当前位置： SCI文献检索 > PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA期刊下所有文献 > A quantitative method for evaluating the stabilities of nucleic acids.

A quantitative method for evaluating the stabilities of nucleic acids.

Abstract：

:We report a general method for screening, in solution, the impact of deviations from canonical Watson-Crick composition on the thermodynamic stability of nucleic acid duplexes. We demonstrate how fluorescence resonance energy transfer (FRET) can be used to detect directly free energy differences between an initially formed "reference" duplex (usually a Watson-Crick duplex) and a related "test" duplex containing a lesion/alteration of interest (e.g., a mismatch, a modified, a deleted, or a bulged base, etc.). In one application, one titrates into a solution containing a fluorescently labeled, FRET-active, reference duplex, an unlabeled, single-stranded nucleic acid (test strand), which may or may not compete successfully to form a new duplex. When a new duplex forms by strand displacement, it will not exhibit FRET. The resultant titration curve (normalized fluorescence intensity vs. logarithm of test strand concentration) yields a value for the difference in stability (free energy) between the newly formed, test strand-containing duplex and the initial reference duplex. The use of competitive equilibria in this assay allows the measurement of equilibrium association constants that far exceed the magnitudes accessible by conventional titrimetric techniques. Additionally, because of the sensitivity of fluorescence, the method requires several orders of magnitude less material than most other solution methods. We discuss the advantages of this method for detecting and characterizing any modification that alters duplex stability, including, but not limited to, mutagenic lesions. We underscore the wide range of accessible free energy values that can be defined by this method, the applicability of the method in probing for a myriad of nucleic acid variations, such as single nucleotide polymorphisms, and the potential of the method for high throughput screening.

journal_name

Proc Natl Acad Sci U S A

journal_title

Proceedings of the National Academy of Sciences of the United States of America

authors

Gelfand CA,Plum GE,Mielewczyk S,Remeta DP,Breslauer KJ

doi

10.1073/pnas.96.11.6113

keywords:

subject

Has Abstract

pub_date

1999-05-25 00:00:00

pages

6113-8

issue

11

eissn

0027-8424

issn

1091-6490

journal_volume

96

pub_type

杂志文章

相关文献

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA文献大全
  • scid mutation in mice confers hypersensitivity to ionizing radiation and a deficiency in DNA double-strand break repair.

    abstract：:C.B-17 severe combined immunodeficient (scid) mice carry the scid mutation and are severely deficient in both T cell- and B cell-mediated immunity, apparently as a result of defective V(D)J joining of the immunoglobulin and T-cell receptor gene elements. In the present studies, we have defined the tissue, cellular, an...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.88.4.1394

    authors： Biedermann KA,Sun JR,Giaccia AJ,Tosto LM,Brown JM

    更新日期：1991-02-15 00:00:00

  • Rous sarcoma virus activates embryonic globin genes in chicken fibroblasts.

    abstract：:Complementary DNA (cDNA) specific for chick globin mRNA sequences fails to hybridize to total RNA extracted from chicken fibroblasts. After infection by Rous sarcoma virus, RNA complementary to globin cDNA is detectable in 100-500 copies per cell. Infection of fibroblasts with the transformation defective (td) deletio...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.72.11.4464

    authors： Groudine M,Weintraub H

    更新日期：1975-11-01 00:00:00

  • Mutations in ionotropic AMPA receptor 3 alter channel properties and are associated with moderate cognitive impairment in humans.

    abstract：:Ionotropic alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors (iGluRs) mediate the majority of excitatory synaptic transmission in the CNS and are essential for the induction and maintenance of long-term potentiation and long-term depression, two cellular models of learning and memory. We identi...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.0708699104

    authors： Wu Y,Arai AC,Rumbaugh G,Srivastava AK,Turner G,Hayashi T,Suzuki E,Jiang Y,Zhang L,Rodriguez J,Boyle J,Tarpey P,Raymond FL,Nevelsteen J,Froyen G,Stratton M,Futreal A,Gecz J,Stevenson R,Schwartz CE,Valle D,Huganir

    更新日期：2007-11-13 00:00:00

  • Reduction of the toxicity and mutagenicity of alkylating agents in mammalian cells harboring the Escherichia coli alkyltransferase gene.

    abstract：:The toxic, mutagenic, and carcinogenic effects of alkylating agents have been attributed to their ability to damage DNA. Reaction at the O6 position of guanine results in miscoding during DNA replication, has been shown to be mutagenic in both bacteriophage and bacteria, and may be responsible for malignant transforma...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.83.17.6292

    authors： Brennand J,Margison GP

    更新日期：1986-09-01 00:00:00

  • Sparsification of neuronal activity in the visual cortex at eye-opening.

    abstract：:Eye-opening represents a turning point in the function of the visual cortex. Before eye-opening, the visual cortex is largely devoid of sensory inputs and neuronal activities are generated intrinsically. After eye-opening, the cortex starts to integrate visual information. Here we used in vivo two-photon calcium imagi...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.0907660106

    authors： Rochefort NL,Garaschuk O,Milos RI,Narushima M,Marandi N,Pichler B,Kovalchuk Y,Konnerth A

    更新日期：2009-09-01 00:00:00

  • Transcriptional patterns in both host and bacterium underlie a daily rhythm of anatomical and metabolic change in a beneficial symbiosis.

    abstract：:Mechanisms for controlling symbiont populations are critical for maintaining the associations that exist between a host and its microbial partners. We describe here the transcriptional, metabolic, and ultrastructural characteristics of a diel rhythm that occurs in the symbiosis between the squid Euprymna scolopes and ...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.0909712107

    authors： Wier AM,Nyholm SV,Mandel MJ,Massengo-Tiassé RP,Schaefer AL,Koroleva I,Splinter-Bondurant S,Brown B,Manzella L,Snir E,Almabrazi H,Scheetz TE,Bonaldo Mde F,Casavant TL,Soares MB,Cronan JE,Reed JL,Ruby EG,McFall-Ngai MJ

    更新日期：2010-02-02 00:00:00

  • Artificial intelligence exploration of unstable protocells leads to predictable properties and discovery of collective behavior.

    abstract：:Protocell models are used to investigate how cells might have first assembled on Earth. Some, like oil-in-water droplets, can be seemingly simple models, while able to exhibit complex and unpredictable behaviors. How such simple oil-in-water systems can come together to yield complex and life-like behaviors remains a ...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.1711089115

    authors： Points LJ,Taylor JW,Grizou J,Donkers K,Cronin L

    更新日期：2018-01-30 00:00:00

  • Cerebellar GABAergic processes: evidence for critical involvement in a form of simple associative learning in the rabbit.

    abstract：:Converging evidence from electrophysiological recording and lesion studies suggests an essential role for the cerebellum in classical conditioning of the nictitating membrane response in the rabbit. The present study begins to delineate within this structure neurotransmitter systems that appear critical for the expres...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.84.7.2101

    authors： Mamounas LA,Thompson RF,Madden J 4th

    更新日期：1987-04-01 00:00:00

  • Interactive effects of age and estrogen on cognition and pyramidal neurons in monkey prefrontal cortex.

    abstract：:We previously reported that long-term cyclic estrogen (E) treatment reverses age-related impairment of cognitive function mediated by the dorsolateral prefrontal cortex (dlPFC) in ovariectomized (OVX) female rhesus monkeys, and that E induces a corresponding increase in spine density in layer III dlPFC pyramidal neuro...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.0704757104

    authors： Hao J,Rapp PR,Janssen WG,Lou W,Lasley BL,Hof PR,Morrison JH

    更新日期：2007-07-03 00:00:00

  • On the mechanism of chaperone activity of the small heat-shock protein of Methanococcus jannaschii.

    abstract：:The small heat-shock protein (sHSP) from Methanococcus jannaschii (Mj HSP16.5) forms a homomeric complex of 24 subunits and has an overall structure of a multiwindowed hollow sphere with an external diameter of approximately 120 A and an internal diameter of approximately 65 A with six square "windows" of approximatel...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.1032940100

    authors： Kim R,Lai L,Lee HH,Cheong GW,Kim KK,Wu Z,Yokota H,Marqusee S,Kim SH

    更新日期：2003-07-08 00:00:00

  • Dominant-negative cyclin-selective ubiquitin carrier protein E2-C/UbcH10 blocks cells in metaphase.

    abstract：:Destruction of mitotic cyclins by ubiquitin-dependent proteolysis is required for cells to complete mitosis and enter interphase of the next cell cycle. In clam eggs, this process is catalyzed by a cyclin-selective ubiquitin carrier protein, E2-C, and the cyclosome/anaphase promoting complex (APC), a 20S particle cont...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.94.6.2362

    authors： Townsley FM,Aristarkhov A,Beck S,Hershko A,Ruderman JV

    更新日期：1997-03-18 00:00:00

  • Precise genome engineering in Drosophila using prime editing.

    abstract：:Precise genome editing is a valuable tool to study gene function in model organisms. Prime editing, a precise editing system developed in mammalian cells, does not require double-strand breaks or donor DNA and has low off-target effects. Here, we applied prime editing for the model organism Drosophila melanogaster and...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.2021996118

    authors： Bosch JA,Birchak G,Perrimon N

    更新日期：2021-01-05 00:00:00

  • Artificial selection for a green revolution gene during japonica rice domestication.

    abstract：:The semidwarf phenotype has been extensively selected during modern crop breeding as an agronomically important trait. Introduction of the semidwarf gene, semi-dwarf1 (sd1), which encodes a gibberellin biosynthesis enzyme, made significant contributions to the "green revolution" in rice (Oryza sativa L.). Here we repo...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.1019490108

    authors： Asano K,Yamasaki M,Takuno S,Miura K,Katagiri S,Ito T,Doi K,Wu J,Ebana K,Matsumoto T,Innan H,Kitano H,Ashikari M,Matsuoka M

    更新日期：2011-07-05 00:00:00

  • Crystallization of myosin subfragment 1.

    abstract：:Crystals of myosin subfragment 1 from avian skeletal muscle have been grown reproducibly. They diffract x-rays to at least 4.5-A resolution. The subfragment 1 crystallizes in space group P2(1)2(1)2(1) where a = 107 A, b = 117 A, and c = 278 A. The cell dimensions and intensity distribution on x-ray diffraction photogr...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：

    authors： Rayment I,Winkelmann DA

    更新日期：1984-07-01 00:00:00

  • Overexpression of LMO4 induces mammary hyperplasia, promotes cell invasion, and is a predictor of poor outcome in breast cancer.

    abstract：:The zinc finger protein LMO4 is overexpressed in a high proportion of breast carcinomas. Here, we report that overexpression of a mouse mammary tumor virus (MMTV)-Lmo4 transgene in the mouse mammary gland elicits hyperplasia and mammary intraepithelial neoplasia or adenosquamous carcinoma in two transgenic strains wit...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.0502990102

    authors： Sum EY,Segara D,Duscio B,Bath ML,Field AS,Sutherland RL,Lindeman GJ,Visvader JE

    更新日期：2005-05-24 00:00:00

  • Hydrodynamic starvation in first-feeding larval fishes.

    abstract：:Larval fishes suffer prodigious mortality rates, eliminating 99% of the brood within a few days after first feeding. Hjort (1914) famously attributed this "critical period" of low survival to the larvae's inability to obtain sufficient food [Hjort (1914) Rapp P-v Réun Cons Int Explor Mer 20:1-228]. However, the cause ...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.1323205111

    authors： China V,Holzman R

    更新日期：2014-06-03 00:00:00

  • Induction of glucose-regulated proteins during anaerobic exposure and of heat-shock proteins after reoxygenation.

    abstract：:In this report we examine the effects of chronic anaerobic exposure and subsequent reoxygenation on protein synthesis patterns in Chinese hamster ovary cells. It is observed by two-dimensional gel electrophoresis (isoelectric focusing/NaDodSO4/PAGE) that the transition from an atmospheric environment to an anaerobic s...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.81.15.4843

    authors： Sciandra JJ,Subjeck JR,Hughes CS

    更新日期：1984-08-01 00:00:00

  • Position of aromatic residues in the S6 domain, not inactivation, dictates cisapride sensitivity of HERG and eag potassium channels.

    abstract：:Unintended block of HERG K+ channels is a side effect of many common medications and is the most common cause of acquired long QT syndrome associated with increased risk of life-threatening arrhythmias. The molecular mechanism of high-affinity HERG block by structurally diverse compounds has been attributed to pi-stac...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.192367299

    authors： Chen J,Seebohm G,Sanguinetti MC

    更新日期：2002-09-17 00:00:00

  • TMEM203 is a binding partner and regulator of STING-mediated inflammatory signaling in macrophages.

    abstract：:Regulation of IFN signaling is critical in host recognition and response to pathogens while its dysregulation underlies the pathogenesis of several chronic diseases. STimulator of IFN Genes (STING) has been identified as a critical mediator of IFN inducing innate immune pathways, but little is known about direct coreg...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.1901090116

    authors： Li Y,James SJ,Wyllie DH,Wynne C,Czibula A,Bukhari A,Pye K,Bte Mustafah SM,Fajka-Boja R,Szabo E,Angyal A,Hegedus Z,Kovacs L,Hill AVS,Jefferies CA,Wilson HL,Yongliang Z,Kiss-Toth E

    更新日期：2019-08-13 00:00:00

  • Dopa decarboxylase activity of the living human brain.

    abstract：:Monoaminergic neurons use dopa decarboxylase (DDC; aromatic-L-amino-acid carboxy-lyase, EC 4.1.1.28) to form dopamine from L-3,4-dihydroxyphenylalanine (L-dopa). We measured regional dopa decarboxylase activity in brains of six healthy volunteers with 6-[18F]fluoro-L-dopa and positron emission tomography. We calculate...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.88.7.2721

    authors： Gjedde A,Reith J,Dyve S,Léger G,Guttman M,Diksic M,Evans A,Kuwabara H

    更新日期：1991-04-01 00:00:00

  • A transmissible plasmid controlling camphor oxidation in Pseudomonas putida.

    abstract：:Earlier papers demonstrated an extensive genetic exchange among fluorescent Pseudomonads; this one documents for genes specifying enzymes of peripheral dissimilation an extrachromosomal array, segregation, and frequent interstrain transfer. An hypothesis is presented of a general mechanism for the formation and mainte...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.70.3.885

    authors： Rheinwald JG,Chakrabarty AM,Gunsalus IC

    更新日期：1973-03-01 00:00:00

  • Characterization of the two-protein complex in Escherichia coli responsible for lipopolysaccharide assembly at the outer membrane.

    abstract：:Lipopolysaccharide (LPS) is the major glycolipid that is present in the outer membranes (OMs) of most Gram-negative bacteria. LPS molecules are assembled with divalent metal cations in the outer leaflet of the OM to form an impervious layer that prevents toxic compounds from entering the cell. For most Gram-negative b...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.0912872107

    authors： Chng SS,Ruiz N,Chimalakonda G,Silhavy TJ,Kahne D

    更新日期：2010-03-23 00:00:00

  • Specific inhibition of Trypanosoma cruzi neuraminidase by the human plasma glycoprotein "cruzin".

    abstract：:Plasma of normal human individuals was shown to contain an inhibitor of Trypanosoma cruzi neuraminidase (NAase; acylneuraminyl hydrolase, sialidase, EC 3.2.1.18). The inhibitor has been purified to homogeneity by PEG precipitation, CM Affi-Gel Blue Sepharose chromatography, and gel filtration. The purified preparation...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.84.10.3097

    authors： Prioli RP,Rosenberg I,Pereira ME

    更新日期：1987-05-01 00:00:00

  • Purification of serine racemase: biosynthesis of the neuromodulator D-serine.

    abstract：:High levels of D-serine occur in mammalian brain, where it appears to be an endogenous ligand of the glycine site of N-methyl-D-aspartate receptors. In glial cultures of rat cerebral cortex, D-serine is enriched in type II astrocytes and is released upon stimulation with agonists of non-N-methyl-D-aspartate glutamate ...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.96.2.721

    authors： Wolosker H,Sheth KN,Takahashi M,Mothet JP,Brady RO Jr,Ferris CD,Snyder SH

    更新日期：1999-01-19 00:00:00

  • Herpes simplex virus 1-infected cell protein 0 contains two E3 ubiquitin ligase sites specific for different E2 ubiquitin-conjugating enzymes.

    abstract：:Infected cell protein 0 (ICP0) of herpes simplex virus 1, a multifunctional ring finger protein, enhances the expression of genes introduced into cells by infection or transfection, interacts with numerous cellular and viral proteins, and is associated with the degradation of several cellular proteins. Sequences encod...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.022531599

    authors： Hagglund R,Van Sant C,Lopez P,Roizman B

    更新日期：2002-01-22 00:00:00

  • Central role for hydrogen peroxide in P2Y1 ADP receptor-mediated cellular responses in vascular endothelium.

    abstract：:ADP activates a family of cell surface receptors that modulate signaling pathways in a broad range of cells. ADP receptor antagonists are widely used to treat cardiovascular disease states. These studies identify a critical role for the stable reactive oxygen species hydrogen peroxide (H2O2) in mediating cellular resp...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.1320854111

    authors： Kalwa H,Sartoretto JL,Martinelli R,Romero N,Steinhorn BS,Tao M,Ozaki CK,Carman CV,Michel T

    更新日期：2014-03-04 00:00:00

  • Machine-learning iterative calculation of entropy for physical systems.

    abstract：:Characterizing the entropy of a system is a crucial, and often computationally costly, step in understanding its thermodynamics. It plays a key role in the study of phase transitions, pattern formation, protein folding, and more. Current methods for entropy estimation suffer from a high computational cost, lack of gen...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.2017042117

    authors： Nir A,Sela E,Beck R,Bar-Sinai Y

    更新日期：2020-12-01 00:00:00

  • MYB30 links ROS signaling, root cell elongation, and plant immune responses.

    abstract：:Reactive oxygen species (ROS) are known to be important signal molecules that are involved in biotic and abiotic stress responses as well as in growth regulation. However, the molecular mechanisms by which ROS act as a growth regulator, as well as how ROS-dependent growth regulation relates to its roles in stress resp...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.1804233115

    authors： Mabuchi K,Maki H,Itaya T,Suzuki T,Nomoto M,Sakaoka S,Morikami A,Higashiyama T,Tada Y,Busch W,Tsukagoshi H

    更新日期：2018-05-15 00:00:00

  • Multimonth controlled small molecule release from biodegradable thin films.

    abstract：:Long-term, localized delivery of small molecules from a biodegradable thin film is challenging owing to their low molecular weight and poor charge density. Accomplishing highly extended controlled release can facilitate high therapeutic levels in specific regions of the body while significantly reducing the toxicity t...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.1323829111

    authors： Hsu BB,Park MH,Hagerman SR,Hammond PT

    更新日期：2014-08-19 00:00:00

  • Co-clustering of denatured hemoglobin with band 3: its role in binding of autoantibodies against band 3 to abnormal and aged erythrocytes.

    abstract：:Precipitates of hemoglobin, termed Heinz bodies, occur in a fraction of erythrocytes after removal of the spleen and are also observed in aged erythrocytes. This implies that precipitates of hemoglobin might play a particular role in senescent cell recognition. By using immunofluorescence microscopy, evidence is prese...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.83.16.6137

    authors： Schlüter K,Drenckhahn D

    更新日期：1986-08-01 00:00:00