Article
Engineering, Environmental
Ke Zhang, Joseph Hodge, Anamika Chatterjee, Tae Seok Moon, Kimberly M. Parker
Summary: Double-stranded RNA undergoes alkaline hydrolysis at orders-of-magnitude slower rates compared to single-stranded RNA, and can remain intact for months at neutral pH. Increasing pH effectively attenuates enzymatic degradation of dsRNA without inducing alkaline hydrolysis, which differs significantly from ssRNA. Understanding these unique properties of dsRNA allows for greater control of stability in RNAi technology and provides insights into various applications, including isolation, detection, and inactivation of dsRNA viruses.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2021)
Article
Agronomy
Ningbo Chen, Xin Dai, Qian Hu, Hongxiao Tan, Liping Qiao, Laifeng Lu
Summary: Postharvest quality deterioration is a major issue in food loss and waste, but the technique of spray-induced gene silencing (SIGS) offers a new solution. By spraying double-stranded RNA (dsRNA) onto the surface of plants, specific genes can be targeted for RNA interference, effectively reducing browning in freshly-cut potatoes. This study highlights the potential application of SIGS in controlling postharvest quality deterioration.
POSTHARVEST BIOLOGY AND TECHNOLOGY
(2023)
Article
Multidisciplinary Sciences
Chen Zhang, Fujia Tian, Ying Lu, Bing Yuan, Zhi-Jie Tan, Xing-Hua Zhang, Liang Dai
Summary: DNA deformations can occur upon environmental changes, and an increase in salt concentration leads to DNA overwinding. Our magnetic tweezers experiments and simulations demonstrate that the twist change induced by salt can be quantitatively explained by the screening of electrostatic repulsion and the coupling between twist and DNA diameter. We determine the coupling constant and predict the temperature dependence of DNA twist, finding that the twist-diameter coupling is a common driving force for salt- and temperature-induced DNA twist changes.
Article
Chemistry, Analytical
Steven R. Strezsak, Penny J. Beuning, Nicholas J. Skizim
Summary: A method for accurately determining the concentration of long dsRNA was developed using nucleic acid digestion and reversed-phase HPLC/UV methods. The study found that sequence design can dramatically change the extinction coefficient of the molecule, with ssRNA overhangs leading to a 5% reduction in the calculated extinction coefficient.
ANALYTICAL METHODS
(2021)
Article
Biochemistry & Molecular Biology
Wenbo Xu, Miao Zhang, Yangcun Li, Wanwan He, Shengchun Li, Jiang Zhang
Summary: RNA interference (RNAi) is an effective technology for pest management. This study demonstrates that RNAi can be used to control the 28-spotted potato ladybird by targeting the beta-Actin gene. Transgenic potato plants expressing the target gene showed enhanced resistance to the pest. These findings expand the application range of RNAi technology to Coccinellidae pests.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2023)
Article
Microbiology
Alexander Stevens, Katherine Muratore, Yanxiang Cui, Patricia J. Johnson, Z. Hong Zhou
Summary: The atomic structure of TVV2 reveals the interactions driving capsid assembly and the properties governing viral genome organization. Comparison with other dsRNA viruses suggests conserved strategies of RNA release and potential domains involved in viral RNA maintenance. This provides insights for future investigations into the interactions between Trichomonas vaginalis and its viruses.
Article
Plant Sciences
Jinqiu Fu, Shijing Xu, Huan Lu, Fanchi Li, Shengchun Li, Ling Chang, David G. Heckel, Ralph Bock, Jiang Zhang
Summary: Plant-mediated RNA interference (RNAi) using dsRNA or siRNA has shown promise in pest control, but little is known about the molecular mechanisms. This study found that siRNAs derived from transgenic plants may be more effective triggers of RNAi in Lepidoptera than dsRNAs.
PLANT CELL AND ENVIRONMENT
(2022)
Article
Agronomy
Danielle Duanis-Assaf, Ilya Shlar, Ortal Galsurker, Olga Davydov, Dalia Maurer, Oleg Feygenberg, Elena Poverenov, Robert Fluhr, Noam Alkan
Summary: By incorporating dsRNA into LDH nano-clays, the stability of dsRNA is improved and it can serve as a long-term controlled-release mechanism to selectively control postharvest pathogen B. cinerea. The LDH-dsRNA complex shows continued efficacy after long-term storage and reduces gray mold development significantly.
POSTHARVEST BIOLOGY AND TECHNOLOGY
(2022)
Article
Endocrinology & Metabolism
Bong Jung Kang, Zakea Sultana, Marcy N. Wilder
Summary: Vitellogenesis-inhibiting hormone (VIH) negatively regulates reproduction in shrimp, and transcriptional silencing of Liv-SGP-G was successfully achieved with dsRNA injections. Although the treatment did not promote ovarian maturation, it was the first report of co-transcriptional repression of Liv-SGP-G using dsRNAs for homologous genes. This study indicates that subadult shrimp can respond to transcriptional silencing techniques.
FRONTIERS IN ENDOCRINOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Danielle Duanis-Assaf, Ortal Galsurker, Olga Davydov, Dalia Maurer, Oleg Feygenberg, Moshe Sagi, Elena Poverenov, Robert Fluhr, Noam Alkan
Summary: Pathogenic fungi cause postharvest losses, prompting the need for new control strategies. The development of dsRNA-ERG effectively inhibits fungal growth and grey-mould development, reducing the required fungicide amount.
PLANT BIOTECHNOLOGY JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Bailing Ren, Jingnan Cao, Yanqiu He, Sheng Yang, Jiang Zhang
Summary: RNA interference is a efficient technology for pest control, and expression of dsRNAs in transplastomic plants may have potential effects on non-target pests. The study showed that ACT plants had cross-resistance to another coleopteran insect with highly conserved nucleotide sequence, providing an opportunity for simultaneous control of different pests.
PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY
(2021)
Article
Virology
Mi-Sun Yoo, A-Tai Truong, Hana Jeong, Do-Hyun Hahn, Ju-Seong Lee, Soon-Seek Yoon, So-Youn Youn, Yun-Sang Cho
Summary: Sacbrood virus (SBV) infection poses a significant threat to Apis cerana colonies in South Korea. RNA interference (RNAi) targeting the VP3 gene is an effective method for protecting and treating SBV in vitro and in infected colonies. Laboratory-based experiments and large-scale field trials demonstrate the safety and efficacy of VP3 double-stranded RNA (dsRNA) treatment in increasing survival rates and preventing symptomatic SBV infections.
Article
Biochemistry & Molecular Biology
Xiaoxiao Zhang, Peng Li, Huanhuan Zhong, Fanming Yang, Fanzhou Liu, Gabriel Yedid, Yan Zeng
Summary: Proteins involved in RNA metabolism possess a double-stranded RNA-binding domain (dsRBD), with variations in sequences and functions. A study showed that a short insertion in the dsRBD of Drosha is important for its function, and extending the L1 region in other dsRBDs reduces RNA binding. This highlights the sensitivity of dsRBDs to perturbations in the L1 region and adds to the understanding of their structural and functional diversity.
ACTA BIOCHIMICA ET BIOPHYSICA SINICA
(2021)
Review
Biochemistry & Molecular Biology
Alexey D. Nikulin
Summary: The review discusses the differences in protein interactions with single- and double-stranded RNA molecules based on the structure of RNA-protein complexes. Proteins interacting with single-stranded RNAs form contacts with RNA bases for recognition of specific nucleotide sequences, while proteins interacting with double-stranded RNAs mainly interact with the RNA sugar-phosphate backbone.
BIOCHEMISTRY-MOSCOW
(2021)
Article
Biotechnology & Applied Microbiology
Shuhei Hashiro, Yasuhiko Chikami, Haruka Kawaguchi, Alexander A. Krylov, Teruyuki Niimi, Hisashi Yasueda
Summary: RNA-based pesticides utilize RNA interference to suppress the expression of essential genes in target pests. Through the development of a cost-competitive dsRNA overproduction system using Corynebacterium glutamicum as a host bacterium, long-chain dsRNAs were efficiently produced and shown to significantly suppress larval growth of pests like the ladybird beetle. This technology has the potential to reduce production costs and find applications in various industries, including agricultural pest control.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2021)
Article
Cell Biology
Phillip George, Nicholas A. Kinney, Jiangtao Liang, Alexey V. Onufriev, Igor V. Sharakhov
Article
Chemistry, Physical
Negin Forouzesh, Abhishek Mukhopadhyay, Layne T. Watson, Alexey Onufriev
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2020)
Article
Biochemistry & Molecular Biology
Parviz Seifpanahi Shabane, Alexey Onufriev
Summary: The study explores the conformational changes of the H4 tail under different charged states. As the charge of the H4 tail is gradually neutralized, its structure transitions from a random coil to a more compact and stable form. Based on ensemble similarity, K -> M is proposed as a possible alternative to the commonly used K -> Q substitution.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Chemistry, Physical
Nicholas P. Bauman, Hongbin Liu, Eric J. Bylaska, Sriram Krishnamoorthy, Guang Hao Low, Christopher E. Granade, Nathan Wiebe, Nathan A. Baker, Bo Peng, Martin Roetteler, Matthias Troyer, Karol Kowalski
Summary: This paper investigates the use of the quantum phase estimation (QPE) algorithm in calculating high-energy excited states characterized by promotion of electrons occupying core-level shells. Results obtained with QPE are compared with various high-accuracy many-body techniques, discussing the feasibility of identifying challenging shake-up states and targeting excitations from specific centers in molecules. Additionally, the application of the lowest-order Trotter formula to reduce complexity of ansatz without affecting error is discussed.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Multidisciplinary Sciences
Yunhui Peng, Shuxiang Li, Alexey Onufriev, David Landsman, Anna R. Panchenko
Summary: This study investigates the roles of histone tails in nucleosomal DNA binding using molecular dynamics simulations, revealing specific binding modes for different types of histone tails and the impact of modifications on interactions. Charge-altering modifications suppress tail-DNA interactions and enhance interactions between nucleosomes and nucleosome-binding proteins.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Physical
Egor S. Kolesnikov, Ivan Yu Gushchin, Petr A. Zhilyaev, Alexey Onufriev
Summary: The distribution of sodium and potassium ions around double-stranded DNA varies depending on the solvent model used, with deeply bound ions showing sensitivity to the solvent model. While monovalent ions bind to DNA regardless of ion type, the behavior of deeply bound ions differs significantly between different solvent models. Despite no single gold standard solvent model, OPC water with J/C ions or TIP3P with J/C + NBFIX may be suitable for practical simulations of ionic atmospheres around DNA.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Entomology
Ksenia S. Onufrieva, Alexey V. Onufriev
Summary: This paper proposes a novel method to estimate insect population density from a single trap catch, which is crucial for improving conservation and management strategies. The method is based on the relationship between experimentally measurable characteristics of insect trap systems and the probability to catch an insect, which has been tested and proven to be applicable across different datasets.
Article
Chemistry, Physical
Alexander Y. Afanasyev, Alexey Onufriev
Summary: This study proposes an approach to interpret polymer force-extension curves with plateau regimes. When combined with a bead-spring dynamic model, the approach accurately reproduces a variety of experimental force-extension curves of DNA and RNA. The researchers provide an algorithm to obtain the model parameters from experimental curves and explore the applicability of the approach to different DNA and RNA structures.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Multidisciplinary
Dan E. Folescu, Alexey Onufriev
Summary: A simple closed-form formula for calculating the apparent surface charge and electric field generated by molecular charge distribution in aqueous solution has been derived. This formula, which does not require any fitted parameters, provides a significant speed-up compared to numerical solutions. It has achieved near-quantitative agreement with the numerical reference for both small and large structures, except in regions of high negative curvature where it is qualitatively correct.
Article
Chemistry, Physical
Yeyue Xiong, Saeed Izadi, Alexey Onufriev
Summary: The article introduces a globally optimal polarizable water model, OPC3-pol, which accurately simulates water molecules at the atomic scale with minimal computational overheads. The model demonstrates improved computational efficiency and structure stability compared to existing approaches.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Proceedings Paper
Computer Science, Hardware & Architecture
Samuel Stein, Nathan Wiebe, Yufei Ding, Peng Bo, Karol Kowalski, Nathan Baker, James Ang, Ang Li
Summary: This paper introduces a virtualized approach for building a quantum backend for variational quantum algorithms (VQA), which involves constructing a quantum ensemble that dynamically distributes quantum tasks and adjusts the ensemble configuration based on machine status. This approach reduces noise and improves training speed for VQA. The paper also presents a novel VQA training framework called EQC, which enables asynchronous parallel training, evaluates circuit output quality, and adjusts the computational contribution of the quantum ensemble based on system performance.
PROCEEDINGS OF THE 2022 THE 49TH ANNUAL INTERNATIONAL SYMPOSIUM ON COMPUTER ARCHITECTURE (ISCA '22)
(2022)
Meeting Abstract
Biophysics
Yoonjin Kim, Alexander Y. Afanasyev, Igor S. Tolokh, Igor V. Sharakhov, Alexey V. Onufriev
BIOPHYSICAL JOURNAL
(2022)
Meeting Abstract
Biophysics
Samira Mali, Igor S. Tolokh, Igor V. Sharakhov, Alexey V. Onufriev
BIOPHYSICAL JOURNAL
(2022)
Meeting Abstract
Biophysics
Alexander Y. Afanasyev, Alexey V. Onufriev
BIOPHYSICAL JOURNAL
(2022)
Meeting Abstract
Biophysics
Igor S. Tolokh, Nicholas A. Kinney, Igor V. Sharakhov, Alexey V. Onufriev
BIOPHYSICAL JOURNAL
(2022)