• Chromomycin A 3 (CHR) binding to the duplex d(CAAGTCTGGCCATCAGTC)· d(GACTGATGGCCAGACTTG) has been studied using quantitative footprinting methods. (syr.edu)
  • An integrated encyclopedia of DNA elements in the human genome. (umassmed.edu)
  • The hexameric MCM complex is conserved throughout archaea and eukaryotic species as the DNA helicase that unwinds the duplex genome providing leading and lagging strand templates for replication. (elifesciences.org)
  • The complex structure and repetitive nature of eukaryotic ribosomal DNA (rDNA) is a challenge for genome assembly, thus the consequences of sequence variation in rDNA remain unexplored. (genetics.org)
  • Thus, genome-wide DH site mapping will be an important tool for systematic identification of all cis -regulatory DNA elements in plants. (plantcell.org)
  • The Arabidopsis DH sites were significantly associated with various cis -regulatory DNA elements previously characterized in the Arabidopsis genome. (plantcell.org)
  • Junk DNA: A Journey Through the Dark Matter of the Genome , by Nessa Carey, ISBN:9780231539418, Columbia University Press, Apr 2015. (panspermia.org)
  • Most recently he is exploring the genome-wide utilization of supercoiled driven changes in DNA to regulate genes in health and disease. (cancer.gov)
  • His work showed that in living cells torque generated during transcription modifies DNA structure dynamically at particular supercoil-sensitive spots in the genome. (cancer.gov)
  • Permanganate/S1 Nuclease Footprinting Reveals Non-B DNA Structures with Regulatory Potential across a Mammalian Genome. (cancer.gov)
  • M. Blanchette , M. Tompa , 'Discovery of regulatory elements by a computational method for phylogenetic footprinting' , Genome Res. (washington.edu)
  • Paix A , Folkmann A , Goldman DH , Kulaga H, Grzelak MJ, Rasoloson D , Paidemarry S, Green R , Reed RR , Seydoux G . (2017) Precision genome editing using synthesis-dependent repair of Cas9-induced DNA breaks. (jhmi.edu)
  • Because retroviruses such as human immunodeficiency virus type 1 (HIV-1) must integrate a DNA copy of their genome into the chromosomal DNA of newly infected cells, it is necessary to characterize the nucleosomal organization of the integrated viral promoter to understand the mechanism(s) associated with the induction of viral transcription. (asm.org)
  • Analysis of T4 DNA polymerase (gp 43) and gp 44/62, gp 45 (T4 DNA replication accessory proteins), and gp 32 (T4 helix destabilizing protein) by DNA footprinting. (neb.com)
  • D. thesis project on control of DNA replication in bacteria. (frankwu.com)
  • our philosophy is that by combining structural and biophysical analysis with biochemical and functional studies, we will be able to build up a complete picture of the mechanism of action of the relevant macromolecules and their role in fundamental biological processes, particularly those related to gene expression and DNA replication. (port.ac.uk)
  • Techniques like DNA footprinting help elucidate which proteins bind to these associated regions of DNA and unravel the complexities of transcriptional control. (wikipedia.org)
  • Any of various techniques used to determine the sites at which proteins bind to DNA or RNA, employed especially in the study of gene expression and regulation. (oxforddictionaries.com)
  • Thus, information on what proteins bind to cis -regulatory DNA elements and when and where these proteins bind is important to understand the regulation and thus function of each gene. (plantcell.org)
  • Ding, ZM, Harshey, RM & Hurley, L 1993, ' (+)-CC-1065 as a structural probe of Mu transposase-induced bending of DNA: Overcoming limitations of hydroxyl-radical footprinting ', Nucleic Acids Research , vol. 21, no. 18, pp. 4281-4287. (elsevier.com)
  • DNA Complexed Structure of the Key Transcription Factor Initiating Development in Sporulating Bacteria Structure (London, England : 1993). (jove.com)
  • Our results show that both the DNA substrate and the C-terminal winged-helix (WH) domain influence the orientation but that translocation on DNA proceeds N-first. (elifesciences.org)
  • The MCM proteins themselves are bilobal with a N-terminal domain (NTD) that acts to stabilize binding to single-strand DNA (ssDNA), a C-terminal domain (CTD) that contains the conserved AAA + (ATPases associated with diverse cellular activities) motor domain that provide energy for translocation and DNA unwinding, and a winged-helix (WH) domain for DNA binding ( Trakselis, 2016 ). (elifesciences.org)
  • These proteins have in common a conserved DNA-binding domain whose structure, as determined for the ETS proteins Fli-1, Ets-1, and PU.1, has an overall topology similar to that of the "winged helix-turn-helix" family of proteins ( 6-9 ). (sciencemag.org)
  • Epigenetic alterations, such as deoxyribonucleic acid (DNA) methylation, play a role in carcinogenesis. (els.net)
  • Some tumours have a very large number of genetic alterations (chromosomal rearrangements, point mutations and DNA methylation), and others have many fewer alterations. (els.net)
  • The generality of the repressive nature of cytosine methylation is widely admitted now, but the role of this DNA modification is still controversial. (embopress.org)
  • Type I enzymes are the most complex, being multi-subunit enzymes with both DNA methylation (MTase) and endonuclease (ENase) activity. (port.ac.uk)
  • Since it has been suggested that CHR binding alters DNA to the A configuration, quantitative footprinting studies using dimethyl sulfate, which alkylates at N-7 of guanine in the major groove, were also carried out. (syr.edu)
  • Nicole Becker received her BS degree in biotechnology from St. Cloud State University and came to Mayo Graduate School to study the potential for monitoring the formation of unusual DNA structures within living cells. (mayo.edu)
  • These structures share the property of having unpaired DNA bases within or adjacent to their location if embedded in B-form DNA. (mayo.edu)
  • These unusual DNA structures then bind by specialized factors to feedback regulate gene expression. (cancer.gov)
  • Note: Maxam-Gilbert chemical DNA sequencing can be run alongside the samples on the polyacrylamide gel to allow the prediction of the exact location of ligand binding site. (wikipedia.org)
  • The DNA template labeled at the 3' or 5' end, depending on the location of the binding site(s). (wikipedia.org)
  • This can limit the precision of predicting a protein's binding site on the DNA molecule. (wikipedia.org)
  • Carey MF, Peterson CL, Smale ST. Experimental strategies for the identification of DNA-binding proteins. (umassmed.edu)
  • Finally, in the paused complexes, the Q DNA-binding element is in a position analogous to binding sites of transcription activators that contact σ 70 region 4 in open complex ( 19 ). (pnas.org)
  • Chromomycin A 3 (CHR) binding to the duplex d(CAAGTCTGGCCATCAGTC)· d(GACTGATGGCCAGACTTG) has been studied using quantitative footprinting methods. (syr.edu)
  • The 5'-phosphate moiety is essential for the binding of Chlorella virus ligase to nicked DNA. (westminster.ac.uk)
  • These results suggest a bipartite domain structure in which the interdomain segment either comprises part of the DNA binding site or undergoes a conformational change upon DNA binding. (westminster.ac.uk)
  • These easily reproducible methods involve sequence recognition properties, as well as physical approaches to measuring both the strength of interaction and the mode of drug binding to DNA. (springer.com)
  • Helicases are composed of two domains, an N- terminal DNA binding domain (NTD) and a C- terminal motor domain (CTD). (elifesciences.org)
  • Wounding and methyl jasmonate treatments induced differently these DNA-binding activities. (plantphysiol.org)
  • Footprinting of DNA-binding proteins in intact cells. (uni-muenchen.de)
  • In the crystal lattice, two molecules form a tandem dimer upon binding to adjacent sites on DNA. (jove.com)
  • The α subunit contains a DNA-binding domain that is a member of the ETS family, whereas the β subunit contains a series of ankyrin repeats. (sciencemag.org)
  • ETS domain proteins make up a large family of DNA-binding proteins found in organisms ranging from fruit flies to humans that play a role in a variety of developmental pathways, in oncogenesis, and in viral gene expression ( 5 ). (sciencemag.org)
  • To investigate how the structurally dissimilar GABP α and β subunits form a tight heterodimer with enhanced DNA-binding affinity, we determined the crystal structure of the GABPα/β ETS domain-ankyrin repeat heterodimer bound to DNA. (sciencemag.org)
  • and behind the pipetters are two 'footprinting' gels which show a protein binding to DNA. (frankwu.com)
  • and iv) isolating said three-stranded DNA molecule bound to said second member of said binding pair. (patentgenius.com)
  • The physicochemical and DNA-binding properties of anticancer 9-aza-anthrapyrazoles (9-aza-APs) were investigated and compared with the carbocyclic analogs losoxantrone (LX) and mitoxantrone (MX). (aspetjournals.org)
  • The 9-aza-APs exhibit prominent affinity for DNA, with an important electrostatic contribution to the binding free energy. (aspetjournals.org)
  • These DNA segments are called transcription factor binding sites (TFBSs). (biomedcentral.com)
  • Guanine‐rich regions of nucleic acids can fold into G‐quadruplex, a secondary structure formed by four strands of deoxyribonucleic acid (DNA) or ribonucleic acid (RNA). (els.net)
  • Hence, bioisosteric substitution and ring-hydroxy deletion play an important role in defining the physicochemical properties and in modulating the affinity of anthrapyrazoles for the nucleic acid, the geometry of the intercalation complex, and the sequence specific contacts along the DNA chain. (aspetjournals.org)
  • Mysterious unchanging DNA finds a purpose in life , by Elizabeth Pennisi, doi:10.1126/science.356.6341.892, Science , 02 Jun 2017. (panspermia.org)
  • Both DNA and RNA G‐quadruplexes are found in biological systems: They have been computationally predicted and experimentally demonstrated by several methods in the genomes of several organisms, including humans, other eukaryotes, bacteria and viruses. (els.net)
  • Expanded encyclopedias of DNA elements in the human and mouse genomes. (washington.edu)
  • The usefulness of DNA cleavage by these naturally recurring restriction enzymes is limited. (google.com)
  • The design and synthesis of sequence-specific DNA recognition and cleaving molecules that go beyond the specificities of the natural restriction enzymes is obviously desirable, as they would provide valuable tools for further research, diagnostics, and chemotherapeutics. (google.com)
  • The path followed by DNA through the complexes is revealed by EM, using an anti-restriction protein that acts as a DNA mimic. (port.ac.uk)
  • This allows the use of promoter bashing to not only discover the location on the DNA strand which affects transcription, but also the proteins which affect that strand. (wikipedia.org)
  • Clone the region of DNA thought to act as a promoter. (wikipedia.org)
  • Allowing activators and repressors to influence sequentially the rate of nucleotide addition between initiation and promoter escape provides a means to sample and integrate the array of DNA-bound transfactors for the genesis of a single transcript. (cancer.gov)
  • Wrapping of upstream DNA around RNAP brings it near the α NTD (which act as hinges at the base of the active site cleft) and also near the downstream cleft, triggering conformational changes in the cleft and in downstream mobile elements (DMEs) of RNAP at the λ P R promoter. (pubmedcentralcanada.ca)
  • 1 , 4 , 12 These conformational changes facilitate bending of the downstream duplex into the cleft to form the most advanced CC prior to opening, in which more than 100 bp of promoter DNA (−82 to +20) interacts with RNAP. (pubmedcentralcanada.ca)
  • The recent discovery that short hybrid RNA:DNA molecules (siHybrids) induce long-term silencing of gene expression in mammalian cells conflicts with the currently hypothesized mechanisms explaining the action of small, interfering RNA (siRNA). (unt.edu)
  • Hsieh et al, "Recombinases can form DNA joint molecules in the absence of strand displacement", Cold Spring Harbor, Sep. (patentgenius.com)
  • Other applications include diagnostic reagents to detect pathogens and aberrant DNA molecules as well as chemotherapeutics. (google.com)
  • Ultraviolet irradiation can be used to excite nucleic acids and create photoreactions, which results in damaged bases in the DNA strand. (wikipedia.org)
  • J. Buhler , T. Ideker , D. Haynor , 'Dapple: Improved Techniques for Finding Spots on DNA Microarrays' , University of Washington Department of Computer Science & Engineering Technical Report UW-CSE-2000-08-05 , (2000) Supplement . (washington.edu)
  • MYC is regulated by a bewildering array of intracellular and extra cellular signals and conditions operating through a host of DNA-bound transfactors. (cancer.gov)
  • This selectivity is partially determined by conformational flexibility of the DNA sequence, and the covalent adduct has a bent DNA structure in which narrowing of the minor groove has occurred. (elsevier.com)
  • Significantly, the locus of bending at these sites is spaced approximately two helical turns apart, and the bending is proposed to occur by narrowing of the minor groove of DNA. (elsevier.com)
  • Register et al, "Electron microscopic visualization of the RecA protein-mediated pairing and branch migration phases of DNA strand exchange", J. Biol. (patentgenius.com)