Hiya Lahiri - Academia.edu (original) (raw)

Papers by Hiya Lahiri

Research paper thumbnail of Supramolecular Sensing Platforms: Techniques for In Vitro Biosensing

ChemEngineering, Jun 28, 2024

Research paper thumbnail of Impact of HMGB1 binding on the structural alterations of platinum drug-treated single dsDNA molecule

Research paper thumbnail of Searching for Blockers of Dengue and West Nile Virus Viroporins

Viruses

Flavivirus infections, such as those caused by dengue and West Nile viruses, emerge as new challe... more Flavivirus infections, such as those caused by dengue and West Nile viruses, emerge as new challenges for the global healthcare sector. It has been found that these two viruses encode ion channels collectively termed viroporins. Therefore, drug molecules that block such ion-channel activity can serve as potential antiviral agents and may play a primary role in therapeutic purposes. We screened 2839 FDA-approved drugs and compounds in advanced experimental phases using three bacteria-based channel assays to identify such ion channel blockers. We primarily followed a negative genetic screen in which the channel is harmful to the bacteria due to excessive membrane permeabilization that can be relieved by a blocker. Subsequently, we cross-checked the outcome with a positive genetic screen and a pH-dependent assay. The following drugs exhibited potential blocker activities: plerixafor, streptomycin, tranexamic acid, CI-1040, glecaprevir, kasugamycin, and mesna were effective against deng...

Research paper thumbnail of XNAs: A Troubleshooter for Nucleic Acid Sensing

Research paper thumbnail of Free-energy-based gene mutation detection using LNA probes

Research paper thumbnail of Protective effect of antioxidant rich aqueous curry leaf (Murraya koenigii) extract against gastro-toxic effects of piroxicam in male Wistar rats

Research paper thumbnail of Molecularly resolved, label-free nucleic acid sensing at solid–liquid interface using non-ionic DNA analogues

RSC Advances, 2022

Improved nucleic acid sensing in terms of single nucleobase mismatch discrimination, as achieved ... more Improved nucleic acid sensing in terms of single nucleobase mismatch discrimination, as achieved by the surface-confined non-ionic PNA and MO capture probes, is exemplified by single molecule force spectroscopy.

Research paper thumbnail of Nanoscale Nucleic Acid Recognition at Solid-liquid Interface using Xeno Nucleic Acid Probes

Langmuir

Challenges in reliable nucleic acid detection are manifold. The major ones are related to false p... more Challenges in reliable nucleic acid detection are manifold. The major ones are related to false positive or negative signals due to a lack of target specificity in detection and to low sensitivity, especially when a plethora of background sequences are present that can mask the specific recognition signal. Utilizing designed synthetic nucleic acids that are commonly called xeno nucleic acids could offer potential routes to meeting such challenges. In this article, we present the general framework of nucleic acid detection, especially for nanoscale applications, and discuss how and why the xeno nucleic acids could be truly an alternative to the DNA probes. Two specific cases, locked nucleic acid (LNA) and peptide nucleic acid (PNA), which are nuclease-resistant and can form thermally stable duplexes with DNA, are addressed. It is shown that the relative ease of the conformationally rigid LNA probe to be oriented upright on the substrate surface and of the nonionic PNA probe to result into high probe density assists in their use in nanoscale nucleic acid recognition. It is anticipated that success with these probes may lead to important developments such as PCR-independent approaches where the major aim is to detect a small number of target sequences present in the analyte medium.

Research paper thumbnail of Discriminating unalike single nucleobase mismatches using a molecularly resolved, label-free, interfacial LNA-based assay

The Analyst, 2016

Molecularly resolved, label-free discrimination of different types of single nucleobase mismatche... more Molecularly resolved, label-free discrimination of different types of single nucleobase mismatches by LNA probes.

Research paper thumbnail of Molecularly resolved label-free sensing of single nucleobase mismatches by interfacial LNA probes

Nucleic Acids Research, 2016

So far, there has been no report on molecularly resolved discrimination of single nucleobase mism... more So far, there has been no report on molecularly resolved discrimination of single nucleobase mismatches using surface-confined single stranded locked nucleic acid (ssLNA) probes. Herein, it is exemplified using a label-independent force-sensing approach that an optimal coverage of 12-mer ssLNA sensor probes formed onto gold(111) surface allows recognition of ssDNA targets with twice stronger force sensitivity than 12-mer ssDNA sensor probes. The force distributions are reproducible and the molecule-by-molecule force measurements are largely in agreement with ensemble on-surface melting temperature data. Importantly, the molecularly resolved detection is responsive to the presence of single nucleobase mismatches in target sequences. Since the labelling steps can be eliminated from protocol, and each force-based detection event occurs within milliseconds' time scale, the force-sensing assay is potentially capable of rapid detection. The LNA probe performance is indicative of versatility in terms of substrate choice-be it gold (for basic research and array-based applications) or silicon (for 'lab-ona-chip' type devices). The nucleic acid microarray technologies could therefore be generally benefited by adopting the LNA films, in place of DNA. Since LNA is nuclease-resistant, unlike DNA, and the LNAbased assay is sensitive to single nucleobase mismatches, the possibilities for label-free in vitro rapid diagnostics based on the LNA probes may be explored.

Research paper thumbnail of Supramolecular Sensing Platforms: Techniques for In Vitro Biosensing

ChemEngineering, Jun 28, 2024

Research paper thumbnail of Impact of HMGB1 binding on the structural alterations of platinum drug-treated single dsDNA molecule

Research paper thumbnail of Searching for Blockers of Dengue and West Nile Virus Viroporins

Viruses

Flavivirus infections, such as those caused by dengue and West Nile viruses, emerge as new challe... more Flavivirus infections, such as those caused by dengue and West Nile viruses, emerge as new challenges for the global healthcare sector. It has been found that these two viruses encode ion channels collectively termed viroporins. Therefore, drug molecules that block such ion-channel activity can serve as potential antiviral agents and may play a primary role in therapeutic purposes. We screened 2839 FDA-approved drugs and compounds in advanced experimental phases using three bacteria-based channel assays to identify such ion channel blockers. We primarily followed a negative genetic screen in which the channel is harmful to the bacteria due to excessive membrane permeabilization that can be relieved by a blocker. Subsequently, we cross-checked the outcome with a positive genetic screen and a pH-dependent assay. The following drugs exhibited potential blocker activities: plerixafor, streptomycin, tranexamic acid, CI-1040, glecaprevir, kasugamycin, and mesna were effective against deng...

Research paper thumbnail of XNAs: A Troubleshooter for Nucleic Acid Sensing

Research paper thumbnail of Free-energy-based gene mutation detection using LNA probes

Research paper thumbnail of Protective effect of antioxidant rich aqueous curry leaf (Murraya koenigii) extract against gastro-toxic effects of piroxicam in male Wistar rats

Research paper thumbnail of Molecularly resolved, label-free nucleic acid sensing at solid–liquid interface using non-ionic DNA analogues

RSC Advances, 2022

Improved nucleic acid sensing in terms of single nucleobase mismatch discrimination, as achieved ... more Improved nucleic acid sensing in terms of single nucleobase mismatch discrimination, as achieved by the surface-confined non-ionic PNA and MO capture probes, is exemplified by single molecule force spectroscopy.

Research paper thumbnail of Nanoscale Nucleic Acid Recognition at Solid-liquid Interface using Xeno Nucleic Acid Probes

Langmuir

Challenges in reliable nucleic acid detection are manifold. The major ones are related to false p... more Challenges in reliable nucleic acid detection are manifold. The major ones are related to false positive or negative signals due to a lack of target specificity in detection and to low sensitivity, especially when a plethora of background sequences are present that can mask the specific recognition signal. Utilizing designed synthetic nucleic acids that are commonly called xeno nucleic acids could offer potential routes to meeting such challenges. In this article, we present the general framework of nucleic acid detection, especially for nanoscale applications, and discuss how and why the xeno nucleic acids could be truly an alternative to the DNA probes. Two specific cases, locked nucleic acid (LNA) and peptide nucleic acid (PNA), which are nuclease-resistant and can form thermally stable duplexes with DNA, are addressed. It is shown that the relative ease of the conformationally rigid LNA probe to be oriented upright on the substrate surface and of the nonionic PNA probe to result into high probe density assists in their use in nanoscale nucleic acid recognition. It is anticipated that success with these probes may lead to important developments such as PCR-independent approaches where the major aim is to detect a small number of target sequences present in the analyte medium.

Research paper thumbnail of Discriminating unalike single nucleobase mismatches using a molecularly resolved, label-free, interfacial LNA-based assay

The Analyst, 2016

Molecularly resolved, label-free discrimination of different types of single nucleobase mismatche... more Molecularly resolved, label-free discrimination of different types of single nucleobase mismatches by LNA probes.

Research paper thumbnail of Molecularly resolved label-free sensing of single nucleobase mismatches by interfacial LNA probes

Nucleic Acids Research, 2016

So far, there has been no report on molecularly resolved discrimination of single nucleobase mism... more So far, there has been no report on molecularly resolved discrimination of single nucleobase mismatches using surface-confined single stranded locked nucleic acid (ssLNA) probes. Herein, it is exemplified using a label-independent force-sensing approach that an optimal coverage of 12-mer ssLNA sensor probes formed onto gold(111) surface allows recognition of ssDNA targets with twice stronger force sensitivity than 12-mer ssDNA sensor probes. The force distributions are reproducible and the molecule-by-molecule force measurements are largely in agreement with ensemble on-surface melting temperature data. Importantly, the molecularly resolved detection is responsive to the presence of single nucleobase mismatches in target sequences. Since the labelling steps can be eliminated from protocol, and each force-based detection event occurs within milliseconds' time scale, the force-sensing assay is potentially capable of rapid detection. The LNA probe performance is indicative of versatility in terms of substrate choice-be it gold (for basic research and array-based applications) or silicon (for 'lab-ona-chip' type devices). The nucleic acid microarray technologies could therefore be generally benefited by adopting the LNA films, in place of DNA. Since LNA is nuclease-resistant, unlike DNA, and the LNAbased assay is sensitive to single nucleobase mismatches, the possibilities for label-free in vitro rapid diagnostics based on the LNA probes may be explored.