Literature DB >> 20446279

Ultrafast vibrational dynamics and local interactions of hydrated DNA.

Łukasz Szyc1, Ming Yang, Erik T J Nibbering, Thomas Elsaesser.   

Abstract

Biochemical processes occur mainly in aqueous environments, where interactions with water molecules play a key role for both the structure and function of biomolecules. Deoxyribonucleic acid (DNA), the basic carrier of genetic information, is characterized by an equilibrium double helix structure which is held together by intermolecular hydrogen bonds between base pairs and hydrated by an environment of water molecules with fluctuating hydrogen bonds. Basic vibrational motions of hydrated DNA and the fastest changes in the DNA-water interactions and hydration geometries occur in less than 1 ps. These processes can be accessed by mapping the vibrational dynamics of DNA and water in a time-resolved way by nonlinear ultrafast vibrational spectroscopy. Recent studies provide a detailed understanding of DNA vibrations and their dynamics, and give insight into nonequilibrium properties and structures of hydrated DNA.

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Year:  2010        PMID: 20446279     DOI: 10.1002/anie.200905693

Source DB:  PubMed          Journal:  Angew Chem Int Ed Engl        ISSN: 1433-7851            Impact factor:   15.336


  15 in total

Review 1.  Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction.

Authors:  Carlos R Baiz; Bartosz Błasiak; Jens Bredenbeck; Minhaeng Cho; Jun-Ho Choi; Steven A Corcelli; Arend G Dijkstra; Chi-Jui Feng; Sean Garrett-Roe; Nien-Hui Ge; Magnus W D Hanson-Heine; Jonathan D Hirst; Thomas L C Jansen; Kijeong Kwac; Kevin J Kubarych; Casey H Londergan; Hiroaki Maekawa; Mike Reppert; Shinji Saito; Santanu Roy; James L Skinner; Gerhard Stock; John E Straub; Megan C Thielges; Keisuke Tominaga; Andrei Tokmakoff; Hajime Torii; Lu Wang; Lauren J Webb; Martin T Zanni
Journal:  Chem Rev       Date:  2020-06-29       Impact factor: 60.622

2.  Conformation of self-assembled porphyrin dimers in liposome vesicles by phase-modulation 2D fluorescence spectroscopy.

Authors:  Geoffrey A Lott; Alejandro Perdomo-Ortiz; James K Utterback; Julia R Widom; Alán Aspuru-Guzik; Andrew H Marcus
Journal:  Proc Natl Acad Sci U S A       Date:  2011-09-22       Impact factor: 11.205

3.  N-H stretching modes of adenosine monomer in solution studied by ultrafast nonlinear infrared spectroscopy and ab initio calculations.

Authors:  Christian Greve; Nicholas K Preketes; Rene Costard; Benjamin Koeppe; Henk Fidder; Erik T J Nibbering; Friedrich Temps; Shaul Mukamel; Thomas Elsaesser
Journal:  J Phys Chem A       Date:  2012-07-18       Impact factor: 2.781

Review 4.  Watching Proteins Wiggle: Mapping Structures with Two-Dimensional Infrared Spectroscopy.

Authors:  Ayanjeet Ghosh; Joshua S Ostrander; Martin T Zanni
Journal:  Chem Rev       Date:  2017-01-06       Impact factor: 60.622

5.  Spectral diffusion at the water/lipid interface revealed by two-dimensional fourth-order optical spectroscopy: a classical simulation study.

Authors:  Yuki Nagata; Shaul Mukamel
Journal:  J Am Chem Soc       Date:  2011-02-18       Impact factor: 15.419

Review 6.  Photoinduced hydrogen-bonding dynamics.

Authors:  Tian-Shu Chu; Jinmei Xu
Journal:  J Mol Model       Date:  2016-08-04       Impact factor: 1.810

7.  Modeling the vibrational couplings of nucleobases.

Authors:  Yaoyukun Jiang; Lu Wang
Journal:  J Chem Phys       Date:  2020-02-28       Impact factor: 3.488

8.  Solution conformation of 2-aminopurine (2-AP) dinucleotide determined by ultraviolet 2D fluorescence spectroscopy (UV-2D FS).

Authors:  Julia R Widom; Neil P Johnson; Peter H von Hippel; Andrew H Marcus
Journal:  New J Phys       Date:  2013-02-01       Impact factor: 3.729

9.  Energetics of base flipping at a DNA mismatch site confined at the latch constriction of α-hemolysin.

Authors:  Robert P Johnson; Rukshan T Perera; Aaron M Fleming; Cynthia J Burrows; Henry S White
Journal:  Faraday Discuss       Date:  2016-12-12       Impact factor: 4.008

10.  Broadband infrared and Raman probes of excited-state vibrational molecular dynamics: simulation protocols based on loop diagrams.

Authors:  Konstantin E Dorfman; Benjamin P Fingerhut; Shaul Mukamel
Journal:  Phys Chem Chem Phys       Date:  2013-06-19       Impact factor: 3.676

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