More Like this

1. Caught in the Middle: A Rigid DNA Label That Provides an Incisive Picture of DNA Conformational Flexibility in Protein–DNA Complexes

   https://doi.org/10.1021/jacs.5c01823  

   Casto, Joshua; Palit, Shramana; Little, Anthony; Hasanbasri, Zikri; Jen-Jacobson, Linda; Saxena, Sunil (May 2025, Journal of the American Chemical Society)
2. Structural predictions of protein–DNA binding: MELD-DNA

   https://doi.org/10.1093/nar/gkad013  

   Esmaeeli, Reza; Bauzá, Antonio; Perez, Alberto (February 2023, Nucleic Acids Research)

   Abstract Structural, regulatory and enzymatic proteins interact with DNA to maintain a healthy and functional genome. Yet, our structural understanding of how proteins interact with DNA is limited. We present MELD-DNA, a novel computational approach to predict the structures of protein–DNA complexes. The method combines molecular dynamics simulations with general knowledge or experimental information through Bayesian inference. The physical model is sensitive to sequence-dependent properties and conformational changes required for binding, while information accelerates sampling of bound conformations. MELD-DNA can: (i) sample multiple binding modes; (ii) identify the preferred binding mode from the ensembles; and (iii) provide qualitative binding preferences between DNA sequences. We first assess performance on a dataset of 15 protein–DNA complexes and compare it with state-of-the-art methodologies. Furthermore, for three selected complexes, we show sequence dependence effects of binding in MELD predictions. We expect that the results presented herein, together with the freely available software, will impact structural biology (by complementing DNA structural databases) and molecular recognition (by bringing new insights into aspects governing protein–DNA interactions). 

   more » « less
3. Specificity versus Processivity in the Sequential Modification of DNA: A Study of DNA Adenine Methyltransferase

   https://doi.org/10.1021/acs.jpcb.7b10349  

   Barel, Itay; Naughton, Brigitte; Reich, Norbert O.; Brown, Frank L. (January 2018, The Journal of Physical Chemistry B)
4. DNA Logic Gates Integrated on DNA Substrates in Molecular Computing

   https://doi.org/10.1002/cbic.202400080  

   Bardales, Andrea C; Smirnov, Viktor; Taylor, Katherine; Kolpashchikov, Dmitry M (April 2024, ChemBioChem)

   Due to nucleic acid's programmability, it is possible to realize DNA structures with computing functions, and thus a new generation of molecular computers is evolving to solve biological and medical problems. Pioneered by Milan Stojanovic, Boolean DNA logic gates created the foundation for the development of DNA computers. Similar to electronic computers, the field is evolving towards integrating DNA logic gates and circuits by positioning them on substrates to increase circuit density and minimize gate distance and undesired crosstalk. In this minireview, we summarize recent developments in the integration of DNA logic gates into circuits localized on DNA substrates. This approach of all‐DNA integrated circuits (DNA ICs) offers the advantages of biocompatibility, increased circuit response, increased circuit density, reduced unit concentration, facilitated circuit isolation, and facilitated cell uptake. DNA ICs can face similar challenges as their equivalent circuits operating in bulk solution (bulk circuits), and new physical challenges inherent in spatial localization. We discuss possible avenues to overcome these obstacles. 

   more » « less
5. DNA Glass: Encasing Diffraction-Quality, Mesoporous DNA Crystals in Silica

   https://doi.org/10.26434/chemrxiv-2025-ppztw  

   Al-Zarah, Hajar; Singh, Vidya R; Woloszyn, Karol; Perren, Lara; Klingsberg, Judah; Posnjak, Gregor; Liedl, Tim; Mandal, Trinanjana; Hihath, Joshua; Mao, Chengde; et al (June 2025, ACS)

   Self-assembling DNA crystals have emerged over the last two decades as an efficient and effective means of organizing matter at the nanoscale, but functionalization of these lattices has proved challenging as physiological buffer conditions are required to maintain structural integrity. In this manuscript, we demonstrate the silicification of porous DNA crystals using sol-gel chemistry. We identify reaction conditions that produce the minimum coating thickness to confer environmental protection, and subsequently measure the protective ability of the silica coating to various stressors, including heat, low ionic strength solution, organic solvents, and unprotected flash freezing. By soaking ions and dyes into the lattice after silica coating, we demonstrate that the crystals maintain their pores, and that the major groove of the DNA can still be used as a site-specific template for chemical modifications. We image a library of different crystal motifs by electron microscopy and confirm the presence of silica using energy dispersive spectroscopy. Finally, we perform X-ray diffraction on these crystals, both with and without cryoprotection and determine the structure of the DNA frame, underscoring the conserved molecular order after coating. We anticipate these mesoporous silica composites for use in applications involving extreme, non-physiological conditions and for experiments which utilize the DNA glass described here as a template for surface science. 

   more » « less