Solution Conformation of [AF]dG Opposite a -2 Deletion Site in a DNA Duplex: Intercalation of the Covalently Attached Aminofluorene Ring into the Helix with Base Displacement of the C8-Modified syn Guanine and Adjacent Unpaired 3'-Adenine into the Major Groove

Biochemistry ◽  
1995 ◽  
Vol 34 (51) ◽  
pp. 16641-16653 ◽  
Author(s):  
Bing Mao ◽  
Brian E. Hingerty ◽  
Suse Broyde ◽  
Dinshaw J. Patel
Keyword(s):  
Major Groove ◽  
Dna Duplex ◽  
Solution Conformation ◽  
Base Displacement

Pyrenemethyl ara-Uridine-2′-carbamate: A Strong Interstrand Excimer in the Major Groove of a DNA Duplex

ChemBioChem ◽  
2003 ◽  
Vol 4 (9) ◽  
pp. 841-847 ◽  
Author(s):  
Natalia N. Dioubankova ◽  
Andrei D. Malakhov ◽  
Dmitry A. Stetsenko ◽  
Michael J. Gait ◽  
Pavel E. Volynsky ◽  
...  
Keyword(s):  
Major Groove ◽  
Dna Duplex

Solution conformation of the (+)- trans-anti -benzo[g]chrysene-dA adduct opposite dT in a DNA duplex 1 1Edited by I. Tinoco

1999 ◽  
Vol 292 (2) ◽  
pp. 289-307 ◽  
Author(s):  
Asif K Suri ◽  
Bing Mao ◽  
Shantu Amin ◽  
Nicholas E Geacintov ◽  
Dinshaw J Patel
Keyword(s):  
Dna Duplex ◽  
Solution Conformation

Investigation of changes in the arrangement of water molecules and salt ions surrounding different atoms of the DNA molecule during the melting process: a molecular dynamics simulation study

2015 ◽  
Vol 93 (3) ◽  
pp. 348-361 ◽  
Author(s):  
C. Izanloo
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Double Helix ◽  
Melting Process ◽  
Minor Groove ◽  
Dynamics Simulation ◽  
Transition Curve ◽  
Water Molecules ◽  
Major Groove ◽  
Dna Duplex

A molecular dynamics simulation was performed on a B-DNA duplex (CGCGAATTGCGC) at different temperatures. The DNA was immerged in a saltwater medium with 1 mol/L NaCl concentration. The arrangements of water molecules and cations around the different atoms of DNA on the melting pathway were investigated. Almost for all atoms of the DNA by double helix → single-stranded transition, the water molecules released from the DNA duplex and cations were close to single-stranded DNA, but this behavior was not clearly seen at melting temperatures. Therefore, release of water molecules and cations approaching the DNA by the increase of temperature does not have any effect on the sharpness of the transition curve. Most of the water molecules and cations were found to be around the negatively charged phosphate oxygen atoms. The number of water molecules released from the first shell hydration upon melting in the minor groove was higher than in the major groove, and intrusion of cations into the minor groove after melting was higher than into the major groove. The hydrations of imino protons were different from each other and were dependent on DNA bases.

Solution conformation of the (+)-cis-anti-[BP]dG adduct in a DNA duplex: Intercalation of the covalently attached benzo[a]pyrenyl ring into the helix and displacement of the modified deoxyguanosine

Biochemistry ◽  
1993 ◽  
Vol 32 (16) ◽  
pp. 4145-4155 ◽  
Author(s):  
Monique Cosman ◽  
Carlos de los Santos ◽  
Radovan Fiala ◽  
Brian E. Hingerty ◽  
Victor Ibanez ◽  
...  
Keyword(s):  
Dna Duplex ◽  
Solution Conformation

Double-Coding Nucleic Acids: Introduction of a Nucleobase Sequence in the Major Groove of the DNA Duplex Using Double-Headed Nucleotides

2014 ◽  
Vol 79 (17) ◽  
pp. 8020-8030 ◽  
Author(s):  
Pawan Kumar ◽  
Antoni Figueras Sorinas ◽  
Lise J. Nielsen ◽  
Maria Slot ◽  
Kirstine Skytte ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Major Groove ◽  
Dna Duplex
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