The fluorescence-based real-time reverse transcription PCR (RT-PCR) is widely used for the quantification of steady-state mRNA levels and is a critical tool for basic research, molecular medicine and biotechnology. Assays are easy to perform, capable of high throughput, and can combine high sensitivity with reliable specificity. The technology is evolving rapidly with the introduction of new enzymes, chemistries and instrumentation. However, while real-time RT-PCR addresses many of the difficulties inherent in conventional RT-PCR, it has become increasingly clear that it engenders new problems that require urgent attention. Therefore, in addition to providing a snapshot of the state-of-the-art in real-time RT-PCR, this review has an additional aim: it will describe and discuss critically some of the problems associated with interpreting results that are numerical and lend themselves to statistical analysis, yet whose accuracy is significantly affected by reagent and operator variability.

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Quantification of mRNA using real-time reverse transcription PCR (RT-PCR): trends and problems.

III. Foldamer Research 3910 A. Overview 3910 B. Motivation 3910 C. Methods 3910 D. General Scope 3912 IV. Peptidomimetic Foldamers 3912 A. The R-Peptide Family 3913 1. Peptoids 3913 2. N,N-Linked Oligoureas 3914 3. Oligopyrrolinones 3915 4. Oxazolidin-2-ones 3916 5. Azatides and Azapeptides 3916 B. The â-Peptide Family 3917 1. â-Peptide Foldamers 3917 2. R-Aminoxy Acids 3937 3. Sulfur-Containing â-Peptide Analogues 3937 4. Hydrazino Peptides 3938 C. The γ-Peptide Family 3938 1. γ-Peptide Foldamers 3938 2. Other Members of the γ-Peptide Family 3941 D. The δ-Peptide Family 3941 1. Alkene-Based δ-Amino Acids 3941 2. Carbopeptoids 3941 V. Single-Stranded Abiotic Foldamers 3944 A. Overview 3944 B. Backbones Utilizing Bipyridine Segments 3944 1. Pyridine−Pyrimidines 3944 2. Pyridine−Pyrimidines with Hydrazal Linkers 3945

A field guide to foldamers.

The long wavelength (far-red to NIR) analyte-responsive fluorescent probes are advantageous for in vivo bioimaging because of minimum photo-damage to biological samples, deep tissue penetration, and minimum interference from background auto-fluorescence by biomolecules in the living systems. Thus, great interest in the development of new long wavelength analyte-responsive fluorescent probes has emerged in recent years. This review highlights the advances in the development of far-red to NIR fluorescent probes since 2000, and the probes are classified according to their organic dye platforms into various categories, including cyanines, rhodamine analogues, BODIPYs, squaraines, and other types (240 references).

Far-red to near infrared analyte-responsive fluorescent probes based on organic fluorophore platforms for fluorescence imaging

Design strategies for water-soluble small molecular chromogenic and fluorogenic probes.

Near-infrared (NIR) fluorescent dyes have emerged as promising modalities for monitoring the levels of various biologically relevant species in cells and organisms. The use of NIR probes enables deep photon penetration in tissue, minimizes photo-damage to biological samples, and produces low background auto-fluorescence from biomolecules present in living systems. The number of new analyte-responsive NIR fluorescent probes has increased substantially in recent years as a consequence of intense research efforts. In this tutorial review, we highlight recent advances (2010–2013) made in the development and applications of NIR fluorescent probes. The review focuses on NIR fluorescent probes that have been devised to sense various biologically important species, including ROS/RNS, metal ions, anions, enzymes and other related species, as well as intracellular pH changes. The basic principles involved in the design of functional NIR fluorescent probes and suggestions about how to expand applications of NIR imaging agents are also described.

Recent progress in the development of near-infrared fluorescent probes for bioimaging applications

New mono- and bis-Cu(II)-triazacyclononane(tacn) complex that conjugated with 9-aminoacridine were synthesized, and their binding modes and DNA cleavage activity were investigated in this study. When the classic intercalator, 9-aminoacridine, was conjugated to mono- and bis-Cu(II)-tacn complexes, a significant red-shift and hypochromism in absorption spectrum was apparent in the acridine absorption region upon binding to DNA. Furthermore, the magnitude of the negative reduced linear dichroism signal in the substrate absorption region appeared to be larger than that in the DNA absorption region. These spectral observations indicated that the acridine moiety intercalated when the Cu(II)-tacn complex was conjugated. In contrast, from a close analysis of the circular and linear dichroism spectrum, the aminoacridine-free bis-Cu(II)-tacn complex was concluded to bind at the phosphate groups of DNA. The 9-aminoacridine-free-bis-Cu(II)-tacn complex produces the nicked and linear DNA. On the other hand, 9-aminoacridine conjugated mono-and bis-Cu(II)-tacn complexes showed unspecific binding with negligible DNA cleavage.

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Cu(II) Complexes Conjugated with 9-Aminoacridine Intercalator: Their Binding Modes to DNA and Activities as Chemical Nuclease

The Z form of poly [d(G-m5C)2], in presence of Mg2+ ion, is found to be transformed into B form upon interaction with 4',6-diamidino-2-phenylindole (DAPI). The Z --> B transformation is complete at a mixing ratio of about 0.07 DAPI per DNA base pairs, i.e., each DAPI molecule may be related to the conversion of 6-7 base pairs. An interaction between DAPI and poly [d(G-m5C)2] in its Z form at low drug: DNA ratios is suggested from optical dichroism and time-resolved luminescence anisotropy results. The spectroscopic behaviour of DAPI indicates that the Z conformation of DNA does not provide normal binding sites for DAPI, such as groove or intercalation sites, but that the initial association may be of external nature. (C) 1993 John Wiley & Sons, Inc.

Z- b transition in poly d(g-m5c)2 induced by interaction with 4',6-diamidino-2-phenylindole

We compared various spectroscopic properties of a norfloxacin-single stranded DNA complex with those of norfloxacin-double stranded DNA complex. Norfloxacin binds to both double-and single stranded DNA, and we observed the following spectroscopic changes for both complexes: hypochromism in the norfloxacin absorption region in the absorption spectrum, the characteristic induced CD spectrum consisting of a weak positive band at 323 nm and a strong positive band at 280-300 nm followed by a negative band in the 260 nm region, a strong decrease in the fluorescence intensity and a red-shift in the fluorescence emission spectrum, and shorter fluorescence decay times. These results indicate that the environments of the bound norfloxacin in both DNAs are similar, although the equilibrium constant of the norfloxacin-single stranded DNA was twice as high as the norfloxacin-double stranded DNA complex. Both complexes were thermodynamically favored with similar negative Δ. Negative Δ terms contribute to these spontaneous reactions; Δ term was unfavorable.

Interaction between Norfloxacin and Single Stranded DNA

Binding of RecA to anti-parallel poly(dA).2poly(dT) triple helix DNA

were calculated using the molecular dynamics (MD) method. The 12 initial structuresthat were investigated in this work included were three ofloxacin: neutrals; zwitterions; and the protonatedspecies, for both the S- and R-enantiomers, each with two starting positions intercalative and minor groove. Thefour final structures with the most favorable free energies from the MD calculations consisted of two categoriesnamely, partial intercalative and the minor groove binding model. In the intercalative model that is found forthe protonated species, the molecular plane of both the S- and R-ofloxacin is inserted between two GC base-pairs with the protonated piperazine ring and the methyl group of the oxazine ring is exposed to the minorgroove. The binding energy of the S-ofloxacin in this model is slightly more favorable than R-ofloxacin.Conversely, even as it began with an initial intercalative structure, the neutral ofloxacin species is bound withinthe minor groove, whereby the molecular plane of ofloxacin tilts between 60-70o with respect to the DNAhelical axis. Two hydrogen bonds are possible for this groove binding model. Finally, the free energy of thezwitterionic ofloxacin is less favorable than that obtained from neutral and protonated species. Key Words : Molecular dynamics, Ofloxacin, Quinolone, DNA, Binding modeIntroductionQuinolone antibiotics exhibit antibacterial activity byinhibiting the action of Topoisomerase II.

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Seog K. Kim

Papers

Cu(II) Complexes Conjugated with 9-Aminoacridine Intercalator: Their Binding Modes to DNA and Activities as Chemical Nuclease

Z- b transition in poly d(g-m5c)2 induced by interaction with 4',6-diamidino-2-phenylindole

Interaction between Norfloxacin and Single Stranded DNA

Binding of RecA to anti-parallel poly(dA).2poly(dT) triple helix DNA

Molecular Dynamics Study on the Binding of S- and R-Ofloxacin to [d(ATAGCGCTAT)] 2 Oligonucleotide: Effects of Protonation States