TY - JOUR

T1 - Механизм диссоциации пары цитозинов, опосредованных ионами серебра

AU - Клюев, Павел Николаевич

AU - Рамазанов, Руслан Рафядинович

PY - 2019

Y1 - 2019

N2 - The development of structured molecular systems based on a nucleic acid framework takes into account the ability of single-stranded DNA to form a stable double-stranded structure due to stacking interactions and hydrogen bonds of complementary pairs of nucleotides. To increase the stability of the DNA double helix and to expand the temperature range in the hybridization protocols, it was proposed to use more stable metal-mediated complexes of nucleotide pairs as an alternative to Watson-Crick hydrogen bonds. One of the most frequently considered options is the use of silver ions to stabilize a pair of cytosines from opposite DNA strands. Silver ions specifically bind to N3 cytosines along the helix axis to form, as is believed, a strong N3–Ag +–N3 bond, relative to which, two rotational isomers, the cis- and trans-configurations of C–Ag +–C can be formed. In present work, a theoretical study and a comparative analysis of the free energy profile of the dissociation of two С–Ag +–C isomers were carried out using the combined method of molecular mechanics and quantum chemistry (QM/MM). As a result, it was shown that the cis-configuration is more favorable in energy than the trans- for a single pair of cytosines, and the geometry of the global minimum at free energy profile for both isomers differs from the equilibrium geometries obtained previously by quantum chemistry methods. Apparently, the silver ion stabilization model of the DNA duplex should take into account not only the direct binding of silver ions to cytosines, but also the presence of related factors, such as stacking interaction in extended DNA, interplanar hydrogen bonds, and metallophilic interaction of neighboring silver ions.

AB - The development of structured molecular systems based on a nucleic acid framework takes into account the ability of single-stranded DNA to form a stable double-stranded structure due to stacking interactions and hydrogen bonds of complementary pairs of nucleotides. To increase the stability of the DNA double helix and to expand the temperature range in the hybridization protocols, it was proposed to use more stable metal-mediated complexes of nucleotide pairs as an alternative to Watson-Crick hydrogen bonds. One of the most frequently considered options is the use of silver ions to stabilize a pair of cytosines from opposite DNA strands. Silver ions specifically bind to N3 cytosines along the helix axis to form, as is believed, a strong N3–Ag +–N3 bond, relative to which, two rotational isomers, the cis- and trans-configurations of C–Ag +–C can be formed. In present work, a theoretical study and a comparative analysis of the free energy profile of the dissociation of two С–Ag +–C isomers were carried out using the combined method of molecular mechanics and quantum chemistry (QM/MM). As a result, it was shown that the cis-configuration is more favorable in energy than the trans- for a single pair of cytosines, and the geometry of the global minimum at free energy profile for both isomers differs from the equilibrium geometries obtained previously by quantum chemistry methods. Apparently, the silver ion stabilization model of the DNA duplex should take into account not only the direct binding of silver ions to cytosines, but also the presence of related factors, such as stacking interaction in extended DNA, interplanar hydrogen bonds, and metallophilic interaction of neighboring silver ions.

KW - Cytosines

KW - DNA

KW - Free energy profile

KW - QM / MM

KW - Silver ions

KW - Cytosines

KW - DNA

KW - Free energy profile

KW - QM / MM

KW - Silver ions

UR - http://www.scopus.com/inward/record.url?scp=85072338020&partnerID=8YFLogxK

UR - http://www.mendeley.com/research/mechanism-dissociation-cytosine-pairs-mediated-silver-ions

U2 - 10.20537/2076-7633-2019-11-4-685-693

DO - 10.20537/2076-7633-2019-11-4-685-693

M3 - статья

VL - 11

SP - 685

EP - 693

JO - КОМПЬЮТЕРНЫЕ ИССЛЕДОВАНИЯ И МОДЕЛИРОВАНИЕ

JF - КОМПЬЮТЕРНЫЕ ИССЛЕДОВАНИЯ И МОДЕЛИРОВАНИЕ

SN - 2076-7633

IS - 4

ER -