Reactivity-Dependent PCR: Direct, Solution-Phase in Vitro Selection for Bond Formation

In vitro selection is a key component of efforts to discover functional nucleic acids and small molecules from libraries of DNA, RNA, and DNA-encoded small molecules. Such selections have been widely used to evolve RNA and DNA catalysts and, more recently, to discover new reactions from DNA-encoded libraries of potential substrates. While effective, current strategies for selections of bond-forming and bond-cleaving reactivity are generally indirect, require the synthesis of biotin-linked substrates, and involve multiple solution-phase and solid-phase manipulations. In this work we report the successful development and validation of reactivity-dependent PCR (RDPCR), a new method that more directly links bond formation or bond cleavage with the amplification of desired sequences and that obviates the need for solid-phase capture, washing, and elution steps. We show that RDPCR can be used to select for bond formation in the context of reaction discovery and for bond cleavage in the context of protease activity profiling.Chemistry and Chemical Biolog

Interaction-Dependent PCR: Identification of Ligand−Target Pairs from Libraries of Ligands and Libraries of Targets in a Single Solution-Phase Experiment

Interaction-dependent PCR (IDPCR) is a solution-phase method to identify binding partners from combined libraries of small-molecule ligands and targets in a single experiment. Binding between DNA-linked targets and DNA-linked ligands induces formation of an extendable duplex. Extension links codes that identify the ligand and target into one selectively amplifiable DNA molecule. In a model selection, IDPCR resulted in the enrichment of DNA encoding all five known protein−ligand pairs out of 67 599 possible sequences.Chemistry and Chemical Biolog

Bone turnover in elderly men: relationships to change in bone mineral density

BACKGROUND: It is not clear whether bone turnover markers can be used to make inference regarding changes in bone mineral density (BMD) in untreated healthy elderly men. The present study was designed to address three specific questions: (i) is there a relationship between bone turnover markers and femoral neck BMD within an individual; (ii) is there a relationship between baseline measurements of bone turnover markers and subsequent change in BMD; and (iii) is there a relationship between changes in bone turnover markers and changes in femoral neck BMD? METHODS: The present study was part of the on-going Dubbo Osteoporosis Epidemiology Study, which was designed as a prospective investigation. Men who had had at least 3 sequential visits with serum samples available during follow-up were selected from the study population. Serum C-terminal telopeptide of type I collagen (sICTP), N-terminal propeptide of type I collagen (sPINP) and femoral neck BMD were measured by competitive radioimmunoassays. Femoral neck bone mineral density (BMD) was measured by a densitometer (GE Lunar Corp, Madison, WI). Various mixed-effects models were used to assess the association between the markers and changes in BMD. RESULTS: One hundred and one men aged 70 ± 4.1 years (mean ± SD) met the criteria of selection for analysis. On average, sPINP decreased by 0.7% per year (p = 0.026), sICTP increased by 1.7% per year (p = 0.0002), and femoral neck BMD decreased by 0.4% per year (p < 0.01). Within-subject analysis indicated that changes in BMD were significantly associated with changes in sPINP (p = 0.022), but not with changes in sICTP (p = 0.84). However, neither baseline sPINP (p = 0.50) nor baseline sICTP (p = 0.63) was associated with subsequent changes in BMD. Moreover, changes in BMD were not significantly associated with previous changes in sPINP (p = 0.13) or sICTP (p = 0.95). CONCLUSION: These results suggest that in elderly men of Caucasian background, changes in sPINP were inversely related to changes in BMD within an individual. However, neither sPINP nor sICTP was sufficiently sensitive to predict the rate of change in BMD for a group of individuals or for an individual

The great screen anomaly—a new frontier in product discovery through functional metagenomics

Functional metagenomics, the study of the collective genome of a microbial community by expressing it in a foreign host, is an emerging field in biotechnology. Over the past years, the possibility of novel product discovery through metagenomics has developed rapidly. Thus, metagenomics has been heralded as a promising mining strategy of resources for the biotechnological and pharmaceutical industry. However, in spite of innovative work in the field of functional genomics in recent years, yields from function-based metagenomics studies still fall short of producing significant amounts of new products that are valuable for biotechnological processes. Thus, a new set of strategies is required with respect to fostering gene expression in comparison to the traditional work. These new strategies should address a major issue, that is, how to successfully express a set of unknown genes of unknown origin in a foreign host in high throughput. This article is an opinionating review of functional metagenomic screening of natural microbial communities, with a focus on the optimization of new product discovery. It first summarizes current major bottlenecks in functional metagenomics and then provides an overview of the general metagenomic assessment strategies, with a focus on the challenges that are met in the screening for, and selection of, target genes in metagenomic libraries. To identify possible screening limitations, strategies to achieve optimal gene expression are reviewed, examining the molecular events all the way from the transcription level through to the secretion of the target gene product