scholarly journals Electrostatically PEGylated DNA enables salt-free hybridization in water

2019 ◽  
Vol 10 (43) ◽  
pp. 10097-10105 ◽  
Author(s):  
Gurudas Chakraborty ◽  
Konstantin Balinin ◽  
Giuseppe Portale ◽  
Mark Loznik ◽  
Evgeny Polushkin ◽  
...  
Keyword(s):  
Aqueous Medium ◽  
Double Helix ◽  
Base Pairing ◽  
Electrostatic Bonding

Electrostatic bonding of PEG molecules onto the backbone of DNA allows Watson–Crick base-pairing between individually PEGylated complementary strands resulting in a double helix with enhanced thermostability in salt-free aqueous medium.

scholarly journals Base pairing structure in the poly d(G-T) double helix: wobble base pairs

1978 ◽  
Vol 5 (6) ◽  
pp. 1955-1970 ◽  
Author(s):  
Thomas A. Early ◽  
John Olmsted ◽  
David R. Kearns ◽  
Axel G. Lezius
Keyword(s):  
Double Helix ◽  
Base Pairing ◽  
Base Pairs

DNA: Not Merely the Secret of Life

2010 ◽  
Author(s):  
Nadrian C. Seeman
Keyword(s):  
Double Helix ◽  
Genetic Material ◽  
Helical Structure ◽  
Prominent Feature ◽  
Base Pairing ◽  
Double Helical Structure ◽  
Reciprocal Exchange ◽  
Sequence Selection ◽  
Living Organisms ◽  
Dna Double Helix

DNA is well-known as the genetic material of living organisms. Its most prominent feature is that it contains information that enables it to replicate itself. This information is contained in the well-known Watson-Crick base pairing interactions, adenine with thymine and guanine with cytosine. The double helical structure that results from this complementarity has become a cultural icon of our era. To produce species more diverse than the DNA double helix, we use the notion of reciprocal exchange, which leads to branched molecules. The topologies of these species are readily programmed through sequence selection; in many cases, it is also possible to program their structures. Branched species can be connected to one another using the same interactions that genetic engineers use to produce their constructs, cohesion by molecules tailed in complementary single-stranded overhangs, known as ‘sticky ends.’ Such sticky-ended cohesion is used to produce N-connected objects and lattices [1]. This notion is shown in the drawing, which shows cohesion between sticky-ended branched species.

scholarly journals A novel form of RNA double helix based on G·U and C·A+wobble base pairing

RNA ◽  
2017 ◽  
Vol 24 (2) ◽  
pp. 209-218 ◽  
Author(s):  
Ankur Garg ◽  
Udo Heinemann
Keyword(s):  
Double Helix ◽  
Base Pairing

Model Calculations on Base-Pair Interactions in DNA

1979 ◽  
Vol 32 (8) ◽  
pp. 1635 ◽  
Author(s):  
RGAR Maclagan
Keyword(s):  
Interaction Energy ◽  
Base Pair ◽  
Double Helix ◽  
Pair Interaction ◽  
Dna Bases ◽  
Base Pairing ◽  
Adjacent Pair ◽  
Model Calculations ◽  
Pair Interaction Energy ◽  
Phosphate Backbone

Calculations are reported using the potential field of Momany, Carruthers, McGuire and Scheraga of the intra-pair interaction energy for all 29 base-pairing schemes proposed by Donohue. Optimized relative orientations and separations of the DNA bases are given. The observed base pairing would appear to be determined principally by the base positions and orientations imposed by the fairly rigid sugar-phosphate backbone. The inter-pair interaction energies for the various possible combinations of the DNA bases in the double-helix models for the A and B forms of DNA are reported. In the model for the B form, the inter-pair interaction energy was found to be almost independent of the base-pair combination. The importance of base overlap in determining the extent to which one base pair is rotated with respect to an adjacent pair was also investigated in a preliminary manner.

Determination of stability of the DNA double helix in an aqueous medium

Biopolymers ◽  
1969 ◽  
Vol 8 (5) ◽  
pp. 559-571 ◽  
Author(s):  
P. L. Privalov ◽  
O. B. Ptitsyn ◽  
T. M. Birshtein
Keyword(s):  
Aqueous Medium ◽  
Double Helix ◽  
Dna Double Helix

scholarly journals Sequence dependence of transient Hoogsteen base-pairing in DNA

2021 ◽  
Author(s):  
Alberto Pérez de Alba Ortíz ◽  
Jocelyne Vreede ◽  
Bernd Ensing
Keyword(s):  
Dynamic Equilibrium ◽  
Double Helix ◽  
Free Energy Calculations ◽  
Dominant Factor ◽  
Base Pairing ◽  
Sequence Dependence ◽  
Purine Base ◽  
Sequence Variations ◽  
Hoogsteen Base Pairing

Hoogsteen (HG) base-pairing is characterized by a 180° rotation of the purine base with respect to the Watson-Crick-Franklin (WCF) motif. Recently, it has been found that both conformations coexist in a dynamical equilibrium and that several biological functions require HG pairs. This relevance has motivated experimental and computational investigations of the base-pairing transition. However, a systematic simulation of sequence variations has remained out of reach. Here, we employ advanced path-based methods to perform unprecedented free-energy calculations. Our methodology enables us to study the different mechanisms of purine rotation, either remaining inside or after flipping outside of the double helix. We study seven different sequences, which are neighbor variations of a well-studied A·T pair in A6-DNA. We observe the known effect of A·T steps favoring HG stability, and find evidence of triple-hydrogen-bonded neighbors hindering the inside transition. More importantly, we identify a dominant factor: the direction of the A rotation, with the 6-ring pointing either towards the longer or shorter segment of the chain, respectively relating to a lower or higher barrier. This highlights the role of DNA's relative flexibility as a modulator of the WCF/HG dynamic equilibrium. Additionally, we provide a robust methodology for future HG proclivity studies.

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