Abstract:
:A quantitative understanding of nucleic acid hybridization is essential to many aspects of biotechnology, such as DNA microarrays, as well as to the structure and folding kinetics of RNA. However, predictions of nucleic acid secondary structures have long been impeded by the presence of helices interior to loops, so-called pseudoknots, which impose complex three-dimensional conformational constraints. In this paper we compute the pseudoknot free energies analytically in terms of known standard parameters, and we show how the results can be included in a kinetic Monte Carlo code to follow the succession of secondary structures during quenched or sequential folding. For the hepatitis delta virus ribozyme, we predict several nonnative stems on the folding path, characterize a kinetically trapped state, interpret several experimentally characterized mutations in terms of the folding path, and suggest how hybridization with other parts of the genome inactivates the newly formed ribozyme.
journal_name
Proc Natl Acad Sci U S Aauthors
Isambert H,Siggia EDdoi
10.1073/pnas.110533697keywords:
subject
Has Abstractpub_date
2000-06-06 00:00:00pages
6515-20issue
12eissn
0027-8424issn
1091-6490pii
110533697journal_volume
97pub_type
杂志文章abstract::The present investigation studied the influence of the blastocyst's state of activity on the "window" of implantation in the receptive uterus in the mouse. The receptive state of the uterus is defined as the limited time when the uterine milieu is favorable to blastocyst acceptance and implantation. In the mouse, impl...
journal_title:Proceedings of the National Academy of Sciences of the United States of America
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doi:10.1073/pnas.90.21.10159
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abstract::The binding of bovine TSH (thyroid stimulating hormone), LH (luteinizing hormone), and their subunits to the TSH receptor of beef thyroid membranes was compared to stimulation by these agents of adenylate cyclase [ATP pyrophosphate-lyase(cyelizing), EC 4.6.1.1] in the same membranes, glucose oxidation in dog thyroid s...
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doi:10.1073/pnas.96.10.5774
更新日期:1999-05-11 00:00:00
abstract::Benthic foraminifers inhabit a wide range of aquatic environments including open marine, brackish, and freshwater environments. Here we show that several different and diverse foraminiferal groups (miliolids, rotaliids, textulariids) and Gromia, another taxon also belonging to Rhizaria, accumulate and respire nitrates...
journal_title:Proceedings of the National Academy of Sciences of the United States of America
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abstract::A fragment of the cloned gene for the human myeloma ND epsilon chain, coding for the second, third, and fourth domains of the immunoglobulin, has been coupled to the tryptophan control region of an expression plasmid and subcloned in Escherichia coli. Induction of gene expression results in the synthesis of the expect...
journal_title:Proceedings of the National Academy of Sciences of the United States of America
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abstract::Recent excavations at Pre-Pottery Neolithic A (PPNA) WF16 in southern Jordan have revealed remarkable evidence of architectural developments in the early Neolithic. This sheds light on both special purpose structures and "domestic" settlement, allowing fresh insights into the development of increasingly sedentary comm...
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journal_title:Proceedings of the National Academy of Sciences of the United States of America
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更新日期:1999-03-02 00:00:00
abstract::Allostatic load (AL) is a measure of overall physiological wear-and-tear over the life course, which could partially be the consequence of early life exposures. AL could allow a better understanding of the potential biological pathways playing a role in the construction of the social gradient in adult health. To explo...
journal_title:Proceedings of the National Academy of Sciences of the United States of America
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更新日期:2015-02-17 00:00:00
abstract::Acute myeloid leukemia subtype M4 with eosinophilia is associated with a chromosome 16 inversion that creates a fusion gene CBFB-MYH11. We have previously shown that CBFB-MYH11 is necessary but not sufficient for leukemogenesis. Here, we report the identification of genes that specifically cooperate with CBFB-MYH11 in...
journal_title:Proceedings of the National Academy of Sciences of the United States of America
pub_type: 杂志文章
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更新日期:2004-04-06 00:00:00
abstract::To elucidate the roles of IgE antibody in host responses to helminth infection, selective IgE-deficient SJA/9 mice were infected with the nematode parasites Nippostrongylus brasiliensis, which elicits remarkable potentiated IgE production, and Trichinella spiralis, which induces strong anti-Trichinella IgE antibody pr...
journal_title:Proceedings of the National Academy of Sciences of the United States of America
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journal_title:Proceedings of the National Academy of Sciences of the United States of America
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更新日期:2008-07-29 00:00:00
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journal_title:Proceedings of the National Academy of Sciences of the United States of America
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journal_title:Proceedings of the National Academy of Sciences of the United States of America
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journal_title:Proceedings of the National Academy of Sciences of the United States of America
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journal_title:Proceedings of the National Academy of Sciences of the United States of America
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更新日期:2010-06-01 00:00:00
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journal_title:Proceedings of the National Academy of Sciences of the United States of America
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journal_title:Proceedings of the National Academy of Sciences of the United States of America
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journal_title:Proceedings of the National Academy of Sciences of the United States of America
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journal_title:Proceedings of the National Academy of Sciences of the United States of America
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journal_title:Proceedings of the National Academy of Sciences of the United States of America
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journal_title:Proceedings of the National Academy of Sciences of the United States of America
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更新日期:2017-08-08 00:00:00
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journal_title:Proceedings of the National Academy of Sciences of the United States of America
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更新日期:2015-09-01 00:00:00
abstract::HU, the major DNA binding protein of Escherichia coli, exists in solution as a heterodimer composed of two highly homologous subunits: HU1, encoded by hupB; HU2, encoded by hupA. The purification of the HU protein from hupA- or hupB- bacteria showed that the hupB mutant strains synthesize normal amounts of the HU2 sub...
journal_title:Proceedings of the National Academy of Sciences of the United States of America
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更新日期:1989-10-01 00:00:00