rearrangement of structured RNA via branch migration structures catalysed by the highly related DEAD-box proteins p68 and p72 Nucleic Acids Res., May 15, 2001; 29(10): 2088 - 2096. [Abstract] [Full Text] [PDF]
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J. Guo, T. Wu, J. Anderson, B. F. Kane, D. G. Johnson, R. J. Gorelick, L. E. Henderson, and J. G. Levin Zinc Finger Structures in the Human Immunodeficiency Virus Type 1 Nucleocapsid Protein Facilitate Efficient Minus- and Plus-Strand Transfer J. Virol., October 1, 2000; 74(19): 8980 - 8988. [Abstract] [Full Text]
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H. Zhang, R. J. Pomerantz, G. Dornadula, and Y. Sun Human Immunodeficiency Virus Type 1 Vif Protein Is an Integral Component of an mRNP Complex of Viral RNA and Could Be Involved in the Viral RNA Folding and Packaging Process J. Virol., September 15, 2000; 74(18): 8252 - 8261. [Abstract] [Full Text]
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E. V. Pilipenko, T. V. Pestova, V. G. Kolupaeva, E. V. Khitrina, A. N. Poperechnaya, V. I. Agol, and C. U.T. Hellen A cell cycle-dependent protein serves as a template-specific translation initiation factor Genes & Dev., August 15, 2000; 14(16): 2028 - 2045. [Abstract] [Full Text]
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S.-J. Chen and K. A. Dill RNA folding energy landscapes PNAS, January 18, 2000; 97(2): 646 - 651. [Abstract] [Full Text] [PDF]
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M. B. Long and B. A. Sullenger Evaluating Group I Intron Catalytic Efficiency in Mammalian Cells Mol. Cell. Biol., October 1, 1999; 19(10): 6479 - 6487. [Abstract] [Full Text] [PDF]
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K. Kossen and O. C. Uhlenbeck Cloning and biochemical characterization of Bacillus subtilis YxiN, a DEAD protein specifically activated by 23S rRNA: delineation of a novel sub-family of bacterial DEAD proteins Nucleic Acids Res., October 1, 1999; 27(19): 3811 - 3820. [Abstract] [Full Text] [PDF]
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T. Wu, J. Guo, J. Bess, L. E. Henderson, and J. G. Levin Molecular Requirements for Human Immunodeficiency Virus Type 1 Plus-Strand Transfer: Analysis in Reconstituted and Endogenous Reverse Transcription Systems J. Virol., June 1, 1999; 73(6): 4794 - 4805. [Abstract] [Full Text]
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J. Bhattacharyya and K. P. Das Molecular Chaperone-like Properties of an Unfolded Protein, alpha s-Casein J. Biol. Chem., May 28, 1999; 274(22): 15505 - 15509. [Abstract] [Full Text] [PDF]
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Y.-X. Feng, S. Campbell, D. Harvin, B. Ehresmann, C. Ehresmann, and A. Rein The Human Immunodeficiency Virus Type 1 Gag Polyprotein Has Nucleic Acid Chaperone Activity: Possible Role in Dimerization of Genomic RNA and Placement of tRNA on the Primer Binding Site J. Virol., May 1, 1999; 73(5): 4251 - 4256. [Abstract] [Full Text]
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N. K. Krishna and A. Schneemann Formation of an RNA Heterodimer upon Heating of Nodavirus Particles J. Virol., February 1, 1999; 73(2): 1699 - 1703. [Abstract] [Full Text]
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 J. S. Rosenblum, L. F. Pemberton, N. Bonifaci, and G. Blobel Nuclear Import and the Evolution of a Multifunctional RNA-binding Protein J. Cell Biol., November 16, 1998; 143(4): 887 - 899. [Abstract] [Full Text] [PDF]
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Z.-S. Huang and H.-N. Wu Identification and Characterization of the RNA Chaperone Activity of Hepatitis Delta Antigen Peptides J. Biol. Chem., October 9, 1998; 273(41): 26455 - 26461. [Abstract] [Full Text] [PDF]
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