Deepak Koirala
Overview
Explore the profile of Deepak Koirala including associated specialties, affiliations and a list of published articles.
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34
Citations
650
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Recent Articles
1.
Ojha M, Hudson L, Photenhauer A, Zang T, Lerew L, Ekesan S, et al.
bioRxiv
. 2025 Mar;
PMID: 40060702
The Rev Response Element (RRE) forms an oligomeric complex with the viral protein Rev to facilitate the nuclear export of intron-retaining viral RNAs during the late phase of HIV-1 infection....
2.
Banna H, Berg K, Sadat T, Das N, Paudel R, DSouza V, et al.
Nucleic Acids Res
. 2024 Dec;
53(4).
PMID: 39739875
Although antibody derivatives, such as Fabs and scFvs, have revolutionized the cellular imaging, quantification and tracking of proteins, analogous tools and strategies are unavailable for cellular RNA visualization. Here, we...
3.
Bu F, Adam Y, Adamiak R, Antczak M, de Aquino B, Badepally N, et al.
Nat Methods
. 2024 Dec;
22(2):399-411.
PMID: 39623050
RNA-Puzzles is a collective endeavor dedicated to the advancement and improvement of RNA three-dimensional structure prediction. With agreement from structural biologists, RNA structures are predicted by modeling groups before publication...
4.
Das N, Vogt J, Patel A, Banna H, Koirala D
Nucleic Acids Res
. 2024 Jul;
52(18):11218-11233.
PMID: 39036953
Enteroviruses contain conserved RNA structures at the extreme 5' end of their genomes that recruit essential proteins 3CD and PCBP2 to promote genome replication. However, the high-resolution structures and mechanisms...
5.
Ojha M, Vogt J, Das N, Redmond E, Singh K, Banna H, et al.
Proc Natl Acad Sci U S A
. 2024 Jan;
121(4):e2313677121.
PMID: 38241435
The genomes of several plant viruses contain RNA structures at their 3' ends called cap-independent translation enhancers (CITEs) that bind the host protein factors such as mRNA 5' cap-binding protein...
6.
Banna H, Das N, Ojha M, Koirala D
BBA Adv
. 2023 Sep;
4:100101.
PMID: 37655005
RNA molecules play essential roles in many biological functions, from gene expression regulation, cellular growth, and metabolism to catalysis. They frequently fold into three-dimensional structures to perform their functions. Therefore,...
7.
Das N, Hollmann N, Vogt J, Sevdalis S, Banna H, Ojha M, et al.
Nat Commun
. 2023 Apr;
14(1):1955.
PMID: 37029118
The extreme 5'-end of the enterovirus RNA genome contains a conserved cloverleaf-like domain that recruits 3CD and PCBP proteins required for initiating genome replication. Here, we report the crystal structure...
8.
Rees H, Gogacz W, Li N, Koirala D, Piccirilli J
ACS Chem Biol
. 2022 Jun;
17(7):1866-1875.
PMID: 35759696
Pepper is a fluorogenic RNA aptamer tag that binds to a variety of benzylidene-cyanophenyl (HBC) derivatives with tight affinity and activates their fluorescence. To investigate how Pepper RNA folds to...
9.
Krochmal D, Shao Y, Li N, DasGupta S, Shelke S, Koirala D, et al.
Nat Chem Biol
. 2022 Jan;
18(4):376-384.
PMID: 35058645
Ribozymes that react with small-molecule probes have important applications in transcriptomics and chemical biology, such as RNA labeling and imaging. Understanding the structural basis for these RNA-modifying reactions will enable...
10.
Swain M, Ageeli A, Kasprzak W, Li M, Miller J, Sztuba-Solinska J, et al.
Nucleic Acids Res
. 2021 Dec;
49(22):13179-13193.
PMID: 34871450
Cellular and virus-coded long non-coding (lnc) RNAs support multiple roles related to biological and pathological processes. Several lncRNAs sequester their 3' termini to evade cellular degradation machinery, thereby supporting disease...