Coupled Schrödinger equations as a model of interchain torsional excitation transport in the DNA model

In this report we consider two weakly coupled Schrödinger equations as a model of interchain energy transport in the DNA double-helix. We employ a reduction of the Yakushevich-type model that considers the torsional dynamics of the DNA. In previous works, only small amplitude excitations and stationary dynamics were investigated, whereas we focus on the nonstationary dynamics of the double helix. In this report we consider two weakly coupled Schrödinger equations as a reduced model of interchain energy transport in the DNA double-helix torsional model. We employ a reduction of the Yakushevich-type model that considers the torsional dynamics of the DNA as effective chains of pendula. In previous works, only small amplitude excitations and stationary dynamics were investigated, whereas we focus on the nonstationary dynamics of the double helix. We consider the system to be a model of two weakly interacting DNA strands. Assuming that initially only one of the chains is excited in the form of a breather, we demonstrate the existence of an invariant that allows us to reduce the order of the problem and examine the system of the phase plane. The analysis demonstrates the utility of an analytical tool for predicting the periodic interchain excitation transitions of its localisation on one of the chains. The technique also takes into account the spreading of the excitations over time.

A hold-and-feed mechanism drives directional DNA loop extrusion by condensin

SMC protein complexes structure genomes by extruding DNA loops, but the molecular mechanism that underlies their activity has remained unknown. We show that the active condensin complex entraps the bases of a DNA loop in two separate chambers. Single-molecule and cryo-electron microscopy provide evidence for a power-stroke movement at the first chamber that feeds DNA into the SMC-kleisin ring upon ATP binding, while the second chamber holds on upstream of the same DNA double helix. Unlocking the strict separation of 'motor' and 'anchor' chambers turns condensin from a one-sided into a bidirectional DNA loop extruder. We conclude that the orientation of two topologically bound DNA segments during the course of the SMC reaction cycle determines the directionality of DNA loop extrusion.

Ionic strength modulates HU protein-induced DNA supercoiling

The histone-like protein from E. coli strain U93 (HU) is an abundant nucleoid-associated protein that contributes to the compaction of the bacterial genome as well as to the regulation of many of its transactions. Despite many years of investigations, the way and extent to which HU binding alters the DNA double helix and/or generates hierarchical structures using DNA as a scaffold is not completely understood. Here we combined single-molecule magnetic measurements with circular dichroism studies to monitor structural changes in the DNA-HU fiber as HU concentration was increased from 0 to 1000 nM under low and physiological monovalent salt conditions. We confirmed that DNA compaction correlated with HU concentration in a biphasic manner but DNA unwinding varied monotonically with HU concentration in 100 mM KCl. Instead, in more physiological 200 mM salt conditions, DNA compaction was monotonic while HU-induced DNA unwinding was negligible. Differential compaction and unwinding of DNA may be part of the response of bacteria to large variations in salt concentrations.

A gyógyszerkutatás új irányzatai: hatékonyság és biztonságosság

Összefoglaló. A betegségek mögött meghúzódó biokémiai, sejtbiológiai változások molekuláris szintű megértése a korszerű gyógyszerkutatás alapját képezi. A kiválasztott biológiai célpont, leggyakrabban egy fehérje, működésének gátlásától vagy fokozásától azt reméljük, hogy elősegíti a gyógyulást. A hagyományos gyógyszerkutatási megközelítések molekuláris alapját a kiválasztott fehérjével való közvetlen kölcsönhatás jelentette. Ugyanakkor a sejten belüli molekuláris biológiai folyamatok részletesebb megértése több új megközelítést nyitott a gyógyszerkutatás számára. A közlemény ezeket a gyógyszerkutatási irányzatokat mutatja be, külön kitérve biztonságosságukra. Summary. Human diseases originate from and are accompanied by changes in the biochemistry of cells. The molecular level understanding of these deviations from normal functioning is key to the curing of the diseases, therefore a principal objective of drug discovery. The key-lock principle postulated by Emil Fischer serves well the understanding of most enzymatic processes and has been helping researchers both in academia and industry to discover new drugs. The binding of a small molecule to the target protein and inhibiting or activating its function is the basis for the efficient functioning of a long list of current drugs. Sometimes the desired biological effect comes from the selective action on a single protein, in other instances it is the combined effect on the working of several proteins. The appropriate selectivity profile is key to the safety and efficiency of the drug in both cases. The completion of the Human Genome Project, in parallel with a significant improvement in the performance of the analytical instrumentation, increased our molecular and systemic level understanding of diseases immensely. Analysis of the differences between healthy and diseased cells and tissues led to the identification of new targets, a lot of which are not classical enzymes but proteins exerting their effect through molecular interactions with other proteins or nucleic acids. Although these proteins were considered undruggable some decades ago, their disease modifying potential led to the discovery of new approaches and modalities to target them. The inhibition of protein-protein interactions, for example, requires the selective targeting of hydrophobic surfaces, sometimes with very high affinity. Drug candidates acting through this molecular mechanism are typically beyond the size of classical drugs that might complicate their development. Besides interacting directly with the protein of interest we might also impact its working through manipulating its quantity within the cell. Interference with the proteasomal degradation of cellular proteins, blocking its working, or hijacking it to selectively increase the degradation of our protein of choice are promising new modalities that are transitioning from research into clinical practice. Alternatively, one might also interfere with the transcriptional machinery. Selective blocking of the messenger RNA responsible for carrying the sequence information of the targeted protein by using so called antisense oligonucleotides, small interfering RNAs, or micro RNAs can result in a decreased synthesis of the protein. Appropriately designed oligonucleotides can also enhance protein synthesis or lead to an alteration of the sequence to synthesize for a given protein. Finally, we might also target the epigenetic regulatory machinery, which is in charge of unpacking the DNA double helix from its storage form and making it available for transcription. This interference typically leads to a more complex change, the parallel modulation of the level of several proteins at the same time.

Expanding the Molecular Alphabet of DNA-Based Data Storage Systems with Neural Network Nanopore Readout Processing

DNA is a promising next-generation data storage medium, but the recording latency and synthesis cost of oligos using the four natural nucleotides remain high. Here, we describe an improved DNA-based storage system that uses an extended 11-letter molecular alphabet combining natural and chemically modified nucleotides. Our extended-alphabet molecular storage paradigm offers a nearly two-fold increase in storage density and potentially the same order of reduction in the recording time. Experimental results involving a library of 77 custom-designed hybrid sequences reveal that one can readily detect and discriminate different combinations and orders of monomers via MspA nanopores. Furthermore, a neural network architecture designed to classify raw current signals generated by Oxford Nanopore Technologies sequencing ensures an average accuracy exceeding 60%, which is 39 times higher than that of random guessing. Molecular dynamics simulations reveal that the majority of modified nucleotides do not induce dramatic disruption of the DNA double helix, making the extended alphabet system potentially compatible with PCR-based random access data retrieval. The methodologies proposed provide a forward path for new implementations of molecular recorders.

Exploring the ATR-CHK1 pathway in the response of doxorubicin-induced DNA damages in acute lymphoblastic leukemia cells

Doxorubicin (Dox) is one of the most commonly used anthracyclines for the treatment of solid and hematological tumors such as B−/T cell acute lymphoblastic leukemia (ALL). Dox compromises topoisomerase II enzyme functionality, thus inducing structural damages during DNA replication and causes direct damages intercalating into DNA double helix. Eukaryotic cells respond to DNA damages by activating the ATM-CHK2 and/or ATR-CHK1 pathway, whose function is to regulate cell cycle progression, to promote damage repair, and to control apoptosis. We evaluated the efficacy of a new drug schedule combining Dox and specific ATR (VE-821) or CHK1 (prexasertib, PX) inhibitors in the treatment of human B−/T cell precursor ALL cell lines and primary ALL leukemic cells. We found that ALL cell lines respond to Dox activating the G2/M cell cycle checkpoint. Exposure of Dox-pretreated ALL cell lines to VE-821 or PX enhanced Dox cytotoxic effect. This phenomenon was associated with the abrogation of the G2/M cell cycle checkpoint with changes in the expression pCDK1 and cyclin B1, and cell entry in mitosis, followed by the induction of apoptosis. Indeed, the inhibition of the G2/M checkpoint led to a significant increment of normal and aberrant mitotic cells, including those showing tripolar spindles, metaphases with lagging chromosomes, and massive chromosomes fragmentation. In conclusion, we found that the ATR-CHK1 pathway is involved in the response to Dox-induced DNA damages and we demonstrated that our new in vitro drug schedule that combines Dox followed by ATR/CHK1 inhibitors can increase Dox cytotoxicity against ALL cells, while using lower drug doses. Graphical abstract • Doxorubicin activates the G2/M cell cycle checkpoint in acute lymphoblastic leukemia (ALL) cells. • ALL cells respond to doxorubicin-induced DNA damages by activating the ATR-CHK1 pathway. • The inhibition of the ATR-CHK1 pathway synergizes with doxorubicin in the induction of cytotoxicity in ALL cells. • The inhibition of ATR-CHK1 pathway induces aberrant chromosome segregation and mitotic spindle defects in doxorubicin-pretreated ALL cells.

Understanding the Origin of Structural Diversity of DNA Double Helix

Deciphering the contribution of DNA subunits to the variability of its 3D structure represents an important step toward the elucidation of DNA functions at the atomic level. In the pursuit of that goal, our previous studies revealed that the essential conformational characteristics of the most populated “canonic” BI and AI conformational families of Watson–Crick duplexes, including the sequence dependence of their 3D structure, preexist in the local energy minima of the elemental single-chain fragments, deoxydinucleoside monophosphates (dDMPs). Those computations have uncovered important sequence-dependent regularity in the superposition of neighbor bases. The present work expands our studies to new minimal fragments of DNA with Watson–Crick nucleoside pairs that differ from canonic families in the torsion angles of the sugar-phosphate backbone (SPB). To address this objective, computations have been performed on dDMPs, cdDMPs (complementary dDMPs), and minimal fragments of SPBs of respective systems by using methods of molecular and quantum mechanics. These computations reveal that the conformations of dDMPs and cdDMPs having torsion angles of SPB corresponding to the local energy minima of separate minimal units of SPB exhibit sequence-dependent characteristics representative of canonic families. In contrast, conformations of dDMP and cdDMP with SPB torsions being far from the local minima of separate SPB units exhibit more complex sequence dependence.

What She Did for Love

This chapter reviews the marked asymmetry exhibited by the Lederberg collaboration. After 1958 when he won the Noble Prize, Joshua’s career took off while Esther’s sharply declined. For the awards ceremonies in Stockholm, Esther was demoted to Nobel wife. Coincidentally, 1958 was the year that Rosalind Franklin died, which disqualified her for sharing the Nobel Prize for the discovery of the DNA double helix. Franklin’s exceptional X-ray diffraction micrographs of DNA provided the critical evidence for Watson and Crick’s chemical model of DNA. In 1947, Gerty and Carl Cori were the first scientific couple to win the Nobel Prize in Physiology or Medicine. An exceptional complementarity distinguished the Cori relationship. More often, husband and wife collaborations are asymmetric: for six out of the seven other couples who earned one Nobel Prize, the husband alone received the award. Unlike most of their colleagues, B. O. Dodge congratulated both Lederbergs for achieving together the Nobel Prize.

A Hidden Legacy

This biography of Esther Zimmer Lederberg highlights the importance of her research work, which revealed the unique features of bacterial sex, essential for our understanding of molecular biology and evolution. A Hidden Legacy relates how, she and her husband Joshua Lederberg established the new field of bacterial genetics together, in the decade leading up to the discovery of the DNA double helix. Their impressive series of achievements include: the discovery of λ‎ bacteriophage and of the first plasmid, known as the F-factor; the demonstration that viruses carry bacterial genes between bacteria; and the elucidation of fundamental properties of bacterial sex. This successful collaboration earned Joshua the 1958 Nobel Prize, which he shared with two of Esther’s mentors, George Beadle and Edward Tatum. Esther Lederberg’s contributions, however, were overlooked by the Nobel committee, an example of institutional discrimination known as the Matilda Effect. Esther Lederberg should also have been recognized for inventing replica plating, an elegant technique that she originated by re-purposing her compact makeup pad as a kind of ink stamp for conveniently transferring bacterial colonies from one petri dish to another. Instead, the credit for the invention is given to her famous husband, or, at best, to Dr. and Mrs. Lederberg. Within a few years of winning the Nobel Prize, Joshua Lederberg divorced his wife, leaving Esther without a laboratory, cut off from research funding, and facing uncertain employment. In response, she created a new social circle made up of artists and musicians, including a new soulmate. She devoted herself to a close-knit musical ensemble, the Mid-Peninsula Recorder Orchestra, an avocation that flourished for over forty years, until the final days of her life.