Chung-ke Chang

Parity-dependent hairpin configurations of repetitive DNA sequence promote slippage associated with DNA expansion

Significance We found that TGGAA DNA repeats, which are involved in the neurological disease spinocerebellar ataxia 31, are capable of assuming two different hairpin structures depending on repeat number parity. We determined the interconversion kinetics by single-molecule spectroscopy and probed the interconversion mechanism through elucidation of the TGGAA repeat stem structure. Our results suggest that the two hairpin structures interconvert through motion slippage, and the process can be explained by the overall stem stability and local destabilization of the kinked GGA motif. Divalent cations and stem length affected the equilibrium and kinetics of slippage. Our findings suggest a mechanism by which a binary dynamic property of DNA repeats may affect repeat expansion and may be applicable to other repetitive DNA systems. Repetitive DNA sequences are ubiquitous in life, and changes in the number of repeats often have various physiological and pathological implications. DNA repeats are capable of interchanging between different noncanonical and canonical conformations in a dynamic fashion, causing configurational slippage that often leads to repeat expansion associated with neurological diseases. In this report, we used single-molecule spectroscopy together with biophysical analyses to demonstrate the parity-dependent hairpin structural polymorphism of TGGAA repeat DNA. We found that the DNA adopted two configurations depending on the repeat number parity (even or odd). Transitions between these two configurations were also observed for longer repeats. In addition, the ability to modulate this transition was found to be enhanced by divalent ions. Based on the atomic structure, we propose a local seeding model where the kinked GGA motifs in the stem region of TGGAA repeat DNA act as hot spots to facilitate the transition between the two configurations, which may give rise to disease-associated repeat expansion.

Recent insights into the development of therapeutics against coronavirus diseases by targeting N protein

n n The advent of severe acute respiratory syndrome (SARS) in the 21st century and the recent outbreak of Middle-East respiratory syndrome (MERS) highlight the importance of coronaviruses (CoVs) as human pathogens, emphasizing the need for development of novel antiviral strategies to combat acute respiratory infections caused by CoVs. Recent studies suggest that nucleocapsid (N) proteins from coronaviruses and other viruses can be useful antiviral drug targets against viral infections. This review aims to provide readers with a concise survey of the structural features of coronavirus N proteins and how these features provide insights into structure-based development of therapeutics against coronaviruses. We will also present our latest results on MERS-CoV N protein and its potential as an antiviral drug target.n n

Crystallographic analysis of the N-terminal domain of Middle East respiratory syndrome coronavirus nucleocapsid protein

Crystals of the N-terminal domain of the nucleocapsid protein from Middle East respiratory syndrome coronavirus that diffracted X-rays to a resolution of at least 2.63u2005Å are described.

UNIVERSAL LENGTHS IN COMPLETE MICROBIAL GENOMES

Statistical analysis of frequency occurrence of short words in complete genomes reveals the existence of a set of universal lengths common to all extant complete microbial genomes. This phenomenon is consistent with a model for genome growth in which primitive genomes grew mainly by maximally stochastic duplications of short segments from an initial length of about 200 nucleotides. The relevance of these results to the so-called RNA world in which life began and evolved before the rise of proteins is discussed.

Cooperative recognition of T:T mismatch by echinomycin causes structural distortions in DNA duplex

Abstract Small-molecule compounds that target mismatched base pairs in DNA offer a novel prospective for cancer diagnosis and therapy. The potent anticancer antibiotic echinomycin functions by intercalating into DNA at CpG sites. Surprisingly, we found that the drug strongly prefers to bind to consecutive CpG steps separated by a single T:T mismatch. The preference appears to result from enhanced cooperativity associated with the binding of the second echinomycin molecule. Crystallographic studies reveal that this preference originates from the staggered quinoxaline rings of the two neighboring antibiotic molecules that surround the T:T mismatch forming continuous stacking interactions within the duplex. These and other associated changes in DNA conformation allow the formation of a minor groove pocket for tight binding of the second echinomycin molecule. We also show that echinomycin displays enhanced cytotoxicity against mismatch repair-deficient cell lines, raising the possibility of repurposing the drug for detection and treatment of mismatch repair-deficient cancers.

A survey of recent unusual high-resolution DNA structures provoked by mismatches, repeats and ligand binding

Abstract The structure of the DNA duplex is arguably one of the most important biological structures elucidated in modern history. DNA duplex structure is closely associated with essential biological functions such as DNA replication and RNA transcription. In addition to the classical A-, B- and Z-DNA conformations, DNA duplexes are capable of assuming a variety of alternative conformations depending on the sequence and environmental context. A considerable number of these unusual DNA duplex structures have been identified in the past decade, and some of them have been found to be closely associated with different biological functions and pathological conditions. In this manuscript, we review a selection of unusual DNA duplex structures, particularly those originating from base pair mismatch, repetitive sequence motifs and ligand-induced structures. Although the biological significance of these novel structures has not yet been established in most cases, the illustrated conformational versatility of DNA could have relevance for pharmaceutical or nanotechnology development. A perspective on the future directions of this field is also presented.

Chapter 6:Binding of Small Molecules to Trinucleotide DNA Repeats Associated with Neurodegenerative Diseases

Repetitive DNA sequences within genes play a vital role in maintaining normal function and pathology. Abnormal increases in the number of repeating units, or expansion, of repetitive sequences have been associated with more than 30 different types of hereditary diseases. Among these, expansion of trinucleotide repeats (TNRs) are arguably the most important, accounting for at least 14 diseases including Huntingtons and fragile X syndrome. Small molecules that bind to specific TNR DNA sequences could find application as diagnostic tools as well as therapeutic agents. Understanding how these compounds interact with TNR DNA should provide clues to their mechanisms of action and empower the development of novel therapeutics. Various biochemical and biophysical methods are required to elucidate the interaction between these compounds and TNR DNA. This chapter will summarize the different types of compounds that interact with abnormal trinucleotide repeat expansions in DNA. We will discuss their respective mechanisms in the light of experimental evidence, and discuss how this information can lead to potential applications.

CoII(Chromomycin)2 Complex Induces a Conformational Change of CCG Repeats from i-Motif to Base-Extruded DNA Duplex

We have reported the propensity of a DNA sequence containing CCG repeats to form a stable i-motif tetraplex structure in the absence of ligands. Here we show that an i-motif DNA sequence may transition to a base-extruded duplex structure with a GGCC tetranucleotide tract when bound to the (CoII)-mediated dimer of chromomycin A3, CoII(Chro)2. Biophysical experiments reveal that CCG trinucleotide repeats provide favorable binding sites for CoII(Chro)2. In addition, water hydration and divalent metal ion (CoII) interactions also play a crucial role in the stabilization of CCG trinucleotide repeats (TNRs). Our data furnish useful structural information for the design of novel therapeutic strategies to treat neurological diseases caused by repeat expansions.