Single-molecule FRET studies of HIV TAR-DNA hairpin unfolding dynamics. 2014

Jixin Chen, and Nitesh K Poddar, and Lawrence J Tauzin, and David Cooper, and Anatoly B Kolomeisky, and Christy F Landes
Department of Chemistry and ‡Department of Electrical and Computer Engineering, Rice University , Houston, Texas 77251-1892, United States.

We directly measure the dynamics of the HIV trans-activation response (TAR)-DNA hairpin with multiple loops using single-molecule Förster resonance energy transfer (smFRET) methods. Multiple FRET states are identified that correspond to intermediate melting states of the hairpin. The stability of each intermediate state is calculated from the smFRET data. The results indicate that hairpin unfolding obeys a "fraying and peeling" mechanism, and evidence for the collapse of the ends of the hairpin during folding is observed. These results suggest a possible biological function for hairpin loops serving as additional fraying centers to increase unfolding rates in otherwise stable systems. The experimental and analytical approaches developed in this article provide useful tools for studying the mechanism of multistate DNA hairpin dynamics and of other general systems with multiple parallel pathways of chemical reactions.

UI MeSH Term Description Entries
D008958 Models, Molecular Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures. Molecular Models,Model, Molecular,Molecular Model
D009690 Nucleic Acid Conformation The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape. DNA Conformation,RNA Conformation,Conformation, DNA,Conformation, Nucleic Acid,Conformation, RNA,Conformations, DNA,Conformations, Nucleic Acid,Conformations, RNA,DNA Conformations,Nucleic Acid Conformations,RNA Conformations
D009691 Nucleic Acid Denaturation Disruption of the secondary structure of nucleic acids by heat, extreme pH or chemical treatment. Double strand DNA is "melted" by dissociation of the non-covalent hydrogen bonds and hydrophobic interactions. Denatured DNA appears to be a single-stranded flexible structure. The effects of denaturation on RNA are similar though less pronounced and largely reversible. DNA Denaturation,DNA Melting,RNA Denaturation,Acid Denaturation, Nucleic,Denaturation, DNA,Denaturation, Nucleic Acid,Denaturation, RNA,Nucleic Acid Denaturations
D011092 Polyethylene Glycols Polymers of ETHYLENE OXIDE and water, and their ethers. They vary in consistency from liquid to solid depending on the molecular weight indicated by a number following the name. They are used as SURFACTANTS, dispersing agents, solvents, ointment and suppository bases, vehicles, and tablet excipients. Some specific groups are NONOXYNOLS, OCTOXYNOLS, and POLOXAMERS. Macrogols,Polyoxyethylenes,Carbowax,Macrogol,Polyethylene Glycol,Polyethylene Oxide,Polyethyleneoxide,Polyglycol,Glycol, Polyethylene,Glycols, Polyethylene,Oxide, Polyethylene,Oxides, Polyethylene,Polyethylene Oxides,Polyethyleneoxides,Polyglycols,Polyoxyethylene
D004279 DNA, Viral Deoxyribonucleic acid that makes up the genetic material of viruses. Viral DNA
D004396 Coloring Agents Chemicals and substances that impart color including soluble dyes and insoluble pigments. They are used in INKS; PAINTS; and as INDICATORS AND REAGENTS. Coloring Agent,Dye,Dyes,Organic Pigment,Stain,Stains,Tissue Stain,Tissue Stains,Organic Pigments,Pigments, Inorganic,Agent, Coloring,Inorganic Pigments,Pigment, Organic,Pigments, Organic,Stain, Tissue,Stains, Tissue
D006678 HIV Human immunodeficiency virus. A non-taxonomic and historical term referring to any of two species, specifically HIV-1 and/or HIV-2. Prior to 1986, this was called human T-lymphotropic virus type III/lymphadenopathy-associated virus (HTLV-III/LAV). From 1986-1990, it was an official species called HIV. Since 1991, HIV was no longer considered an official species name; the two species were designated HIV-1 and HIV-2. AIDS Virus,HTLV-III,Human Immunodeficiency Viruses,Human T-Cell Lymphotropic Virus Type III,Human T-Lymphotropic Virus Type III,LAV-HTLV-III,Lymphadenopathy-Associated Virus,Acquired Immune Deficiency Syndrome Virus,Acquired Immunodeficiency Syndrome Virus,Human Immunodeficiency Virus,Human T Cell Lymphotropic Virus Type III,Human T Lymphotropic Virus Type III,Human T-Cell Leukemia Virus Type III,Immunodeficiency Virus, Human,Immunodeficiency Viruses, Human,Virus, Human Immunodeficiency,Viruses, Human Immunodeficiency,AIDS Viruses,Human T Cell Leukemia Virus Type III,Lymphadenopathy Associated Virus,Lymphadenopathy-Associated Viruses,Virus, AIDS,Virus, Lymphadenopathy-Associated,Viruses, AIDS,Viruses, Lymphadenopathy-Associated
D001483 Base Sequence The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence. DNA Sequence,Nucleotide Sequence,RNA Sequence,DNA Sequences,Base Sequences,Nucleotide Sequences,RNA Sequences,Sequence, Base,Sequence, DNA,Sequence, Nucleotide,Sequence, RNA,Sequences, Base,Sequences, DNA,Sequences, Nucleotide,Sequences, RNA
D013816 Thermodynamics A rigorously mathematical analysis of energy relationships (heat, work, temperature, and equilibrium). It describes systems whose states are determined by thermal parameters, such as temperature, in addition to mechanical and electromagnetic parameters. (From Hawley's Condensed Chemical Dictionary, 12th ed) Thermodynamic
D014508 Urea A compound formed in the liver from ammonia produced by the deamination of amino acids. It is the principal end product of protein catabolism and constitutes about one half of the total urinary solids. Basodexan,Carbamide,Carmol

Related Publications

Jixin Chen, and Nitesh K Poddar, and Lawrence J Tauzin, and David Cooper, and Anatoly B Kolomeisky, and Christy F Landes
January 2020, The journal of physical chemistry. B,
Jixin Chen, and Nitesh K Poddar, and Lawrence J Tauzin, and David Cooper, and Anatoly B Kolomeisky, and Christy F Landes
April 2020, Chemistry (Weinheim an der Bergstrasse, Germany),
Jixin Chen, and Nitesh K Poddar, and Lawrence J Tauzin, and David Cooper, and Anatoly B Kolomeisky, and Christy F Landes
July 2014, The journal of physical chemistry. B,
Jixin Chen, and Nitesh K Poddar, and Lawrence J Tauzin, and David Cooper, and Anatoly B Kolomeisky, and Christy F Landes
February 2012, European biophysics journal : EBJ,
Jixin Chen, and Nitesh K Poddar, and Lawrence J Tauzin, and David Cooper, and Anatoly B Kolomeisky, and Christy F Landes
March 2006, Journal of molecular biology,
Jixin Chen, and Nitesh K Poddar, and Lawrence J Tauzin, and David Cooper, and Anatoly B Kolomeisky, and Christy F Landes
January 2016, Methods in enzymology,
Jixin Chen, and Nitesh K Poddar, and Lawrence J Tauzin, and David Cooper, and Anatoly B Kolomeisky, and Christy F Landes
September 2008, Current protocols in nucleic acid chemistry,
Jixin Chen, and Nitesh K Poddar, and Lawrence J Tauzin, and David Cooper, and Anatoly B Kolomeisky, and Christy F Landes
October 2013, The journal of physical chemistry. B,
Jixin Chen, and Nitesh K Poddar, and Lawrence J Tauzin, and David Cooper, and Anatoly B Kolomeisky, and Christy F Landes
January 2019, Methods in enzymology,
Jixin Chen, and Nitesh K Poddar, and Lawrence J Tauzin, and David Cooper, and Anatoly B Kolomeisky, and Christy F Landes
November 2017, Progress in biophysics and molecular biology,
Copied contents to your clipboard!