Research
Research Interests
As chemists, we are intensely interested in the field of nucleic acid, and value in-depth investigation of the subject and its challenges.
G-quadruplex nucleic acid
G-quadruplex represents one of the conformational variations in the domain of nucleic acid. It comprises a planar arrangement of four guanine nucleobases, which is inherently stabilized by hydrogen bonding interactions via Hoogsteen faces and folds in the presence of Na(I) or K(I). Notably, the sequences that are potential to fold into G4-conformation, are not located randomly, but rather found in the regulatory region of the human chromosome. In fact, G-quadruplex offers a new modality for targeting DNA, a way to moving beyond the current ‘blunderbuss’ approach with cytotoxic drugs. It is assumed that the molecule which can induce the formation or stabilize the G-tetrad conformation can be applied as anticancer drugs.
Key questions in focus:
-
Can we contribute, as chemists, in controlling the G-quadruplex function?
-
Can we aim to harness the structural complexity of the coordination complex in targeting the G-quadruplex?
Prebiotic Chemistry
This is a very exciting time for research on the origin of life, and we, as chemists, believe in the existence of a 'chemical evolution' before the much known 'Darwinian evolution'. Relatively little is known about how the simple organic molecules present on early earth evolved into a complex system with enormous precision. The research in prebiotic chemistry attempts to solve this issue theoretically and experimentally. The challenges in this study lie in the fact that direct evidence is long gone, and we have to work by using plausible inference. The origin-of-life researchers need to solve numerous puzzles, and it’s a long way from slime to Mozart.
Key questions in focus:
-
Can we explore the possible involvement of metal ions in solving some of the prehistoric puzzles?
All projects typically require the involvement of synthetic organic chemistry, coordination chemistry, and nucleic acid chemistry.
More details are coming soon.
Research Experience (Before joining IIT Kgp)
Metal-mediated base pairing and potential application (PhD research)
DNA is a biopolymer with a specific array of four nucleobases, which is responsible for storage, transport, and decoding of genetic information from parent to offspring, according to central dogma of molecular biology.[1] Not only that, DNA provided a new horizon to supramolecular chemistry for its unique self-assembly and molecular recognition behavior, which can be manipulated in a predetermined fashion for the construction of supramolecular nanoarchitecture.[2]
The concept of metal-mediated base pairing leads to an influx of new ideas in the context of site-specific functionalization of nucleic acid scaffold. In terms of supramolecular chemistry, it can be interpreted as a site-specific metal-ligand coordination reaction in the presence of multiple potential donors within the ligand scaffold. In here, the constituent nucleobases are held together by coordinate bonds to the metal ions in the center, formally replacing the hydrogen-bond-mediated base pairs.[3] Over the years, several applications have been found in this context, which eventually boosted up the ongoing research of metal-mediated base pairing. Possible applications include charge transfer through DNA, DNA-templated nanoparticle generation, DNA-based hybrid catalysis etc. The site-specific functionalization ability of metal-mediated base pairing further leads to the generation of metal-ion sensors, recognition of oligonucleotide sequence, metal-responsive materials, expansion of genetic four letter code, etc.[3]
In here, we introduced a GNA-functionalized imidazole appended derivative of 1,10-phenanthroline into DNA oligonucleotide. Using that artificial nucleobase, we successfully introduced different metal ions (ex Ag(I), Cu(I), Zn(II), Hg(II) etc.) into different DNA topologies, like antiparallel duplex, parallel-stranded duplex, three-way junction, etc, under precise control over their positions.[4] Based on those results, we were able to develop a fluorescence sensor by which the identity of the pyrimidine nucleobases can be discriminated by the virtue of metal-mediated base pairing.[5] This molecular beacon performed well in the detection of biologically relevant single nucleotide polymorphisms.[6] Besides, the acquired knowledges of different metal-mediated base pairs were efficiently implemented to generate a DNA-programmed heterometallic assembly within a parallel-stranded duplex scaffold. [7]
Reference.
1. F. Crick, Nature 1970, 227, 561.
2. Y. Takezawa, M. Shionoya, Acc. Chem. Res. 2012, 45, 2066.
3. B. Jash, J. Müller, Chem. Eur. J. 2017, 23, 17166.
4. a) B. Jash, J. Neugebauer, J. Müller, Inorg. Chim. Act. 2016, 452, 181.
b) B. Jash, J. Müller, Angew. Chem. Int. Ed. 2018, 57, 9524.
5. B. Jash, P. Scharf, N. Sandmann, C. Fonseca Guerra, D. A. Megger, J. Müller, Chem. Sci. 2017, 8, 1337.
6. B. Jash, J. Müller, Eur. J. Inorg. Chem. 2017, 3857.
7. B. Jash, J. Müller, Chem. Eur. J. 2018, 24, 10636.
Ribosome-free capture and translation (Postdoc research at University of Stuttgart)
This process of transforming genetic instructions into extra-genetic form is called translation. Translation occurs in all living systems, and it links between genotype and phenotype at the molecular level. Over the past few decades, biology and chemistry have joined hands to investigate the mechanism of ribosome-based translational machinery. What has been unearthed, as a result, is an intricate network of multiple processes: involvement of aminoacyl tRNA synthetases, tRNA carrying amino acids to the ribosomes, recognition of the correct binding site at the mRNA, elongation of the peptide chain, and termination factors. The process is ultra-complex, to say the least. However, it is extremely unlikely that massive ribosomal machinery for polypeptide synthesis existed in the primitive world.[1] The mystery lies in how the early, crude form of polypeptide formation in the primitive, enzyme-free world emerged to become the synchronized process of protein synthesis as we see it today. Nobel laureate Francis Crick described the origin of protein synthesis as a notoriously difficult problem.[2]
The very first fundamental question that makes us think how the simplest building blocks of RNA and protein may have been interconnected in the prebiotic world. In this regard, Richert lab reported a molecule called peptido RNA, which forms spontaneously in a salt-rich condensation buffer containing amino acid and ribonucleotide, which are the simplest form of protein and RNA, respectively.[3] This observation set the stage to template-directed anchoring of the carboxy-terminus of the peptido RNA to the oligonucleotide. And that, in turn, led to the formation of charged RNA that relies on RNA-mediated molecular recognition beyond that of free amino acids and ribonucleotides.[4] Next, our goal was to reveal the process of ribosome-free translation with the involvement of a charged species, and an RNA template – one that can be produced in the condensation buffer by spontaneous oligomerization. We showed how the reaction of 2',3'-esters of ribonucleotides (tNMPs) and phosphoramidate-linked aminoacidyl oligoribonucleotides leads to the formation of specific dipeptides. In our simplified ribosomal reaction centre, the RNA template acts as a mimic of messenger RNA, and tNMP acts as a mimic of charged tRNA. This experimental observation augments the importance of the base pairing efficiency of the RNA template to drive significantly high-yielding coupling of the tNMPs in comparison to the background reaction. When the mixture of charged tNMPs was employed in the presence of different templates, we found incorporation of the encoded amino acid as the dominant product. Additionally, these results tell us that selectivity could be enhanced even further by using aminoacyl dinucleotides / trinucleotides, as it could facilitate stronger binding to the template in comparison to the aminoacyl mononucleotide – the canonical form which can encode only four amino acids.[5]
We did succeed, in our own small way. We hope that our findings serve as a starting point and a clue for other investigators – fellow researchers uncovering the obscure evolution of protein-synthesis.
Reference.
1. H. F. Noller, Cold Spring Harb. Perspect. Biol. 2012, 4, a003681.
2. F. H. C. Crick, S. Brenner, A. Klug, G. Pieczenik, Orig. Life 1976, 7, 389.
3. M. Jauker, H. Griesser, C. Richert, Angew. Chem. Int. Ed. 2015, 54, 14564.
4. B. Jash, C. Richert, Chem. Sci. 2020, 11, 3487.
5. B. Jash, P. Tremmel, D. Jovanovic, C. Richert, Nat. Chem. 2021, 13, 751.
RNA Chemical Biology (Postdoc research at Stanford University)
RNA transfers genetic information from DNA to the ribosomal protein machinery at the molecular level.[1] Notably, researchers hypothesize that we are in the process of genomic evolution, and many of the RNA functions within the cell are yet to be discovered.[2] Thus, it is important to develop robust chemical methods that could be useful in exploring the function and properties of RNA.[3] Regardless the sequence, the presence of the 2'-OH group in the ribose sugar of RNA is considered as one of the major differences between DNA and RNA molecules. Over the past two decades, the covalent modification at the 2'-OH group gained significant attention due to easier implementation than the usual enzymatic approach for monitoring RNA structure and dynamics.[4] Among the various chemical tools for synthetic and transcribed RNA, selective hydroxyl acylation analyzed by primer extension (SHAPE), is found to be one of the useful methods for RNA structure analysis based on the elevated reactivity of unpaired or conformationally unconstrained nucleotides relative to those in helices.[5] Apart from structural mapping, acylation of 2'-OH group has got significant attention in RNA conjugation chemistry.
We herein attempted to understand various effects that control the reactivity of the RNA 2’-OH towards acylation reaction from a standpoint of chemist.[6] We believe that a proper chemical insight will be helpful in the designing of reagents for RNA conjugation and methods for functionalizing RNAs for applied science in future.
Reference.
1. D. L. Nelson, M. M. Cox, Lehninger principles of biochemistry, fourth edition 4th Ed. 2005, WH Freeman and Company, New York.
2. T. R. Cech, J. A. Steitz, Cell 2014, 157, 77.
3. W. A. Velema, E. T. Kool, Nat. Rev. Chem. 2020, 4, 22.
4. E. Paredes, M. Evans, S. R. Das, Methods 2011, 54, 251.
5. S. A. Mortimer, K. M. Weeks, J. Am. Chem. Soc. 2007, 129, 4144.
6. B. Jash, E. T. Kool, Chem. Commun. 2022, 58, 3693.