Mechanisms of Small Molecule-DNA Interactions Probed by Single-molecule Force Spectroscopy

There is a wide range of applications for non-covalent DNA binding ligands, and optimization of such interactions requires detailed understanding of the binding mechanisms. One important class of these ligands is that of intercalators, which bind DNA by inserting aromatic moieties between adjacent DNA base pairs. Characterizing the dynamic and equilibrium aspects of DNA-intercalator complex assembly may allow optimization of DNA binding for specific functions. Single-molecule force spectroscopy studies have recently revealed new details about the molecular mechanisms governing DNA intercalation. These studies can provide the binding kinetics and affinity as well as determining the magnitude of the double helix structural deformations during the dynamic assembly of DNA–ligand complexes. These results may in turn guide the rational design of intercalators synthesized for DNA-targeted drugs, optical probes, or integrated biological self-assembly processes. Herein, we survey the progress in experimental methods as well as the corresponding analysis framework for understanding single molecule DNA binding mechanisms. We discuss briefly minor and major groove binding ligands, and then focus on intercalators, which have been probed extensively with these methods. Conventional mono-intercalators and bis-intercalators are discussed, followed by unconventional DNA intercalation. We then consider the prospects for using these methods in optimizing conventional and unconventional DNA-intercalating small molecules

Strong DNA Deformation Required for Extremely Slow DNA Threading Intercalation by a Binuclear Ruthenium Complex

DNA intercalation by threading is expected to yield high affinity and slow dissociation, properties desirable for DNA-targeted therapeutics. To measure these properties, we utilize single molecule DNA stretching to quantify both the binding affinity and the force-dependent threading intercalation kinetics of the binuclear ruthenium complex Δ,Δ-[μ‐bidppz‐(phen)4Ru2]4+ (Δ,Δ-P). We measure the DNA elongation at a range of constant stretching forces using optical tweezers, allowing direct characterization of the intercalation kinetics as well as the amount intercalated at equilibrium. Higher forces exponentially facilitate the intercalative binding, leading to a profound decrease in the binding site size that results in one ligand intercalated at almost every DNA base stack. The zero force Δ,Δ-P intercalation Kd is 44 nM, 25-fold stronger than the analogous mono-nuclear ligand (Δ-P). The force-dependent kinetics analysis reveals a mechanism that requires DNA elongation of 0.33 nm for association, relaxation to an equilibrium elongation of 0.19 nm, and an additional elongation of 0.14 nm from the equilibrium state for dissociation. In cells, a molecule with binding properties similar to Δ,Δ-P may rapidly bind DNA destabilized by enzymes during replication or transcription, but upon enzyme dissociation it is predicted to remain intercalated for several hours, thereby interfering with essential biological processes

Perioperative events influence cancer recurrence risk after surgery.

Surgery is a mainstay treatment for patients with solid tumours. However, despite surgical resection with a curative intent and numerous advances in the effectiveness of (neo)adjuvant therapies, metastatic disease remains common and carries a high risk of mortality. The biological perturbations that accompany the surgical stress response and the pharmacological effects of anaesthetic drugs, paradoxically, might also promote disease recurrence or the progression of metastatic disease. When cancer cells persist after surgery, either locally or at undiagnosed distant sites, neuroendocrine, immune, and metabolic pathways activated in response to surgery and/or anaesthesia might promote their survival and proliferation. A consequence of this effect is that minimal residual disease might then escape equilibrium and progress to metastatic disease. Herein, we discuss the most promising proposals for the refinement of perioperative care that might address these challenges. We outline the rationale and early evidence for the adaptation of anaesthetic techniques and the strategic use of anti-adrenergic, anti-inflammatory, and/or antithrombotic therapies. Many of these strategies are currently under evaluation in large-cohort trials and hold promise as affordable, readily available interventions that will improve the postoperative recurrence-free survival of patients with cancer

Impact of left ventricular dysfunction on early and late outcomes in patients undergoing concomitant aortic valve replacement and coronary artery bypass graft surgery

Background: An increasing proportion of patients present for concomitant aortic valve replacement (AVR) and coronary artery bypass grafting (CABG) with left ventricular (LV) dysfunction. The aim of this study was to evaluate the early outcomes and late survival of patients with different degrees of LV function undergoing concomitant AVR and CABG. Methods: Between June 2001 and December 2009, patients undergoing concomitant AVR-CABG were identified from the Australian and New Zealand Society of Cardiac and Thoracic Surgeons Cardiac Surgery Database Program. Demographic, operative data and post-operative outcomes were compared between patients with normal (> 60%), moderately impaired (30-60%), and severely impaired (< 30%) estimated LV ejection fraction (LVEF). Independent risk factors for short-and long-term mortality were identified using binary logistic and Cox regression, respectively. Results: AVR-CABG was performed in 2,563 patients with a mean follow up of 36 months (range 0-106). 144 (5.6%) had severely impaired LVEF, 983 (38.3%) had moderately impaired LVEF while the remaining 1377 (53.7%) had normal LVEF. The 30-day mortality in patients with severely impaired, moderately impaired and normal LVEF was 9.0%, 4.3% and 2.9%, respectively. This was significant on univariate (p < 0.001) but not multivariate analysis (p = NS). Severely impaired, moderately impaired and normal LVEF patients experienced 5-year survivals of 63.7%, 77.1% and 82.5%, respectively. Severely impaired LVEF was an independent multivariable predictor of late mortality (HR 1.71; 95% CI 1.22-2.40; p = 0.002). Conclusions: Patients with severely impaired LVEF experience worse outcomes. However, in the era of modern surgery, this alone should not predicate exclusion, given the established benefits of surgery in this high-risk group. © 2013 Via Medica

The effect of residents’ personality, emotional solidarity, and community commitment on support for tourism development

Residents' personality and their perspectives about community and those visiting can play an important role in forming overall support for tourism development. This study examined how residents' personality, emotional solidarity, and community commitment impact perceptions of tourism, which ultimately explain support for tourism development. To test the theoretical framework, survey data were collected from 340 residents living in two Malaysian tourism destinations. Structural equation modelling was utilized to assess the proposed model. Results revealed that sympathetic understanding and welcoming nature were the strongest factors influencing residents' attitudes towards tourism development while the effect was different among males and females with differing personality traits. Further analysis showed that the effect of welcoming nature and emotional closeness on residents’ attitude towards tourism development was different among residents with personalities of high agreeableness and extraversion, while openness to experience, conscientiousness, and neuroticism did not have a significant effect on these relationships