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Nucleic Acid Denaturation (0):
Recent article
Nucleic Acid Denaturation
Abstract
We present a systematic review of published microsatellite primer notes and show that, on average, about half of all candidate loci are lost due to insufficient PCR amplification, monomorphism or multicopy status in the genome, no matter what isolation strategy is used. Thus, the screening of candid...
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PMID: 21847526
PDF is available here.
PDF is available here.
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Abstract
These results were confirmed by direct DNA sequencing and by high-resolution melting analysis. The costs and time constraints of each detection method were compared at the same time. In conclusion, our newly designed multiplex SNaPshot assay is a fast, inexpensive, sensitive, and robust technique fo...
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PMID: 21742054
PDF is available here.
PDF is available here.
Abstract
The V600E mutation in the BRAF oncogene is associated with colorectal carcinomas, with mismatch-repair deficiency and, recently, with nonresponse to epidermal growth factor receptor inhibitor therapy. The use of reliable techniques for its detection is important. The aim of our study...
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PMID: 21708284
PDF is available here.
PDF is available here.
Abstract
Base pairs formed by the inosine nucleoside (I) play an important role in many physiological processes as well as in various DNA technologies. Relative stabilities and favored base pair geometries of free inosine wobble base pairs in aprotic solvents have been determined through (1)H NMR measurements...
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PMID: 21644523
PDF is available here.
PDF is available here.
Audio, Transactions of the IRE Professional Group on (Chapter 17) 2011
Abstract
Multidimensional "3D" melting curves for G-quadruplexes are obtained by recording whole spectra (absorbance, CD, fluorescence) as a function of temperature, rather than the common approach of recording the spectral response to temperature at a single wavelength. 3D melting curves are...
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PMID: 21638271
PDF is available here.
PDF is available here.
Physical Chemistry (62)1 2011
Abstract
This review discusses multiscale modeling and simulations of macromolecules and macromolecular systems in the context of two specific examples. In the first, recent attempts to develop coarse-grained representations of DNA are reviewed, and a discussion of recent predictions of such models is present...
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PMID: 21219152
PDF is available here.
PDF is available here.
médecine/sciences (27)4 2011
Abstract
Abstract
Neoplasia cells exfoliated from colorectal epithelium have dysfunctional apoptotic mechanisms, thus it is possible to identify high-molecular weight DNA fragments in feces. This prospective single-center study was performed to evaluate the sensitivity and specificity of fecal-based DNA integrity vers...
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PMID: 21225430
PDF is available here.
PDF is available here.
Abstract
We hereby explored two dual-labeled, self-quenched probes, TaqMan and shared-stem molecular beacons, in their ability to conduct FMCA. Both probes could be directly used for FMCA and readily integrated with closed-tube amplicon hybridization under asymmetric PCR conditions. Improved flexibility of F...
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PMID: 21552536
PDF is available here.
PDF is available here.
Abstract
Universal newborn hearing screening (UNHS) is of paramount importance for early identification and management of hearing impairment in children. However, infants with slight/mild, progressive, or late-onset hearing impairment might be missed in conventional UNHS. To investigate whether genetic screen...
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PMID: 21811586
PDF is available here.
PDF is available here.
Abstract
Identification of somatic mutations in cancer is a major goal for understanding and monitoring the events related to cancer initiation and progression. High resolution melting (HRM) curve analysis represents a fast, post-PCR high-throughput method for scanning somatic sequence altera...
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PMID: 21264207
PDF is available here.
PDF is available here.
American Surgeon (11) 2011
Abstract
Abstract
We previously showed by NMR and molecular modeling that the unexpectedly high binding affinity of 2'F-ANA is largely due to a C-H···F-C pseudohydrogen bond at pyrimidine-purine steps. Comparisons of the melting of duplexes with identical sequence composition but a rearranged sequence confirm that...
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PMID: 21171597
PDF is available here.
PDF is available here.
Abstract
3-Aminophenyl-modified analogues of the bicyclic nucleoside N-methyl-3H-pyrrolo[2,3-d]pyrimidin-2(7H)-one were synthesised and incorporated directly into triplex-forming oligonucleotides in order to utilise their extended hydrogen bonding motif for recognition of the CG base pair. All analogues demo...
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PMID: 20835452
PDF is available here.
PDF is available here.
Radiation Research (174)5 2010
Abstract
This study reports the effects of denaturation and deoxygenation on radiation-induced formation of 2-deoxyribonolactone (2-dL) and 5'-aldehyde (5'-Ald) lesions in highly polymerized DNA. The radiation-chemical yields of 2-dL were determined through quantification of its dephosphorylation product 5-m...
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PMID: 20954863
PDF is available here.
PDF is available here.
ISME Journal (4)11 2010
Abstract
Lonar Lake is a unique saline and alkaline ecosystem formed by meteor impact in the Deccan basalts in India around 52,000 years ago. To investigate the role of methylotrophy in the cycling of carbon in this unusual environment, stable-isotope probing (SIP) was carried out using the o...
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PMID: 20555363
PDF is available here.
PDF is available here.
Analyst (Cambridge UK) (135)11 2010
Abstract
Remarkable direct electrochemical behaviors of thermally denatured calf thymus DNA (ssDNA) on the poly(methyl methacrylate)-graphite powder microcomposite electrode (PMMA/GME) were observed and investigated. The result indicated that the PMMA/GME showed great promotion of the electrochemical respons...
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PMID: 20877834
PDF is available here.
PDF is available here.
Abstract
We evaluated this method of mutation screening for the two major breast and ovarian cancer susceptibility genes BRCA1 and BRCA2. Screening of these two genes is time-consuming and must include exploration of large rearrangements that represent 5% to 15% of the alterations observed in these genes. To...
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PMID: 20858050
PDF is available here.
PDF is available here.
Abstract
We have demonstrated and validated a novel quantitative method based on a DNA integrity assay and mutation in faeces of CRC patients using denaturing high performance liquid chromatography (dHPLC).
Faecal DNA (fDNA) was isolated from 28 CRC, 96 healthy and 61 patients with adenomas. Adenomatosis pol...
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PMID: 20504269
PDF is available here.
PDF is available here.
Abstract
A new ligand DBHIP and its two ruthenium(II) complexes [Ru(dmb)(2)(DBHIP)](ClO(4))(2) (1) and [Ru(dmp)(2)(DBHIP)](ClO(4))(2) (2) have been synthesized and characterized. The cytotoxicity of DBHIP and complexes 1 and 2 has been assessed by MTT assay. The apoptosis studies were carried out with acridi...
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PMID: 20422275
PDF is available here.
PDF is available here.
Abstract
We previously confirmed that they conferred GCV resistance to recombinant baculoviruses (Nakano et al., J. Virol. Methods 161:223-230, 2009). Six characterized mutations, including a previously reported one that encodes a GCV-sensitive kinase-activity mutant (Isegawa et al., J. Clin. Virol. 44:15-19...
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PMID: 20083192
PDF is available here.
PDF is available here.
Abstract
We evaluated several methods and approaches for determining diversity including AP-PCR, chromosomal DNA fingerprinting, denaturing gradient gel electrophoresis, and 16S rRNA gene sequencing. Central to these methods was the gathering and screening of isolates from cultivation medium. Using various e...
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PMID: 20573585
PDF is available here.
PDF is available here.
EMBO Journal (29)15 2010
Abstract
We show that Lpm targets the sigma(70) subunit region 3.2 and the RNAP beta' subunit switch-2 element, which controls the clamping of promoter DNA in the RNAP active-site cleft. Lpm abolishes isomerization of the 'closed'-promoter complex to the transcriptionally competent 'open' complex and blocks...
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PMID: 20562828
PDF is available here.
PDF is available here.
Abstract
The molecular and ultrastructural profiles of the symbionts found in the midgut and ileum of Cephalotes atratus, Cephalotes clypeatus, and Cephalotes pusillus were determined using the V3 region of the bacterial 16S rDNA gene and transmission electron microscopy (T.E.M.). Two samples of C. atratus,...
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PMID: 20202856
PDF is available here.
PDF is available here.
Nanotechnology (21)25 2010
Abstract
We observed that TiO(2) nanoparticles of approximately 25 nm diameter caused significant enhancement of PCR efficiency for various types of templates (namely plasmid DNA, genomic DNA and complementary DNA). By a series of experiments, the optimal TiO(2) concentration was determined to be 0.4 nM, whi...
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PMID: 20516586
PDF is available here.
PDF is available here.
Journal of Hazardous Materials (178)1-3 2010
Abstract
Real-time polymerase chain reaction (PCR), denaturing gradient gel electrophoresis (DGGE), and the culture-based method were applied in the intrinsic bioremediation study at a petroleum-hydrocarbon contaminated site. The genes of phenol hydroxylase (PHE), ring-hydroxylating toluene monooxygenase (RM...
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PMID: 20185233
PDF is available here.
PDF is available here.
Journal of Hazardous Materials (178)1-3 2010
Abstract
This study was conducted with column experiments, batch experiments, and bench-scale permeable reactive barrier (PRB) for monitoring the PRB in the relation between BTEX (benzene, toluene, ethylbenzene, and p-xylene) decomposition efficiency and the distribution of a microbial community. To obtain t...
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PMID: 20122795
PDF is available here.
PDF is available here.
Abstract
(19)F NMR spectroscopy offers an efficient tool for monitoring RNA invasion. The invasion of 2'-O-methyl oligoribonucleotides into a (19)F-labeled HIV-1 TAR RNA model and the temperature-dependent behavior of the complexes obtained have been examined.
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PMID: 20521791
PDF is available here.
PDF is available here.
Abstract
Recombinant simian virus 40 (rSV40)-derived vectors are particularly useful for gene delivery to bone marrow progenitor cells and their differentiated derivatives, certain types of epithelial cells (e.g., hepatocytes), and central nervous system neurons and microglia. They integrate rapidly into cel...
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PMID: 20516175
PDF is available here.
PDF is available here.
Abstract
We describe the use of straightforward Tris borate, EDTA (TBE) gels for routine analysis. These gels are appropriate for determining the quantity and integrity of RNA before using it for other applications. This procedure should not be used to determine size with accuracy, because the RNA will not r...
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PMID: 20516183
PDF is available here.
PDF is available here.
Marine Biotechnology (12)3 2010
Abstract
We investigated microorganisms associated with a deep-sea sponge, Characella sp. (Pachastrellidae) collected at a hydrothermal vent site (686 m depth) in the Sumisu Caldera, Ogasawara Island chain, Japan, and with two sponges, Pachastrella sp. (Pachastrellidae) and an unidentified Poecilosclerida sp...
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PMID: 20221658
PDF is available here.
PDF is available here.
Abstract
Series of novel peptide-bridged bis-phenanthridine derivatives as well as corresponding monomers were prepared by solid phase peptide synthesis, which allowed easy and fast tuning of compound properties. Interactions of new derivatives with double stranded DNA were strongly structure-dependent, amon...
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PMID: 20202724
PDF is available here.
PDF is available here.
Abstract
Benzo[c][1,7] and [1,8]phenanthroline substituted by dialkylaminoalkyl side chains at position C2 and C1, respectively, were synthesized and their biological activity evaluated. These compounds displayed more potent cytotoxicity toward L1210 cells than the parent unsubstituted compounds, associated...
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PMID: 20236738
PDF is available here.
PDF is available here.
Nucleic Acids Research (38)11 2010
Abstract
We investigated the thermodynamic stability of the temperature labile hairpin 2 of the Salmonella fourU RNA thermometer over a broad temperature range and determined free energy, enthalpy and entropy values for the base-pair opening of individual nucleobases by measuring the temperature dependence o...
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PMID: 20211842
PDF is available here.
PDF is available here.
Nucleic Acids Research (38)11 2010
Abstract
We have recently described a Dilute-'N'-Go protocol that greatly simplifies preparation and sequencing of both strands of an amplicon generated using linear-after-the-exponential (LATE)-PCR, an advanced form of asymmetric PCR . The same protocol can also be used to sequence all limiting primer stran...
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PMID: 20189962
PDF is available here.
PDF is available here.
Abstract
We characterize the initial encounter between the enhancer-dependent Esigma(54) and its cognate activator AAA+ ATPase protein, before ADP+P(i) formation, using a small primed RNA (spRNA) synthesis assay. The results show that in a prehydrolysis state, sufficient activator-dependent rearrangements in...
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PMID: 20439713
PDF is available here.
PDF is available here.
Abstract
We employed DNA-functionalized gold nanoparticles (AuNPs) as a model system and found that if the alcohol content is less than approximately 30%, more alcohol leads to a faster DNA hybridization, although with a decreased melting temperature. The generality of this observation was independently veri...
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PMID: 20402504
PDF is available here.
PDF is available here.
Abstract
Despite progress with triplex-forming oligonucleotides or helix-invading peptide nucleic acids (PNAs), there remains a need for probes facilitating sequence-unrestricted targeting of double stranded DNA (dsDNA) at physiologically relevant conditions. Invader LNA probes, i.e., DNA duplexes with "+1 i...
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PMID: 20401378
PDF is available here.
PDF is available here.
FEMS Microbiology Letters (306)2 2010
Abstract
We examined changes in the bacterial community composition in the rape phyllosphere after treatment with dichlorvos, an organophosphorus pesticide. Results indicate that the bacterial community showed marked changes after treatment. We evaluated the rate of dichlorvos degradation by a natural microb...
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PMID: 20529133
PDF is available here.
PDF is available here.
Abstract
We study the thermally driven denaturation of a double-stranded polymer in the presence of a stretching force via Monte-Carlo simulations. When one strand only is stretched, the denaturation transition is first order, while when both strands are stretched, melting is second order. By revisiting the...
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PMID: 20866280
PDF is available here.
PDF is available here.
Clinica Chimica Acta (411)9-10 2010
Abstract
HRM analysis can be successfully applied to screen ETFDH mutations. Since riboflavin-responsive MADD is often treatable, especially with mutations in ETFDH, identifying ETFDH mutations is crucial for these patients.
Copyright 2010 Elsevier B.V. All rights reserved....
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PMID: 20138856
PDF is available here.
PDF is available here.
Abstract
We not only developed a few new compounds showing the AIE phenomena but also controlled the AIE through environmental stimulation and demonstrated that the new AIE molecules are suitable for pH and biomacromolecule sensing....
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PMID: 20112939
PDF is available here.
PDF is available here.
Abstract
A high-resolution melt (HRM) assay using a Rotor-Gene 6000 instrument was developed to characterize the codon for glycine 54 in the cyp51A genes from 13 reference isolates and 12 clinical isolates of Aspergillus fumigatus. Mutations in this codon confer reduced susceptibility to itraconazole and pos...
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PMID: 20194699
PDF is available here.
PDF is available here.
Methods in Molecular Biology (639)639 2010
Abstract
In plants, small RNA (microRNAs and other endogenous small RNAs)-guided target gene expression is vital for a wide variety of biological processes including adaptation to stress conditions. Identification of stress-regulated microRNAs or other classes of endogenous small RNAs advances our understand...
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PMID: 20387050
PDF is available here.
PDF is available here.
Abstract
After the identification of the human interferon-gamma (IFNG) variant G54D (c.287G>A, ss105106770) in DNA samples from Ghana, West Africa, systematic mutation screening of IFNG by the LightCycler((R))-based procedure of high-resolution melting (HRM) revealed additional rare mutations. All variants o...
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PMID: 20038203
PDF is available here.
PDF is available here.
Abstract
We report the basic principles and first applications of a new statistical approach to HRM analysis addressing these concerns. Our method allows automated genotyping of unknown samples coupled with formal statistical information on the likelihood, if an unknown sample is of a known genotype (by disc...
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PMID: 20146938
PDF is available here.
PDF is available here.
Medical Science Monitor (16)3 2010
Abstract
A rapid IL-6 gene genotyping assay was developed. The clinical data revealed that the -572G/C polymorphism in the IL-6 gene promoter region is involved in the pathogenesis and progression of CHD in the Han Chinese....
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PMID: 20190679
PDF is available here.
PDF is available here.
Clinical Biochemistry (43)4-5 2010
Abstract
The developed HRM method is efficient and reproducible for detection of SLC4A1 mutations and polymorphisms.
Copyright 2009 Elsevier Inc. All rights reserved....
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PMID: 20035734
PDF is available here.
PDF is available here.
Abstract
We evaluated the composition of the microbiota of supra- and subgingival plaque samples collected from 75 adult subjects with different drinking habits (drinkers of coffee, red wine, or water for at least 2 years) by analyzing the microbial population through the separation of PCR-amplified fragment...
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PMID: 19955272
PDF is available here.
PDF is available here.
Abstract
DNA Parallel clamps with a polypurine strand linked to a polypyrimidine Hoogsteen strand containing locked nucleic acids bind their corresponding polypyrimidine targets with high affinity.
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PMID: 20151386
PDF is available here.
PDF is available here.
Abstract
We devised a method to detect low mutation levels in brain DNA. Different proportions of a known SOD1 mutation were prepared to determine the sensitivity of DHPLC. The fraction containing the mutant signal was collected and re-amplified ('enriched') to increase sensitivity and to dideoxy sequence th...
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PMID: 20184515
PDF is available here.
PDF is available here.
Clinical laboratory (56)9-10 2010
Abstract
We investigated two populations, a mental disease group and a healthy control group, to identify whether these two genetic variants are correlated with the general development of a mental disorder and if they could potentially be used as predictive markers for manifestation of the same.
Using specif...
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PMID: 21086794
PDF is available here.
PDF is available here.
BMC Genetics (11)1 2010
Abstract
Although variations may occur, our results indicate that DHPLC and Dot Blot hybridization can be used as reliable screening methods for TP53 codon 72 polymorphism detection, especially in molecular epidemiologic studies, where high throughput methodologies are required....
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PMID: 20504317
PDF is available here.
PDF is available here.
Clinical laboratory (56)5-6 2010
Abstract
This study showed that HRM is a reliable screening method to identify mutations in the KRAS gene, and the PE can be used as a diagnostic method to accurately pinpoint the nature of mutations....
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PMID: 20575464
PDF is available here.
PDF is available here.
Upgrading SELEX technology by using lambda exonuclease digestion for single-stranded DNA generation.
Abstract
We demonstrate the considerable benefits of ssDNA production by lambda exonuclease digestion for in vitro selection of DNA aptamers. We believe that the generation of ssDNA aptamers using this method will greatly improve the success rate of SELEX experiments concerning the recovery of target-specifi...
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PMID: 20110867
PDF is available here.
PDF is available here.
Abstract
We describe methods for the construction and testing of sequence probes based on engineered zinc finger DNA-binding proteins. Background is reduced using split-reporter molecules, and signal is amplified using enzymatic reporters. The resulting sequence-enabled reassembly (SEER) probes can be config...
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PMID: 20680847
PDF is available here.
PDF is available here.
Abstract
The DNA x RNA hybrid duplexes are functionally important structures in gene expression that are underutilized as potential drug targets. Several tools are described here for the discovery and characterization of small molecules capable of the selective recognition of DNA x RNA hybrid structures. Com...
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PMID: 19997877
PDF is available here.
PDF is available here.
Abstract
We have used DGGE to screen hMLH1 and hMSH2 mutations and have shown high detection rate....
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PMID: 20721744
PDF is available here.
PDF is available here.
Abstract
We describe s-RT-MELT, a novel technology that enables expanded-throughput enzymatic mutation scanning in clinical cancer samples for germline or low-level somatic mutations, or for SNP genotyping. GC-clamp-containing PCR products from tumor and normal cells are hybridized to generate mismatches at...
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PMID: 20721745
PDF is available here.
PDF is available here.
Abstract
Denaturing high performance liquid chromatography (DHPLC) facilitates automated mutation scanning of PCR products with the ability to detect nearly 100% of sequence variants including single nucleotide substitutions and small insertions or deletions. It has particular application for genetic screeni...
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PMID: 20721741
PDF is available here.
PDF is available here.