Single-molecule fluorescence spectroscopy of TOTO on poly-AT and poly-GC DNA

Excited state lifetime and amplitude measurements were made on thiazole orange dimer (TOTO), a dimeric DNA-intercalating fluorophore, at single-molecule concentrations. As expected from previous study, the excited state lifetime of TOTO intercalated in DNA is dependent on the sequence of the double-stranded DNA, having values of 2.2 ns in poly-GC DNA and 1.8 ns in poly-AT DNA. The distribution of excited state lifetimes of single molecules of TOTO intercalated into oligonucleotides having varying proportions of poly-GC sequences relative to poly-AT sequences were analyzed as a function of the fraction of poly-GC. By using excited state lifetime distributions from the purely GC and purely AT oligonucleotides as a basis set, it was possible to estimate the GC content of oligonucleotides with intermediate GC composition to within a few percent error. This serves as a model for the analysis of equilibrium binding distributions in DNA using single-molecule methods.     

A dual-column HPLC method for the simultaneous determination of DHPG (9-[(1,3-dihydroxy-2-propoxy)methyl]guanine) and its mono and diesters in biological samples

A convenient method for the simultaneous determination of various DHPG species present in biological samples is presented. This method utilizes a cation exchange column (25 cm X 4.6 mm i.d.) coupled in series to a short reversed-phase column (5 cm X 4.6 mm i.d.). The mobile phase consists of methanol:0.005M ammonium phosphate buffer, pH 2.5. There is a large polarity difference between DHPG and its esters due to the non-polar side chain of the ester moiety. The simultaneous determination of the diesters, monoesters, and DHPG in these samples using only the cation exchange or the reversed-phase column is not possible without time-consuming gradient elution. In the reversed-phase mode alone, the esters are highly retained relative to DHPG, whereas the esters are only slightly retained on a cation exchange column and are insensitive to changes in pH and ionic strength of the mobile phase. However, a combination of these two columns provides interesting selectivity for these compounds and offers a unique way of controlling the retention times of these species relative to each other. The retention time of esters can be selectively altered (with respect to DHPG) by changing the composition of methanol in the mobile phase. In contrast, the retention time of DHPG is controlled by changing the buffer strength and pH of the mobile phase.     

Chemical modification of polymer surfaces: a review

The main approaches that have been taken to chemically modify polymer surfaces are introduced and reviewed. These are wet chemical oxidation, plasma treatment, classical organic chemistry, and attachment of polymer chains. The extent to which each of these approaches can produce the specific modifications desired is discussed, and any unwanted effects that commonly occur are cited. Finally, the need for using several methods of surface analysis in concert to obtain adequate surface characterization is described.     

The importance of ground-state vibronic mixing in molecular Raman scattering

We consider Albrecht's theory for Raman scattering of fundamentals in the far and pre-resonance regions. Destructive interferences inherent to the A and B terms augment the conventionally suppressed C term dramatically. Raman excitation profiles for the ν₁(a_1g) and ν₆(e_2g fundamentals in benzene can be well fitted with theoretical C-term profiles involving the ¹E_1u(π-π^*) state at 1800 A.     

Structural basis for recognition of bacterial cell wall teichoic acid by pseudo-symmetric SH3b-like repeats of a viral peptidoglycan hydrolase

Endolysins are bacteriophage-encoded peptidoglycan hydrolases targeting the cell wall of host bacteria via their cell wall-binding domains (CBDs). The molecular basis for selective recognition of surface carbohydrate ligands by CBDs remains elusive. Here, we describe, in atomic detail, the interaction between the Listeria phage endolysin domain CBD500 and its cell wall teichoic acid (WTA) ligands. We show that 3′O-acetylated GlcNAc residues integrated into the WTA polymer chain are the key epitope recognized by a CBD binding cavity located at the interface of tandem copies of beta-barrel, pseudo-symmetric SH3b-like repeats. This cavity consists of multiple aromatic residues making extensive interactions with two GlcNAc acetyl groups via hydrogen bonds and van der Waals contacts, while permitting the docking of the diastereomorphic ligands. Our multidisciplinary approach tackled an extremely challenging protein–glycopolymer complex and delineated a previously unknown recognition mechanism by which a phage endolysin specifically recognizes and targets WTA, suggesting an adaptable model for regulation of endolysin specificity.

Combining genetic, biochemical and computational approaches, we elucidated the molecular mechanisms underlying the recognition of Listeria wall teichoic acid by bacteriophage-encoded SH3b repeats.     

Rapid synthesis of pomalidomide-conjugates for the development of protein degrader libraries

Current methods for the preparation of heterobifunctional pomalidomide-conjugates rely on methods that are often low yielding and produce intractable byproducts. Herein we describe our strategy for the reliable and succinct preparation of pomalidomide-linkers which is essential to the formation of these conjugates. We present the preparation of 18 pomalidomide-linkers in high yield compared to current literature methods. Our findings show that secondary amines consistently afford greater yields than their primary counterparts, a trend that we were able to exploit in the synthesis of several new pomalidomide homo-dimers in enhanced yields compared to similar literature syntheses. This trend was further utilised to develop the first one-pot synthesis of JQ1-pomalidomide conjugates in yields up to 62%, providing a method that is suited to rapid preparation of conjugate libraries as is frequently required for the development of new protein degraders.

Current methods for the preparation of heterobifunctional pomalidomide-conjugates rely on methods that are often low yielding and produce intractable byproducts. Herein we describe our strategy for the succinct preparation of pomalidomide-linkers.     

ZIF-8 degrades in cell media,serum, and some—but not all—common laboratory buffers

ABSTRACT

Drug delivery using metal-organic frameworks (MOF) has elicited interest in their biocompatibility; however, few studies have been conducted on their stability in common buffers, cell media, and blood proteins. In particular, the use of ZIF-8, a MOF interconnected by Zn and methylimidazole, has been frequently employed. In this study, we tested single crystals of ZIF-8 with common laboratory buffers, cell media, and serum, and noted several issues. Buffers containing phosphate and bicarbonate alter the appearance and composition of ZIF-8; however, these buffers do not appear to cause cargo to leak out even when the ZIF-8 itself is displaced by phosphates. On the other hand, serum dissolves ZIF-8, causing premature cargo release. Our results show that ZIF-8 undergoes surface chemistry changes that may affect the interpretation of cellular uptake and cargo release data. On the other hand, it provides a rational explanation as to how ZIF-8 neatly dissolves in vivo.     

Appointment-driven queueing systems with non-punctual customers

Queueing Systems - We consider a single-server queueing system where a finite number of customers arrive over time to receive service. Arrivals are driven by appointments, with a scheduled...     

q-polymatroids and their relation to rank-metric codes

Journal of Algebraic Combinatorics - It is well known that linear rank-metric codes give rise to q-polymatroids. Analogously to matroid theory, one may ask whether a given q-polymatroid is...