@article { ISI:000372562000005,
	title = {Influence of ionic liquids on thermodynamics of small molecule DNA interaction: the binding of ethidium bromide to calf thymus DNA},
	journal = {Journal of Physical Chemistry B},
	volume = {120},
	number = {10},
	year = {2016},
	month = {MAR},
	pages = {2691-2700},
	publisher = {AMER CHEMICAL SOC},
	address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA},
	abstract = {<p>Ionic liquids (ILs) are salts with poor ionic coordination, resultantly remaining in liquid state below 100 degrees C and some may retain liquid state even at room temperature. ILs are known to provide a conducive environment for many biological enzymatic reactions, but their interaction with biomacromolecules are poorly understood. In the present study, we investigate the effect of various ionic liquids on DNA small molecule interaction using calf thymus DNA (ctDNA) ethidium bromide (EB) as a model system. The effect of various ionic liquids on these interactions is studied by an array of techniques such as circular dichroism (CD), UV melting, fluorescence exclusion and isothermal titration calorimetry. Interestingly, we observed that presence of IL increased the stability of ctDNA without altering its structure. The binding affinities Kbs for EB binding to ctDNA in the presence of 300 mM ILs are about half order of magnitude smaller than the Kbs in absence of ILs and correspond to a less favorable free energy. We noted that, when adjusted to corresponding buffer condition, the unfavorable shift in AG of ctDNA-EB interaction is attributed to decreased entropy in the case of ILs, whereas the same effect by NaCI was due to increased enthalpy.</p>},
	issn = {1520-6106},
	doi = {10.1021/acs.jpcb.5b11823},
	author = {Mishra, Arpit and Ekka, Mary Krishna and Maiti, Souvik}
}
@article {46331,
	title = {Francisella novicida Cas9 interrogates genomic DNA with very high specificity and can be used for mammalian genome editing},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	volume = {116},
	year = {2019},
	month = {OCT},
	pages = {20959-20968},
	type = {Article},
	abstract = {<p>Genome editing using the CRISPR/Cas9 system has been used to make precise heritable changes in the DNA of organisms. Although the widely used Streptococcus pyogenes Cas9 (SpCas9) and its engineered variants have been efficiently harnessed for numerous gene-editing applications across different platforms, concerns remain regarding their putative off-targeting at multiple loci across the genome. Here we report that Francisella novicida Cas9 (FnCas9) shows a very high specificity of binding to its intended targets and negligible binding to off-target loci. The specificity is determined by its minimal binding affinity with DNA when mismatches to the target single-guide RNA (sgRNA) are present in the sgRNA:DNA heteroduplex. FnCas9 produces staggered cleavage, higher homology-directed repair rates, and very low nonspecific genome editing compared to SpCas9. We demonstrate FnCas9-mediated correction of the sickle cell mutation in patient-derived induced pluripotent stem cells and propose that it can be used for precise therapeutic genome editing for a wide variety of genetic disorders.</p>
},
	keywords = {CRISPR Cas9, gene therapy, Genome editing, iPSCs, sickle cell anemia},
	issn = {0027-8424},
	doi = {10.1073/pnas.1818461116},
	author = {Acharya, Sundaram and Mishra, Arpit and Paul, Deepanjan and Ansari, Asgar Hussain and Azhar, Mohd and Kumar, Manoj and Rauthan, Riya and Sharma, Namrata and Aich, Meghali and Sinha, Dipanjali and Sharma, Saumya and Jain, Shivani and Ray, Arjun and Jain, Suman and Ramalingam, Sivaprakash and Maiti, Souvik and Chakraborty, Debojyoti}
}
