G-Quadruplex-Forming DNA Aptamers Inhibit the DNA-Binding Function of HupB and Mycobacterium tuberculosis Entry into Host Cells

Kalra, Priya; Mishra, Subodh Kumar; Kaur, Surinder; Kumar, Amit; Prasad, H. K.; Sharma, Tarun; Tyagi, Jaya Sivaswami

doi:10.1016/j.omtn.2018.08.011

Cited by 34 publications

(39 citation statements)

References 59 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The PPK2 G9 aptamer was demonstrated to bind strongly to the protein and efficiently inhibit its polyphosphate-dependent nucleoside diphosphate kinase (NDK) activities, resulting in Mtb inhibition. The other examples of aptamers having therapeutic applications against Mtb are HupB-4T and HupB-13T, both of which form a parallel G4 structure [139]. They demonstrated high stability, affinity, and selectivity for HupB protein.…”

Section: Other Applicationsmentioning

confidence: 99%

G-Quadruplex-Forming Aptamers—Characteristics, Applications, and Perspectives

2019

View full text Add to dashboard Cite

G-quadruplexes constitute a unique class of nucleic acid structures formed by G-rich oligonucleotides of DNA- or RNA-type. Depending on their chemical nature, loops length, and localization in the sequence or structure molecularity, G-quadruplexes are highly polymorphic structures showing various folding topologies. They may be formed in the human genome where they are believed to play a pivotal role in the regulation of multiple biological processes such as replication, transcription, and translation. Thus, natural G-quadruplex structures became prospective targets for disease treatment. The fast development of systematic evolution of ligands by exponential enrichment (SELEX) technologies provided a number of G-rich aptamers revealing the potential of G-quadruplex structures as a promising molecular tool targeted toward various biologically important ligands. Because of their high stability, increased cellular uptake, ease of chemical modification, minor production costs, and convenient storage, G-rich aptamers became interesting therapeutic and diagnostic alternatives to antibodies. In this review, we describe the recent advances in the development of G-quadruplex based aptamers by focusing on the therapeutic and diagnostic potential of this exceptional class of nucleic acid structures.

show abstract

Section: Other Applicationsmentioning

confidence: 99%

G-Quadruplex-Forming Aptamers—Characteristics, Applications, and Perspectives

2019

View full text Add to dashboard Cite

show abstract

“…It is also noted that MutS can bind to G-quadruplex structures [ 34 ] and may also afford a level of stabilization leading to increased deletion. Finally, other indirect effects may be due to sRNA-based regulation of some transcription factors [ 86 ] or of other nucleoid proteins that could influence quadruplex stability [ 87 , 88 ].…”

Section: Discussionmentioning

confidence: 99%

Crucial Role of the C-Terminal Domain of Hfq Protein in Genomic Instability

et al. 2020

View full text Add to dashboard Cite

G-rich DNA repeats that can form G-quadruplex structures are prevalent in bacterial genomes and are frequently associated with regulatory regions of genes involved in virulence, antigenic variation, and antibiotic resistance. These sequences are also inherently mutagenic and can lead to changes affecting cell survival and adaptation. Transcription of the G-quadruplex-forming repeat (G3T)n in E. coli, when mRNA comprised the G-rich strand, promotes G-quadruplex formation in DNA and increases rates of deletion of G-quadruplex-forming sequences. The genomic instability of G-quadruplex repeats may be a source of genetic variability that can influence alterations and evolution of bacteria. The DNA chaperone Hfq is involved in the genetic instability of these G-quadruplex sequences. Inactivation of the hfq gene decreases the genetic instability of G-quadruplex, demonstrating that the genomic instability of this regulatory element can be influenced by the E. coli highly pleiotropic Hfq protein, which is involved in small noncoding RNA regulation pathways, and DNA organization and packaging. We have shown previously that the protein binds to and stabilizes these sequences, increasing rates of their genomic instability. Here, we extend this analysis to characterize the role of the C-terminal domain of Hfq protein in interaction with G-quadruplex structures. This allows to better understand the function of this specific region of the Hfq protein in genomic instability.

show abstract

“…PCR cycle numbers were optimized in order to avoid formation of any undesired high-molecular-weight amplicon. Subsequently, ssDNA was prepared using alkaline treatment as described previously 40 , 41 and used in the next round of SELEX. The rigorousness of selection was intensified in every successive round of SELEX by increasing the strength of Tween 20 during washing and by decreasing the interaction time with the target during selection.…”

Section: Methodsmentioning

confidence: 99%

Theranostic Application of a Novel G-Quadruplex-Forming DNA Aptamer Targeting Malate Synthase of Mycobacterium tuberculosis

Dhiman

Kumar

Mishra

et al. 2019

Molecular Therapy - Nucleic Acids

Self Cite

View full text Add to dashboard Cite

The successful management of tuberculosis (TB) requires efficient diagnosis and treatment. Further, the increasing prevalence of drug-resistant TB highlights the urgent need to develop novel inhibitors against both drug-susceptible and drug-resistant forms of disease. Malate synthase (MS), an enzyme of the glyoxylate pathway, plays a vital role in mycobacterial persistence, and therefore it is considered as an attractive target for novel anti-TB drug development. Recent studies have also ascribed an adhesin function to MS and established it as a potent diagnostic biomarker. In this study, a panel of Mycobacterium tuberculosis (Mtb) MS-specific single-stranded DNA aptamers was identified by Systematic Evolution of Ligands by EXponential enrichment (SELEX). The best-performing G-quadruplex-forming 44-mer aptamer, MS10, was optimized post-SELEX to generate an 11-mer aptamer, MS10-Trunc. This aptamer was characterized by various biochemical, biophysical, and in silico techniques. Its theranostic activity toward Mtb was established using enzyme inhibition, host cell binding, and invasion assays. MS10-Trunc aptamer exhibited high affinity for MS (equilibrium dissociation constant [KD] ∼19 pM) and displayed robust inhibition of MS enzyme activity with IC50 of 251.1 nM and inhibitor constant (Ki) of 230 nM. This aptamer blocked mycobacterial entry into host cells by binding to surface-associated MS. In addition, we have also demonstrated its application in the detection of tuberculous meningitis (TBM) in patients with sensitivity and specificity each of >97%.

show abstract

G-Quadruplex-Forming DNA Aptamers Inhibit the DNA-Binding Function of HupB and Mycobacterium tuberculosis Entry into Host Cells

Cited by 34 publications

References 59 publications

G-Quadruplex-Forming Aptamers—Characteristics, Applications, and Perspectives

G-Quadruplex-Forming Aptamers—Characteristics, Applications, and Perspectives

Crucial Role of the C-Terminal Domain of Hfq Protein in Genomic Instability

Theranostic Application of a Novel G-Quadruplex-Forming DNA Aptamer Targeting Malate Synthase of Mycobacterium tuberculosis

Contact Info

Product

Resources

About